diff --git a/.dockerignore b/.dockerignore index 3b15d33c..67ef5242 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,6 +1,7 @@ # Git .git .gitignore +.github create_permissions.log # Logs log/* @@ -9,4 +10,8 @@ tmp/* # Editor temp files *.swp *.swo -test/solr +coverage +# Ignore generated test data +test/data/uploaded_ontologies/**/* +test/data/ontology_files/repo/**/* +test/log diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 212d5dcd..d9af054d 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -1,85 +1,92 @@ -# Workflow for deploying ontologies_api to stage/prod systems via capistrano. -# This workflow runs after a successeful execution of the unit test workflow and it -# can also be triggered manually. +# Workflow to deploy OntoPortal API to stage/prod systems # # Required github secrets: # -# CONFIG_REPO - github repo containing config and customizations for the API. Format 'author/private_config_repo' +# CONFIG_REPO - github repo containing config and customizations for API. Format 'author/private_config_repo' # it is used for getting capistrano deployment configuration for stages on the github actions runner and -# PRIVATE_CONFIG_REPO env var is constructed from it which is used by capistrano on the remote servers for pulling configs. +# PRIVATE_CONFIG_REPO env var is constructed from it which is used by capistrano on the API hosts for pulling configs. # -# GH_PAT - github Personal Access Token for accessing PRIVATE_CONFIG_REPO +# GH_PAT - github Personal Access Token for accessing private config repo # -# SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if app servers are hosted on private network. +# SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if API nodes live on private network. +# SSH_JUMPHOST_USER - username to use to connect to the ssh jump/proxy. # -# DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/deploy_id_rsa_enc (see miloserdow/capistrano-deploy) -# this SSH key is used for accessing jump host, UI nodes, and private github repo. +# DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/ +# this SSH key is used for accessing jump host, API nodes, and private github repo. name: Capistrano Deployment # Controls when the action will run. on: - # Trigger deployment to staging after unit test action completes - workflow_run: - workflows: ["Ruby Unit Tests"] - types: - - completed - branches: [master, develop] + push: + branches: + - stage + - test # Allows running this workflow manually from the Actions tab workflow_dispatch: - branches: [master, develop] inputs: BRANCH: - description: 'Branch/tag to deploy' - default: develop + description: "Branch/tag to deploy" + options: + - stage + - test + - master + default: stage required: true environment: - description: 'target environment to deploy to' + description: "target environment to deploy to" type: choice options: - staging - - production - default: staging - + - agroportal + - test + default: stage jobs: deploy: runs-on: ubuntu-latest - # run deployment only if "Ruby Unit Tests" workflow completes sucessefully or when manually triggered - if: ${{ (github.event.workflow_run.conclusion == 'success') || (github.event_name == 'workflow_dispatch') }} env: - BUNDLE_WITHOUT: default #install gems required primarily for the deployment in order to speed this workflow + BUNDLE_WITHOUT: default #install gems required primarely for deployment in order to speed up workflow PRIVATE_CONFIG_REPO: ${{ format('git@github.com:{0}.git', secrets.CONFIG_REPO) }} # Steps represent a sequence of tasks that will be executed as part of the job steps: - - name: set branch/tag and environment to deploy from inputs - run: | - # workflow_dispatch default input doesn't get set on push so we need to set defaults - # via shell parameter expansion - # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g - USER_INPUT_BRANCH=${{ inputs.branch }} - echo "BRANCH=${USER_INPUT_BRANCH:-develop}" >> $GITHUB_ENV - USER_INPUT_ENVIRONMENT=${{ inputs.environment }} - echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v3 - - uses: ruby/setup-ruby@v1 - with: - ruby-version: 2.7.6 # Not needed with a .ruby-version file - bundler-cache: true # runs 'bundle install' and caches installed gems automatically - - name: get-deployment-config - uses: actions/checkout@v3 - with: - repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings - token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT - path: deploy_config - - name: copy-deployment-config - run: cp -r deploy_config/ontologies_api/* . - # add ssh hostkey so that capistrano doesn't complain - - name: Add jumphost's hostkey to Known Hosts - run: | - mkdir -p ~/.ssh - ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts - shell: bash - - uses: miloserdow/capistrano-deploy@master - with: - target: ${{ env.TARGET }} # which environment to deploy - deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project + - name: set branch/tag and environment to deploy from inputs + run: | + # workflow_dispatch default input doesn't get set on push so we need to set defaults + # via shell parameter expansion + # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g + USER_INPUT_BRANCH=${{ inputs.branch }} + echo "BRANCH=${USER_INPUT_BRANCH:github.head_ref:-master}" >> $GITHUB_ENV + + USER_INPUT_ENVIRONMENT=${{ inputs.environment }} + echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV + + CONFIG_REPO=${{ secrets.CONFIG_REPO }} + GH_PAT=${{ secrets.GH_PAT }} + echo "PRIVATE_CONFIG_REPO=https://${GH_PAT}@github.com/${CONFIG_REPO}" >> $GITHUB_ENV + + echo "SSH_JUMPHOST=${{ secrets.SSH_JUMPHOST }}" >> $GITHUB_ENV + echo "SSH_JUMPHOST_USER=${{ secrets.SSH_JUMPHOST_USER }}" >> $GITHUB_ENV + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - uses: actions/checkout@v3 + - uses: ruby/setup-ruby@v1 + with: + ruby-version: 2.7.8 # Not needed with a .ruby-version file + bundler-cache: true # runs 'bundle install' and caches installed gems automatically + - name: get-deployment-config + uses: actions/checkout@v3 + with: + repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings + token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT + path: deploy_config + - name: copy-deployment-config + run: cp -r deploy_config/ontologies_api/${{ inputs.environment }}/* . + # add ssh hostkey so that capistrano doesn't complain + - name: Add jumphost's hostkey to Known Hosts + run: | + mkdir -p ~/.ssh + echo "${{ secrets.SSH_JUMPHOST }}" + ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts + shell: bash + - uses: miloserdow/capistrano-deploy@master + with: + target: ${{ env.TARGET }} # which environment to deploy + deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project diff --git a/.gitignore b/.gitignore index 8b568832..c525d7c8 100644 --- a/.gitignore +++ b/.gitignore @@ -36,7 +36,6 @@ config/environments/* !config/environments/config.rb.sample #ignore capistrano deployment -config/deploy/* config/*.p12 # Ignore generated test data @@ -56,8 +55,6 @@ test/data/ontology_files/repo/**/* *.swp -.ruby-version - config/environments/console.rb config/environments/development.rb.sample diff --git a/.ruby-version b/.ruby-version new file mode 100644 index 00000000..818bd47a --- /dev/null +++ b/.ruby-version @@ -0,0 +1 @@ +3.0.6 diff --git a/Capfile b/Capfile index f86314f3..3bf9ae11 100644 --- a/Capfile +++ b/Capfile @@ -16,12 +16,12 @@ install_plugin Capistrano::SCM::Git # https://github.com/capistrano/rails # # require 'capistrano/rvm' -# require 'capistrano/rbenv' +require 'capistrano/rbenv' # require 'capistrano/chruby' require 'capistrano/bundler' # require 'capistrano/rails/assets' # require 'capistrano/rails/migrations' require 'capistrano/locally' - +require 'new_relic/recipes' # announce deployments in NewRelic # Loads custom tasks from `lib/capistrano/tasks' if you have any defined. Dir.glob('lib/capistrano/tasks/*.cap').each { |r| import r } diff --git a/Dockerfile b/Dockerfile index 4dcc0c72..a2bed486 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -ARG RUBY_VERSION +ARG RUBY_VERSION=3.0 ARG DISTRO_NAME=bullseye FROM ruby:$RUBY_VERSION-$DISTRO_NAME diff --git a/Gemfile b/Gemfile index d939e422..19f5d75b 100644 --- a/Gemfile +++ b/Gemfile @@ -1,25 +1,25 @@ source 'https://rubygems.org' - -gem 'activesupport', '~> 3.2' +gem 'activesupport', '~> 5' # see https://github.com/ncbo/ontologies_api/issues/69 -gem 'bigdecimal', '1.4.2' -gem 'faraday', '~> 1.9' +gem 'bigdecimal' +# gem 'faraday', '~> 1.9' gem 'json-schema', '~> 2.0' -gem 'multi_json', '~> 1.0' +gem 'multi_json' gem 'oj' gem 'parseconfig' gem 'rack' gem 'rake', '~> 10.0' +gem 'rexml' # Investigate why unicorn fails to start under ruby 3 without adding rexml gem to the Gemfile gem 'sinatra', '~> 1.0' gem 'sinatra-advanced-routes' gem 'sinatra-contrib', '~> 1.0' gem 'request_store' gem 'parallel' gem 'json-ld' - +gem 'google-protobuf', '3.25.3' # Rack middleware -gem 'ffi', '~> 1.15.5' +gem 'ffi', '~> 1.16.3' gem 'rack-accept', '~> 0.4' gem 'rack-attack', '~> 6.6.1', require: 'rack/attack' gem 'rack-cache', '~> 1.13.0' @@ -35,7 +35,7 @@ gem 'redis-store', '~>1.10' # Monitoring gem 'cube-ruby', require: 'cube' -gem 'newrelic_rpm' +gem 'newrelic_rpm', group: [:default, :deployment] # HTTP server gem 'unicorn' @@ -53,7 +53,14 @@ gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'developm gem 'ontologies_linked_data', git: 'https://github.com/lifewatch-eric/ontologies_linked_data.git', branch: 'master' gem 'ncbo_cron', git: 'https://github.com/lifewatch-eric/ncbo_cron.git', branch: 'master' + group :development do + # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42 + gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo' + gem 'rubocop' +end + +group :deployment do # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42 gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0', require: false gem 'capistrano', '~> 3', require: false @@ -61,8 +68,6 @@ group :development do gem 'capistrano-locally', require: false gem 'capistrano-rbenv', require: false gem 'ed25519', '>= 1.2', '< 2.0', require: false - gem 'pry' - gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo' end @@ -71,10 +76,13 @@ group :profiling do end group :test do - gem 'minitest', '~> 4.0' + gem 'crack', '0.4.5' + gem 'minitest', '~> 5.0' + gem 'minitest-hooks', "~> 1.5" gem 'minitest-stub_any_instance' gem 'rack-test' gem 'simplecov', require: false gem 'simplecov-cobertura' # for codecov.io gem 'webmock', '~> 3.19.1' + gem 'webrick' end \ No newline at end of file diff --git a/Gemfile.lock b/Gemfile.lock index 4067e9e4..ab9c63dd 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -17,7 +17,7 @@ GIT GIT remote: https://github.com/lifewatch-eric/ontologies_linked_data.git - revision: c212a601a796e43c6ede014afe74da78858612a3 + revision: 32ee5870e220b62678b8dd81e6f29087678b9446 branch: master specs: ontologies_linked_data (0.0.1) @@ -37,7 +37,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: 013abea4af3b10910ec661dbb358a4b6cae198a4 + revision: 9dbd4f179e42c52095129d353a5ac584e9bd47f3 branch: master specs: ncbo_ontology_recommender (0.0.1) @@ -48,7 +48,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: a95245b8c964431505ca6315907440996c59a00d + revision: f8ac7b00e8d8b46d1eea04de014175525c1cdd83 branch: development specs: goo (0.0.2) @@ -103,26 +103,29 @@ GIT GEM remote: https://rubygems.org/ specs: - activesupport (3.2.22.5) - i18n (~> 0.6, >= 0.6.4) - multi_json (~> 1.0) + activesupport (5.2.8.1) + concurrent-ruby (~> 1.0, >= 1.0.2) + i18n (>= 0.7, < 2) + minitest (~> 5.1) + tzinfo (~> 1.1) addressable (2.8.7) public_suffix (>= 2.0.2, < 7.0) - airbrussh (1.5.2) + airbrussh (1.5.3) sshkit (>= 1.6.1, != 1.7.0) + ast (2.4.2) backports (3.25.0) base64 (0.2.0) bcrypt (3.1.20) bcrypt_pbkdf (1.1.1) bcrypt_pbkdf (1.1.1-x86_64-darwin) - bigdecimal (1.4.2) + bigdecimal (3.1.8) builder (3.3.0) capistrano (3.19.1) airbrussh (>= 1.0.0) i18n rake (>= 10.0.0) sshkit (>= 1.9.0) - capistrano-bundler (2.1.0) + capistrano-bundler (2.1.1) capistrano (~> 3.1) capistrano-locally (0.3.0) capistrano (~> 3.0) @@ -130,42 +133,25 @@ GEM capistrano (~> 3.1) sshkit (~> 1.3) coderay (1.1.3) - concurrent-ruby (1.3.3) + concurrent-ruby (1.3.4) connection_pool (2.4.1) - crack (1.0.0) - bigdecimal + crack (0.4.5) rexml cube-ruby (0.0.3) dante (0.2.0) date (3.3.4) declarative (0.0.20) - docile (1.4.0) + docile (1.4.1) domain_name (0.6.20240107) ed25519 (1.3.0) - faraday (1.10.3) - faraday-em_http (~> 1.0) - faraday-em_synchrony (~> 1.0) - faraday-excon (~> 1.1) - faraday-httpclient (~> 1.0) - faraday-multipart (~> 1.0) - faraday-net_http (~> 1.0) - faraday-net_http_persistent (~> 1.0) - faraday-patron (~> 1.0) - faraday-rack (~> 1.0) - faraday-retry (~> 1.0) + faraday (2.8.1) + base64 + faraday-net_http (>= 2.0, < 3.1) ruby2_keywords (>= 0.0.4) - faraday-em_http (1.0.0) - faraday-em_synchrony (1.0.0) - faraday-excon (1.1.0) - faraday-httpclient (1.0.1) - faraday-multipart (1.0.4) - multipart-post (~> 2) - faraday-net_http (1.0.1) - faraday-net_http_persistent (1.2.0) - faraday-patron (1.0.0) - faraday-rack (1.0.0) - faraday-retry (1.0.3) - ffi (1.15.5) + faraday-net_http (3.0.2) + faraday-retry (2.2.1) + faraday (~> 2.0) + ffi (1.16.3) gapic-common (0.21.1) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) @@ -176,76 +162,73 @@ GEM grpc (~> 1.59) get_process_mem (0.2.7) ffi (~> 1.0) - google-analytics-data (0.6.0) + google-analytics-data (0.6.1) google-analytics-data-v1beta (>= 0.11, < 2.a) google-cloud-core (~> 1.6) - google-analytics-data-v1beta (0.12.0) + google-analytics-data-v1beta (0.13.1) gapic-common (>= 0.21.1, < 2.a) google-cloud-errors (~> 1.0) google-apis-analytics_v3 (0.16.0) google-apis-core (>= 0.15.0, < 2.a) - google-apis-core (0.15.0) + google-apis-core (0.15.1) addressable (~> 2.5, >= 2.5.1) googleauth (~> 1.9) - httpclient (>= 2.8.1, < 3.a) + httpclient (>= 2.8.3, < 3.a) mini_mime (~> 1.0) + mutex_m representable (~> 3.0) retriable (>= 2.0, < 4.a) - rexml - google-cloud-core (1.7.0) + google-cloud-core (1.7.1) google-cloud-env (>= 1.0, < 3.a) google-cloud-errors (~> 1.0) google-cloud-env (2.1.1) faraday (>= 1.0, < 3.a) google-cloud-errors (1.4.0) - google-protobuf (3.25.3) google-protobuf (3.25.3-x86_64-darwin) google-protobuf (3.25.3-x86_64-linux) googleapis-common-protos (1.6.0) google-protobuf (>= 3.18, < 5.a) googleapis-common-protos-types (~> 1.7) grpc (~> 1.41) - googleapis-common-protos-types (1.15.0) + googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) - googleauth (1.11.0) + googleauth (1.11.2) faraday (>= 1.0, < 3.a) google-cloud-env (~> 2.1) jwt (>= 1.4, < 3.0) multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.64.0) - google-protobuf (~> 3.25) - googleapis-common-protos-types (~> 1.0) - grpc (1.64.0-x86_64-darwin) - google-protobuf (~> 3.25) + grpc (1.65.2-x86_64-darwin) + google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.64.0-x86_64-linux) - google-protobuf (~> 3.25) + grpc (1.65.2-x86_64-linux) + google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) haml (5.2.2) temple (>= 0.8.0) tilt - hashdiff (1.1.0) + hashdiff (1.1.1) htmlentities (4.3.4) http-accept (1.7.0) - http-cookie (1.0.6) + http-cookie (1.0.7) domain_name (~> 0.5) httpclient (2.8.3) - i18n (0.9.5) + i18n (1.14.6) concurrent-ruby (~> 1.0) - json (2.7.2) + json (2.7.4) json-ld (3.0.2) multi_json (~> 1.12) rdf (>= 2.2.8, < 4.0) json-schema (2.8.1) addressable (>= 2.4) - jwt (2.8.2) + jwt (2.9.3) base64 kgio (2.11.4) + language_server-protocol (3.17.0.3) libxml-ruby (5.0.3) link_header (0.0.8) - logger (1.6.0) + logger (1.6.1) macaddr (1.7.2) systemu (~> 2.6.5) mail (2.8.1) @@ -254,19 +237,22 @@ GEM net-pop net-smtp method_source (1.1.0) - mime-types (3.5.2) + mime-types (3.6.0) + logger mime-types-data (~> 3.2015) - mime-types-data (3.2024.0702) + mime-types-data (3.2024.1001) mini_mime (1.1.5) - minitest (4.7.5) + minitest (5.25.1) + minitest-hooks (1.5.2) + minitest (> 5.3) minitest-stub_any_instance (1.0.3) mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) - multipart-post (2.4.1) - net-http-persistent (4.0.2) + mutex_m (0.2.0) + net-http-persistent (4.0.4) connection_pool (~> 2.2) - net-imap (0.4.14) + net-imap (0.4.17) date net-protocol net-pop (0.1.2) @@ -279,21 +265,28 @@ GEM net-ssh (>= 5.0.0, < 8.0.0) net-smtp (0.5.0) net-protocol - net-ssh (7.2.3) + net-ssh (7.3.0) netrc (0.11.0) - newrelic_rpm (9.11.0) - oj (3.16.1) + newrelic_rpm (9.14.0) + oj (3.16.6) + bigdecimal (>= 3.0) + ostruct (>= 0.2) omni_logger (0.1.4) logger os (1.1.4) - parallel (1.25.1) + ostruct (0.6.0) + parallel (1.26.3) parseconfig (1.1.2) + parser (3.3.5.0) + ast (~> 2.4.1) + racc pony (1.13.1) mail (>= 2.0) pry (0.14.2) coderay (~> 1.1) method_source (~> 1.0) public_suffix (5.1.1) + racc (1.8.1) rack (1.6.13) rack-accept (0.4.5) rack (>= 0.4) @@ -310,6 +303,7 @@ GEM rack-test (2.1.0) rack (>= 1.3) rack-timeout (0.7.0) + rainbow (3.1.1) raindrops (0.20.1) rake (10.5.0) rdf (3.2.11) @@ -328,15 +322,16 @@ GEM rdf (~> 3.2) rexml (~> 3.2) redcarpet (3.6.0) - redis (5.2.0) + redis (5.3.0) redis-client (>= 0.22.0) redis-client (0.22.2) connection_pool redis-rack-cache (2.2.1) rack-cache (>= 1.10, < 2) redis-store (>= 1.6, < 2) - redis-store (1.10.0) + redis-store (1.11.0) redis (>= 4, < 6) + regexp_parser (2.9.2) representable (3.2.0) declarative (< 0.1.0) trailblazer-option (>= 0.1.1, < 0.2.0) @@ -349,11 +344,23 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.1) - strscan + rexml (3.3.9) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) + rubocop (1.67.0) + json (~> 2.3) + language_server-protocol (>= 3.17.0) + parallel (~> 1.10) + parser (>= 3.3.0.2) + rainbow (>= 2.2.2, < 4.0) + regexp_parser (>= 2.4, < 3.0) + rubocop-ast (>= 1.32.2, < 2.0) + ruby-progressbar (~> 1.7) + unicode-display_width (>= 2.4.0, < 3.0) + rubocop-ast (1.32.3) + parser (>= 3.3.1.0) + ruby-progressbar (1.13.0) ruby-xxHash (0.4.0.2) ruby2_keywords (0.0.5) rubyzip (2.3.2) @@ -371,7 +378,7 @@ GEM simplecov-cobertura (2.1.0) rexml simplecov (~> 0.19) - simplecov-html (0.12.3) + simplecov-html (0.13.1) simplecov_json_formatter (0.1.4) sinatra (1.4.8) rack (~> 1.5) @@ -386,20 +393,22 @@ GEM rack-test sinatra (~> 1.4.0) tilt (>= 1.3, < 3) - sshkit (1.23.0) + sshkit (1.23.2) base64 net-scp (>= 1.1.2) net-sftp (>= 2.1.2) net-ssh (>= 2.8.0) - strscan (3.1.0) + ostruct systemu (2.6.5) temple (0.10.3) + thread_safe (0.3.6) tilt (2.4.0) timeout (0.4.1) trailblazer-option (0.1.2) - tzinfo (2.0.6) - concurrent-ruby (~> 1.0) + tzinfo (1.2.11) + thread_safe (~> 0.1) uber (0.1.0) + unicode-display_width (2.6.0) unicorn (6.1.0) kgio (~> 2.6) raindrops (~> 0.7) @@ -412,31 +421,33 @@ GEM addressable (>= 2.8.0) crack (>= 0.3.2) hashdiff (>= 0.4.0, < 2.0.0) + webrick (1.8.2) PLATFORMS - ruby x86_64-darwin-23 x86_64-linux DEPENDENCIES - activesupport (~> 3.2) + activesupport (~> 5) bcrypt_pbkdf (>= 1.0, < 2.0) - bigdecimal (= 1.4.2) + bigdecimal capistrano (~> 3) capistrano-bundler capistrano-locally capistrano-rbenv + crack (= 0.4.5) cube-ruby ed25519 (>= 1.2, < 2.0) - faraday (~> 1.9) - ffi (~> 1.15.5) + ffi (~> 1.16.3) goo! + google-protobuf (= 3.25.3) haml (~> 5.2.2) json-ld json-schema (~> 2.0) - minitest (~> 4.0) + minitest (~> 5.0) + minitest-hooks (~> 1.5) minitest-stub_any_instance - multi_json (~> 1.0) + multi_json ncbo_annotator! ncbo_cron! ncbo_ontology_recommender! @@ -445,7 +456,6 @@ DEPENDENCIES ontologies_linked_data! parallel parseconfig - pry rack rack-accept (~> 0.4) rack-attack (~> 6.6.1) @@ -461,6 +471,8 @@ DEPENDENCIES redis-rack-cache (~> 2.0) redis-store (~> 1.10) request_store + rexml + rubocop shotgun! simplecov simplecov-cobertura @@ -471,6 +483,7 @@ DEPENDENCIES unicorn unicorn-worker-killer webmock (~> 3.19.1) + webrick BUNDLED WITH 2.4.22 diff --git a/config/deploy.rb b/config/deploy.rb index 322d0ba9..bb8baf8b 100644 --- a/config/deploy.rb +++ b/config/deploy.rb @@ -1,4 +1,6 @@ -# config valid only for Capistrano 3 +set :author, "ontoportal-lirmm" +set :application, "ontologies_api" +set :repo_url, "https://github.com/#{fetch(:author)}/#{fetch(:application)}.git" APP_PATH = '/srv/ontoportal' @@ -11,7 +13,7 @@ # ask :branch, proc { `git rev-parse --abbrev-ref HEAD`.chomp } # Default deploy_to directory is /var/www/my_app -set :deploy_to, "#{APP_PATH}/#{fetch(:application)}" +set :deploy_to, "/srv/ontoportal/#{fetch(:application)}" # Default value for :scm is :git # set :scm, :git @@ -20,7 +22,7 @@ # set :format, :pretty # Default value for :log_level is :debug -# set :log_level, :debug +set :log_level, :error # Default value for :pty is false # set :pty, true @@ -45,11 +47,39 @@ # required for restarting unicorn with sudo set :pty, true # Default value for default_env is {} -set :default_env, { -} +# set :default_env, { path: "/opt/ruby/bin:$PATH" } # Default value for keep_releases is 5 set :keep_releases, 5 +set :config_folder_path, "#{fetch(:application)}/#{fetch(:stage)}" + +# If you want to restart using `touch tmp/restart.txt`, add this to your config/deploy.rb: + +SSH_JUMPHOST = ENV.include?('SSH_JUMPHOST') ? ENV['SSH_JUMPHOST'] : 'jumpbox.hostname.com' +SSH_JUMPHOST_USER = ENV.include?('SSH_JUMPHOST_USER') ? ENV['SSH_JUMPHOST_USER'] : 'username' + +JUMPBOX_PROXY = "#{SSH_JUMPHOST_USER}@#{SSH_JUMPHOST}" +set :ssh_options, { + user: 'ontoportal', + forward_agent: 'true', + keys: %w(config/deploy_id_rsa), + auth_methods: %w(publickey), + # use ssh proxy if API servers are on a private network + proxy: Net::SSH::Proxy::Command.new("ssh #{JUMPBOX_PROXY} -W %h:%p") +} + +# private git repo for configuraiton +PRIVATE_CONFIG_REPO = ENV.include?('PRIVATE_CONFIG_REPO') ? ENV['PRIVATE_CONFIG_REPO'] : 'https://your_github_pat_token@github.com/your_organization/ontoportal-configs.git' +desc "Check if agent forwarding is working" +task :forwarding do + on roles(:all) do |h| + if test("env | grep SSH_AUTH_SOCK") + info "Agent forwarding is up to #{h}" + else + error "Agent forwarding is NOT up to #{h}" + end + end +end # inspired by http://nathaniel.talbott.ws/blog/2013/03/14/post-deploy-smoke-tests/ desc 'Run smoke test' @@ -77,7 +107,6 @@ end end - namespace :deploy do desc 'Incorporate the private repository content' @@ -85,10 +114,10 @@ # or get config from local directory if LOCAL_CONFIG_PATH env var is set task :get_config do if defined?(PRIVATE_CONFIG_REPO) - TMP_CONFIG_PATH = "/tmp/#{SecureRandom.hex(15)}" + TMP_CONFIG_PATH = "/tmp/#{SecureRandom.hex(15)}".freeze on roles(:app) do execute "git clone -q #{PRIVATE_CONFIG_REPO} #{TMP_CONFIG_PATH}" - execute "rsync -av #{TMP_CONFIG_PATH}/#{fetch(:application)}/ #{release_path}/" + execute "rsync -av #{TMP_CONFIG_PATH}/#{fetch(:config_folder_path)}/ #{release_path}/" execute "rm -rf #{TMP_CONFIG_PATH}" end elsif defined?(LOCAL_CONFIG_PATH) @@ -101,10 +130,10 @@ desc 'Restart application' task :restart do on roles(:app), in: :sequence, wait: 5 do - # Your restart mechanism here, for example: - # execute :touch, release_path.join('tmp/restart.txt') - execute 'sudo systemctl restart unicorn' - execute 'sleep 5' + # Your restart mechanism here, for example: + # execute :touch, release_path.join('tmp/restart.txt') + execute 'sudo systemctl restart unicorn' + execute 'sleep 5' end end diff --git a/config/deploy/agroportal.rb b/config/deploy/agroportal.rb new file mode 100644 index 00000000..c01f3fb9 --- /dev/null +++ b/config/deploy/agroportal.rb @@ -0,0 +1,17 @@ +# Simple Role Syntax +# ================== +# Supports bulk-adding hosts to roles, the primary +# server in each group is considered to be the first +# unless any hosts have the primary property set. +# Don't declare `role :all`, it's a meta role +role :app, %w[agroportal.lirmm.fr] +role :db, %w[agroportal.lirmm.fr] # sufficient to run db:migrate only on one system +set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'master' +# Extended Server Syntax +# ====================== +# This can be used to drop a more detailed server +# definition into the server list. The second argument +# something that quacks like a hash can be used to set +# extended properties on the server. +# server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value +set :log_level, :error diff --git a/config/deploy/staging.rb b/config/deploy/staging.rb new file mode 100644 index 00000000..47b158ae --- /dev/null +++ b/config/deploy/staging.rb @@ -0,0 +1,17 @@ +# Simple Role Syntax +# ================== +# Supports bulk-adding hosts to roles, the primary +# server in each group is considered to be the first +# unless any hosts have the primary property set. +# Don't declare `role :all`, it's a meta role +role :app, %w{stageportal.lirmm.fr} +role :db, %w{stageportal.lirmm.fr} # sufficient to run db:migrate only on one system +set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'stage' +# Extended Server Syntax +# ====================== +# This can be used to drop a more detailed server +# definition into the server list. The second argument +# something that quacks like a hash can be used to set +# extended properties on the server. +#server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value +set :log_level, :error diff --git a/config/deploy/test.rb b/config/deploy/test.rb new file mode 100644 index 00000000..fcbe1efc --- /dev/null +++ b/config/deploy/test.rb @@ -0,0 +1,17 @@ +# Simple Role Syntax +# ================== +# Supports bulk-adding hosts to roles, the primary +# server in each group is considered to be the first +# unless any hosts have the primary property set. +# Don't declare `role :all`, it's a meta role +role :app, %w{testportal.lirmm.fr} +role :db, %w{testportal.lirmm.fr} # sufficient to run db:migrate only on one system +# Extended Server Syntax +# ====================== +# This can be used to drop a more detailed server +# definition into the server list. The second argument +# something that quacks like a hash can be used to set +# extended properties on the server. +#server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value +set :log_level, :error +set :branch, ENV.include?('BRANCH') ? ENV['BRANCH'] : 'test' diff --git a/config/environments/config.rb.sample b/config/environments/config.rb.sample index f143b8f9..4e7900b7 100644 --- a/config/environments/config.rb.sample +++ b/config/environments/config.rb.sample @@ -87,6 +87,37 @@ LinkedData.config do |config| link: 'https://www.googleapis.com/oauth2/v3/userinfo' } } + config.ui_name = 'Bioportal' + config.title = 'NCBO BioPortal' + config.description = "The world's most comprehensive repository of biomedical ontologies " + config.color = '#234979' + config.logo = '' + config.fundedBy = [ + { + img_src: 'https://identity.stanford.edu/wp-content/uploads/sites/3/2020/07/block-s-right.png', + url: 'https://www.stanford.edu', + + }, + { + img_src: 'https://ontoportal.org/images/logo.png', + url: 'https://ontoportal.org/', + } + ] + config.federated_portals = { + 'agroportal' => { + api: 'http://data.agroportal.lirmm.fr', + ui: 'http://agroportal.lirmm.fr', + apikey: '1cfae05f-9e67-486f-820b-b393dec5764b', + color: '#1e2251' + }, + 'bioportal' => { + api: 'http://data.bioontology.org', + ui: 'http://bioportal.bioontology.org', + apikey: '4a5011ea-75fa-4be6-8e89-f45c8c84844e', + color: '#234979' + }, + + } end Annotator.config do |config| diff --git a/config/environments/test.rb b/config/environments/test.rb index 0b68cc3b..2cef531a 100644 --- a/config/environments/test.rb +++ b/config/environments/test.rb @@ -1,4 +1,11 @@ -# This file is designed to be used for unit testing with docker-compose +# conig file for unit tests + +# GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : "AG" +# GOO_HOST = ENV.include?("GOO_HOST") ? ENV["GOO_HOST"] : "localhost" +# GOO_PATH_QUERY = ENV.include?("GOO_PATH_QUERY") ? ENV["GOO_PATH_QUERY"] : "/repositories/bioportal" +# GOO_PATH_DATA = ENV.include?("GOO_PATH_DATA") ? ENV["GOO_PATH_DATA"] : "/repositories/bioportal/statements" +# GOO_PATH_UPDATE = ENV.include?("GOO_PATH_UPDATE") ? ENV["GOO_PATH_UPDATE"] : "/repositories/bioportal/statements" +# GOO_PORT = ENV.include?("GOO_PORT") ? ENV["GOO_PORT"] : 10035 GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : "4store" GOO_PATH_QUERY = ENV.include?("GOO_PATH_QUERY") ? ENV["GOO_PATH_QUERY"] : "/sparql/" @@ -6,7 +13,8 @@ GOO_PATH_UPDATE = ENV.include?("GOO_PATH_UPDATE") ? ENV["GOO_PATH_UPDATE"] : "/update/" GOO_PORT = ENV.include?("GOO_PORT") ? ENV["GOO_PORT"] : 9000 GOO_HOST = ENV.include?("GOO_HOST") ? ENV["GOO_HOST"] : "localhost" -REDIS_HOST = ENV.include?("REDIS_HOST") ? ENV["REDIS_HOST"] : "localhost" +REDIS_HTTP_CACHE_HOST = ENV.include?("REDIS_HTTP_CACHE_HOST") ? ENV["REDIS_HTTP_CACHE_HOST"] : "localhost" +REDIS_PERSISTENT_HOST = ENV.include?("REDIS_PERSISTENT_HOST") ? ENV["REDIS_PERSISTENT_HOST"] : "localhost" REDIS_PORT = ENV.include?("REDIS_PORT") ? ENV["REDIS_PORT"] : 6379 SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr" SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr" @@ -31,11 +39,11 @@ config.goo_path_query = GOO_PATH_QUERY.to_s config.goo_path_data = GOO_PATH_DATA.to_s config.goo_path_update = GOO_PATH_UPDATE.to_s - config.goo_redis_host = REDIS_HOST.to_s + config.goo_redis_host = REDIS_PERSISTENT_HOST.to_s config.goo_redis_port = REDIS_PORT.to_i - config.http_redis_host = REDIS_HOST.to_s + config.http_redis_host = REDIS_HTTP_CACHE_HOST.to_s config.http_redis_port = REDIS_PORT.to_i - config.ontology_analytics_redis_host = REDIS_HOST.to_s + config.ontology_analytics_redis_host = REDIS_PERSISTENT_HOST.to_s config.ontology_analytics_redis_port = REDIS_PORT.to_i config.search_server_url = SOLR_TERM_SEARCH_URL.to_s config.property_search_server_url = SOLR_PROP_SEARCH_URL.to_s @@ -79,22 +87,20 @@ end Annotator.config do |config| - config.annotator_redis_host = REDIS_HOST.to_s + config.annotator_redis_host = REDIS_PERSISTENT_HOST.to_s config.annotator_redis_port = REDIS_PORT.to_i config.mgrep_host = MGREP_HOST.to_s config.mgrep_port = MGREP_PORT.to_i config.mgrep_dictionary_file = "./test/data/dictionary.txt" end -OntologyRecommender.config do |config| -end - LinkedData::OntologiesAPI.config do |config| - config.http_redis_host = REDIS_HOST.to_s + config.http_redis_host = REDIS_HTTP_CACHE_HOST.to_s config.http_redis_port = REDIS_PORT.to_i end NcboCron.config do |config| - config.redis_host = REDIS_HOST.to_s + config.redis_host = REDIS_PERSISTENT_HOST.to_s config.redis_port = REDIS_PORT.to_i +# config.ontology_report_path = REPORT_PATH end diff --git a/config/rack_attack.rb b/config/rack_attack.rb index 88a3e8d6..4612b493 100644 --- a/config/rack_attack.rb +++ b/config/rack_attack.rb @@ -1,6 +1,8 @@ # frozen_string_literal: true -puts "(API) >> Throttling enabled at #{LinkedData::OntologiesAPI.settings.req_per_second_per_ip} req/sec" +limit_req_ip = LinkedData::OntologiesAPI.settings.req_per_second_per_ip +limit_req_ip_heavy = limit_req_ip / 5 +puts "(API) >> Throttling enabled at #{limit_req_ip} req/sec" require 'rack/attack' use Rack::Attack @@ -27,11 +29,12 @@ request.env['REMOTE_USER']&.admin? end -Rack::Attack.throttle('requests by ip', - limit: LinkedData::OntologiesAPI.settings.req_per_second_per_ip, - period: 1.second -) do |request| - request.ip +Rack::Attack.throttle('req/ip/heavy', limit: limit_req_ip_heavy, period: 1.second) do |req| + req.ip if req.path.include?('/recommender') || req.path.include?('/annotator') +end + +Rack::Attack.throttle('req/ip', limit: limit_req_ip, period: 1.second) do |req| + req.ip end Rack::Attack.throttled_responder = lambda do |request| diff --git a/controllers/agents_controller.rb b/controllers/agents_controller.rb index 1bf86321..0b47c0c2 100644 --- a/controllers/agents_controller.rb +++ b/controllers/agents_controller.rb @@ -1,8 +1,29 @@ class AgentsController < ApplicationController - %w[/agents /Agents].each do |namespace| - namespace namespace do - # Display all agents + get '/ontologies/:acronym/agents' do + ont = Ontology.find(params["acronym"]).first + latest = ont.latest_submission(status: :any) + latest.bring(*OntologySubmission.agents_attrs) + properties_agents= {} + OntologySubmission.agents_attrs.each do |attr| + properties_agents[attr] = Array(latest.send(attr)) + end + + agents = [] + properties_agents.each do |key, value| + agents.concat(value.map{ |agent| agent.bring_remaining}) + end + agents.uniq! + + if includes_param.include?(:all) || includes_param.include?(:usages) + LinkedData::Models::Agent.load_agents_usages(agents) + end + + reply agents + end + + %w[agents Agents].each do |namespace| + namespace "/#{namespace}" do get do check_last_modified_collection(LinkedData::Models::Agent) query = LinkedData::Models::Agent.where @@ -147,4 +168,4 @@ def update_agent(agent, params) end end -end \ No newline at end of file +end diff --git a/controllers/home_controller.rb b/controllers/home_controller.rb index c2a67fb4..29aa851c 100644 --- a/controllers/home_controller.rb +++ b/controllers/home_controller.rb @@ -4,7 +4,7 @@ class HomeController < ApplicationController CLASS_MAP = { - Property: "LinkedData::Models::ObjectProperty" + Property: "LinkedData::Models::ObjectProperty" } namespace "/" do @@ -13,25 +13,37 @@ class HomeController < ApplicationController expires 3600, :public last_modified @@root_last_modified ||= Time.now.httpdate routes = routes_list + #TODO: delete when ccv will be on production routes.delete("/ccv") if LinkedData.settings.enable_resource_index == false routes.delete("/resource_index") end + + routes.delete('/Agents') + routes_hash = {} context = {} routes.each do |route| next if route.length < 3 || route.split("/").length > 2 route_no_slash = route.gsub("/", "") context[route_no_slash] = route_to_class_map[route].type_uri.to_s if route_to_class_map[route] && route_to_class_map[route].respond_to?(:type_uri) - routes_hash[route_no_slash] = LinkedData.settings.rest_url_prefix+route_no_slash + routes_hash[route_no_slash] = LinkedData.settings.rest_url_prefix + route_no_slash end - routes_hash["@context"] = context - reply ({links: routes_hash}) + + config = LinkedData::Models::PortalConfig.current_portal_config + + federated_portals = config.federated_portals + federated_portals. transform_values! { |v| v.delete(:apikey) ; v } + config.init_federated_portals_settings(federated_portals) + config.id = RDF::URI.new(LinkedData.settings.id_url_prefix) + config.class.link_to *routes_hash.map { |key, url| LinkedData::Hypermedia::Link.new(key, url, context[key]) } + + reply config end get "documentation" do - @metadata_all = metadata_all.sort {|a,b| a[0].name <=> b[0].name} + @metadata_all = metadata_all.sort { |a, b| a[0].name <=> b[0].name } haml "documentation/documentation".to_sym, :layout => "documentation/layout".to_sym end diff --git a/controllers/ontologies_controller.rb b/controllers/ontologies_controller.rb index 493c9bd0..3d77f8e1 100644 --- a/controllers/ontologies_controller.rb +++ b/controllers/ontologies_controller.rb @@ -70,6 +70,25 @@ class OntologiesController < ApplicationController end end + # on demand ontology pull + post "/:acronym/pull" do + LOGGER.info "Forcing the pull and processing of ontology #{params['acronym']}" + actions = NcboCron::Models::OntologySubmissionParser::ACTIONS.dup + actions[:remote_pull] = true + ont = Ontology.find(params["acronym"]).first + error 404, "You must provide a valid `acronym` to retrieve an ontology" if ont.nil? + ont.bring(:acronym, :submissions, :viewingRestriction, :administeredBy) + check_write_access(ont) + latest = ont.latest_submission(status: :any) + error 404, "Ontology #{params["acronym"]} contains no submissions" if latest.nil? + check_last_modified(latest) + latest.bring(*OntologySubmission.goo_attrs_to_load(includes_param)) + error 404, "Ontology #{params["acronym"]} is not configured to be remotely pulled" unless latest.remote_pulled? + NcboCron::Models::OntologySubmissionParser.new.queue_submission(latest, actions) + LOGGER.info "Ontology #{params['acronym']} has been queued for pull and processing" + halt 204 + end + ## # Update latest submission of an ontology REQUIRES_REPROCESS = ["prefLabelProperty", "definitionProperty", "synonymProperty", "authorProperty", "classType", "hierarchyProperty", "obsoleteProperty", "obsoleteParent"] @@ -140,8 +159,8 @@ class OntologiesController < ApplicationController get '/:acronym/download' do acronym = params["acronym"] ont = Ontology.find(acronym).include(Ontology.goo_attrs_to_load).first - ont.bring(:viewingRestriction) if ont.bring?(:viewingRestriction) error 422, "You must provide an existing `acronym` to download" if ont.nil? + ont.bring(:viewingRestriction) if ont.bring?(:viewingRestriction) check_access(ont) restricted_download = LinkedData::OntologiesAPI.settings.restrict_download.include?(acronym) error 403, "License restrictions on download for #{acronym}" if restricted_download && !current_user.admin? diff --git a/controllers/ontology_submissions_controller.rb b/controllers/ontology_submissions_controller.rb index 5b72cce2..d11d9267 100644 --- a/controllers/ontology_submissions_controller.rb +++ b/controllers/ontology_submissions_controller.rb @@ -60,6 +60,7 @@ class OntologySubmissionsController < ApplicationController # Display a submission get '/:ontology_submission_id' do ont = Ontology.find(params["acronym"]).include(:acronym).first + error 422, "Ontology #{params["acronym"]} does not exist" unless ont check_last_modified_segment(LinkedData::Models::OntologySubmission, [ont.acronym]) ont.bring(:submissions) ont_submission = ont.submission(params["ontology_submission_id"]) @@ -161,6 +162,25 @@ class OntologySubmissionsController < ApplicationController end end + get '/:ontology_submission_id/diff' do + acronym = params["acronym"] + submission_attributes = [:submissionId, :submissionStatus, :diffFilePath] + ont = Ontology.find(acronym).include(:submissions => submission_attributes).first + error 422, "You must provide an existing `acronym` to download" if ont.nil? + ont.bring(:viewingRestriction) + check_access(ont) + ont_restrict_downloads = LinkedData::OntologiesAPI.settings.restrict_download + error 403, "License restrictions on download for #{acronym}" if ont_restrict_downloads.include? acronym + submission = ont.submission(params['ontology_submission_id'].to_i) + error 404, "There is no such submission for download" if submission.nil? + file_path = submission.diffFilePath + if File.readable? file_path + reply submission.parse_diff_report + else + error 500, "Cannot read submission diff file: #{file_path}" + end + end + ## # Download a submission diff file get '/:ontology_submission_id/download_diff' do diff --git a/controllers/properties_controller.rb b/controllers/properties_controller.rb index f98e9016..c20bc532 100644 --- a/controllers/properties_controller.rb +++ b/controllers/properties_controller.rb @@ -24,7 +24,9 @@ class PropertiesController < ApplicationController get '/:property' do prop = params[:property] ont, submission = get_ontology_and_submission - p = ont.property(prop, submission) + bring_unmapped = bring_unmapped?(includes_param) + + p = ont.property(prop, submission, display_all_attributes: bring_unmapped) error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil? reply 200, p end @@ -51,7 +53,7 @@ class PropertiesController < ApplicationController get '/:property/tree' do prop = params[:property] ont, submission = get_ontology_and_submission - p = ont.property(prop, submission) + p = ont.property(prop, submission, display_all_attributes: false) error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil? root_tree = p.tree @@ -79,7 +81,7 @@ class PropertiesController < ApplicationController get '/:property/ancestors' do prop = params[:property] ont, submission = get_ontology_and_submission - p = ont.property(prop, submission) + p = ont.property(prop, submission, display_all_attributes: false) error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil? ancestors = p.ancestors p.class.in(submission).models(ancestors).include(:label, :definition).all @@ -91,7 +93,7 @@ class PropertiesController < ApplicationController get '/:property/descendants' do prop = params[:property] ont, submission = get_ontology_and_submission - p = ont.property(prop, submission) + p = ont.property(prop, submission, display_all_attributes: false) error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil? descendants = p.descendants p.class.in(submission).models(descendants).include(:label, :definition).all @@ -103,7 +105,7 @@ class PropertiesController < ApplicationController get '/:property/parents' do prop = params[:property] ont, submission = get_ontology_and_submission - p = ont.property(prop, submission) + p = ont.property(prop, submission, display_all_attributes: false) error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil? p.bring(:parents) @@ -120,7 +122,7 @@ class PropertiesController < ApplicationController get '/:property/children' do prop = params[:property] ont, submission = get_ontology_and_submission - p = ont.property(prop, submission) + p = ont.property(prop, submission, display_all_attributes: false) error 404, "Property #{prop} not found in ontology #{ont.id.to_s}" if p.nil? p.bring(:children) diff --git a/controllers/recommender_v1_controller.rb b/controllers/recommender_v1_controller.rb index 5b0123a9..29991299 100644 --- a/controllers/recommender_v1_controller.rb +++ b/controllers/recommender_v1_controller.rb @@ -1,17 +1,10 @@ class RecommenderController < ApplicationController namespace "/recommender_v1" do - # execute an annotator query + # Mark this route as deprecated get do - text = params["text"] - raise error 400, "A text to be analyzed by the recommender must be supplied using the argument text=" if text.nil? || text.strip.empty? - acronyms = restricted_ontologies_to_acronyms(params) - display_classes = params['display_classes'].eql?('true') # default will be false - recommender = Recommender::Models::NcboRecommender.new - recommendations = recommender.recommend(text, acronyms, display_classes) - reply 200, recommendations + reply 410, { message: "This API endpoint has been deprecated and is no longer available. Please use /recommender or refer to the API documentation for updated routes." } end end end - diff --git a/controllers/search_controller.rb b/controllers/search_controller.rb index 9f701714..ce34d51d 100644 --- a/controllers/search_controller.rb +++ b/controllers/search_controller.rb @@ -63,7 +63,7 @@ class SearchController < ApplicationController page_size: page_size, sort: sort }) - + total_found = page_data.aggregate ontology_rank = LinkedData::Models::Ontology.rank docs = {} @@ -153,11 +153,17 @@ class SearchController < ApplicationController fq = "agentType_t:#{type}" if type - qf = [ - "acronymSuggestEdge^25 nameSuggestEdge^15 emailSuggestEdge^15 identifiersSuggestEdge^10 ", # start of the word first - "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10 ", # full word match - "acronymSuggestNgram^2 nameSuggestNgram^1.5 email_text^1" # substring match last - ].join(' ') + if params[:qf] + qf = params[:qf] + else + qf = [ + "acronymSuggestEdge^25 nameSuggestEdge^15 emailSuggestEdge^15 identifiersSuggestEdge^10 ", # start of the word first + "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10 ", # full word match + "acronymSuggestNgram^2 nameSuggestNgram^1.5 email_text^1" # substring match last + ].join(' ') + end + + if params[:sort] sort = "#{params[:sort]} asc, score desc" @@ -230,6 +236,9 @@ def process_search(params = nil) doc[:submission] = submission doc[:ontology_rank] = (ontology_rank[doc[:submissionAcronym]] && !ontology_rank[doc[:submissionAcronym]].empty?) ? ontology_rank[doc[:submissionAcronym]][:normalizedScore] : 0.0 doc[:properties] = MultiJson.load(doc.delete(:propertyRaw)) if include_param_contains?(:properties) + + doc = filter_attrs_by_language(doc) + instance = doc[:provisional] ? LinkedData::Models::ProvisionalClass.read_only(doc) : LinkedData::Models::Class.read_only(doc) docs.push(instance) end diff --git a/controllers/users_controller.rb b/controllers/users_controller.rb index 58e7667f..ce77c161 100644 --- a/controllers/users_controller.rb +++ b/controllers/users_controller.rb @@ -16,7 +16,7 @@ class UsersController < ApplicationController end ## - # This endpoint will create a token and store it on the user + # This endpoint will create a token and store it on the use- # An email is generated with this token, which allows the user # to click and login to the UI. The token can then be provided to # the /reset_password endpoint to actually reset the password. @@ -48,7 +48,7 @@ class UsersController < ApplicationController if token_accepted reply user else - error 403, "Password reset not authorized with this token" + error 401, "Password reset not authorized with this token" end end @@ -92,6 +92,7 @@ class UsersController < ApplicationController # Delete a user delete '/:username' do + error 403, "Access denied" unless current_user.admin? User.find(params[:username]).first.delete halt 204 end diff --git a/dip.yml b/dip.yml index c4c12684..c829068f 100644 --- a/dip.yml +++ b/dip.yml @@ -7,7 +7,7 @@ version: '7.1' compose: files: - - .docker-compose.yml + - docker-compose.yml project_name: ontologies_api interaction: @@ -34,14 +34,14 @@ interaction: # A shortcut to run unit tests test: - description: Run minitest unit tests + description: Run unit tests with 4store triplestore service: api - command: bundle exec rake test + command: bundle exec rake test TESTOPTS='-v' test-ag: - description: Run minitest unit tests + description: Run unit tests with AllegroGraph triplestore service: api-agraph - command: bundle exec rake test + command: bundle exec rake test TESTOPTS='-v' rackup: description: Run onotlogies_api service via rack up commands diff --git a/docker-compose.yml b/docker-compose.yml index a75136d7..2a08a35e 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -31,6 +31,7 @@ services: environment: <<: *env BUNDLE_APP_CONFIG: /srv/ontoportal/ontologies_api/.bundle + profiles: - 4store depends_on: @@ -48,7 +49,7 @@ services: - "9393:9393" volumes: # bundle volume for hosting gems installed by bundle; it speeds up gem install in local development - - app_api:/srv/ontoportal/ontologies_api + - .:/srv/ontoportal/ontologies_api - repository:/srv/ontoportal/data/repository ncbo_cron: @@ -198,3 +199,4 @@ volumes: mgrep: logs: history: + diff --git a/fix_purls.rb b/fix_purls.rb deleted file mode 100755 index 2f8f7a98..00000000 --- a/fix_purls.rb +++ /dev/null @@ -1,136 +0,0 @@ -require 'ontologies_linked_data' -require 'ncbo_annotator' -require_relative 'config/config' -require_relative 'config/environments/production' -# require_relative 'config/environments/stage' - - -purl_client = LinkedData::Purl::Client.new - - -# acronyms = ["AAO", "ABA-AMB", "ACGT-MO", "AI-RHEUM", "APAONTO", "ATC", "AURA", "BCGO", "BCTEO", "BHN", "BILA", -# "CANONT", "CCO", "CCON", "CHD", "CHEMBIO", "CLIN-EVAL", "CNO", "CO", "CO-WHEAT", "CPRO", "CPTH", "CRISP", -# "CTONT", "DC-CL", "DIAGONT", "DIKB", "DOCCC", "DSO", "DWC-TEST", "ELIG", "EPILONT", "EPSO", "ERO", "FB-SP", -# "FIRE", "FLO", "FLU", "GCC", "GENE-CDS", "GENETRIAL", "GEOSPECIES", "GEXO", "GLYCANONT", "GLYCOPROT", "GMO", -# "GPI", "GRO-CPD", "GRO-CPGA", "HCPCS-HIMC", "HIMC-CPT", "HINO", "HIV", "HOM-TEST", "I2B2-LOINC", "ICD0", -# "ICD09", "ICD11-BODYSYSTEM", "IDOMAL", "IEV", "IMMDIS", "IMR", "LHN", "LSM", "MCCL", "MIXSCV", "MPO", "MS", -# "MSTDE", "MSTDE-FRE", "NBO", "NCC", "NCCO", "NEOMARK3", "NEOMARK4", "NHSQI2009", "NIC", "NONRCTO", "OBOREL", -# "OBR-Scolio", "OFP", "OGSF", "OMIT", "ONTF", "ONTOAD", "ONTODM-CORE", "OntoOrpha", "ORTHO", "PHARMGKB", -# "PHENOMEBLAST", "PHENOSCAPE-EXT", "PHYFIELD", "PIERO", "PLATSTG", "PPIO", "PRO-ONT", "PROVO", "PSDS", -# "PSIMOD", "PTRANS", "RBSCI", "RCTONT", "RETO", "REXO", "RGMU", "RGMU2", "RNIMU", "SBRO", "SENTI", "STY", -# "TAXRANK", "TEST-PROD", "TEST1015", "TESTONTO", "TESTONTO2", "TESTONTOO", "TST-PAUL2", "TTTTHHHH", "TYPON", -# "UDEF", "UNITSONT", "VBCV", "WB-BT", "WB-LS", "WB-PHENOTYPE", "WH", "WSIO", "XEO", "ZIP3", "ZIP5"] - - -# acronyms = ["HOM-PROCS2.owl", "HOM-DXVCODES2.owl", "HOM-ICD9.owl", "HOM-PROCS_OSHPD.owl", "HOM-ICD9-PROCS_OSHPD.owl", -# "HOM-ICD9-ECODES_OSHPDowl", "HOM-ICD9_DXandVCODES_OSHPD.owl", "HOM-MDCDRG_OSHPD.owl", -# "HOM-ICD9-ECODES_OSHPD.owl", "HOM-PROCS2", "HOM-PROCS2", "HOM-DXVCODES2", "FBbt", "FBdv", "FAO", "EMAP", -# "ECO", "EV", "CL", "CHEBI", "DDANAT", "DOID", "MA", "BTO", "ProPreO", "MOD", "MI", "PW", "MPATH", "TO", -# "EO", "MFO", "MAO", "TGMA", "EHDA", "EHDAA", "MP", "FBbi", "CARO", "FBsp", "SOPHARM", "PRO", "SNPO", -# "ClinicalTrialOntology", "basic-vertebrate-gross-anatomy", "RID", "ZFA", "amino-acid", "WBbt", "WBls", -# "SEP", "SBO", "OBO_REL", "REX", "SPD", "birnlex", "MHC", "nif", "GRO", "TTO", "BSPO", "MIRO", "OCRe", "GO", -# "ENVO", "WBPhenotype", "TADS", "BOOTStrep", "PATO", "SO", "TAO", "UO", "YPO", "IDO", "TRANS", "XAO", "ATMO", -# "OGI", "ICD-9", "BRO", "DC_CL", "EP", "BPMetadata", "ECG", "RS", "DermLex", "VO", "MAT", "SPO", "BHO", "HP", -# "OBI", "MO", "FHHO", "OPB", "EFO", "NEMO"] - -# acronyms = ["HOM-PROCS2", "TADS", "HOM", "ABA", "CLKB", "CST", "ICPC", "BFO", "PEO", "SYMP", "SitBAC", "PLO", "APO", -# "MeGO", "gsontology", "NIF_Dysfunction", "ATO", "Field", "LDA", "GAZ", "SSO", "IAO", "LNC", "PDQ", "OMIM", -# "MEDLINEPLUS", "WHO", "SNOMEDCT", "NDFRT", "MSH", "PKO", "ICF", "KiSAO", "ICNP", "POL", "k2p", "NIF_Cell", -# "TOK", "RXNORM", "MDR", "OGMS", "CTCAE", "ICPC2P", "AIR", "BTC", "NDDF", "ICD10PCS", "MDDB", "RCD", "GFO", -# "GFO-Bio", "CHEMINF", "bioportal", "bioportal", "npo", "npo.owl", "bioportal.owl", "bro.owl", "BRO-Core", -# "bro", "MS", "EDAM", "EDAM", "HL7", "PD_ST", "JERM", "CLO", "NCBITaxon", "pma", "NCIM", "IMGT", "TMA", -# "bodysystem", "TMO", "ICECI", "MTHCH", "INO", "ICPS", "RNAO", "CPT", "ICD10", "FMA", "NCIt", "SIO", -# "SNOMED-Ethnic-Group", "SNOMEDCT-MAS", "BAO", "EHDAA2", "BO", "DDI", "NIGO", "RoleO", "HL7_UCSF_DSCHRG", -# "HL7_Dschrg", "HOM-ICD9"] - - -# acronyms = ["HOM-PROCS2/", "bioportal/", "bioportal", "npo/", "bro/", "MS/", "EDAM/", "apollo", "HOM_Discharge", -# "UCSF_TSI_Discharge", "HOM_ICD9", "HOM_ICD9", "SNOMED-Clinical-Findings", "SNOMEDCT-CF", "CO_Wheat", "REPO", -# "GALEN", "VAO", "ExO", "HPI", "vHOG", "UCare_Demographics", "UCare-Demographics", "TM-MER", -# "TM-SIGNS-AND-SYMPTS", "TM-OTHER-FACTORS", "TM-CONST", "obi-device", "OGMD", "FDA-MedDevice", "HOM-EHS", -# "PVOnto", "CELDAC", "PHARE", "1580", "AERO", "COA", "BP", "PO", "COR", "PR", "CMO", "XCO", "MMO", -# "Chem2Bio2OWL", "PRePPO", "PhylOnt", "IxnO", "BDO", "OntoDT", "OMRSE", "HLTH_INDICS", "FBcv", "HUGO", -# "CogPO", "ICD10CM", "NMR", "CSP", "OBOE", "oboe-sbc", "NeuMORE", "MCBCC", "LiPrO", "NeoMarkOntology", -# "ACGT", "BT", "CDAO", "CPTAC", "OGR", "ODGI", "CBO", "CPR", "pseudo", "SAO", "ZEA", "UBERON", "fged-obi", -# "obi-fged", "ICD9_PROCEDURES", "OPL", "HOMERUN_UHC", "BiositemapIM", "BRO-Activity", "BRO-AreaOfResearch", -# "BRO-Chinese", "cogat", "EMO", "HC", "OntoDM", "NCBI_NMOsp", "invertebrata", "VT", "IDOBRU"] - -# acronyms = ["HOM-DATASOURCE_OSHPD", "EPIC-SRC", "HOM-EPIC", "HOMERUN", "HOM-TX", "HPIO", "SHR", "MFOEM", "PedTerm", -# "AEO", "OAE", "FYPO", "HOM-CPT", "SYN", "DATASRC-ORTHO", "HOM-ORTHO", "vivo", "OPB.properties", -# "proftest.4205", "PO_PAE", "PO_PSDS", "GRO_CPD", "GRO_CPGA", "VSAO", "RH-MESH", "BAO-GPCR", "FMA-SUBSET", -# "COSTART", "ORDO", "FB-CV", "cms.36739", "chi.76398", "chi.41353", "I9I10CMMOST", "project", "DTVPrecision", -# "bibliographic", "dcterms", "foaf", "SciRes", "BRIDG", "ICD9CM-PROC", "CPT-mod", "SWEET", -# "cms.29622", "HOM-CHI", "nhds.7763", "NIF-RTH", "shrine.20924", "IDODEN", "gs1", "MEDO", "IFAR", "PathLex", -# "journal-test", "testvdb", "UCSF-ICD910CM", "Pizza-Example", "OPE", "NCBO_TEST_NOTES", "CABRO", "MTHMSTFRE", -# "GCO", "pomoc", "bco", "OVAE", "GOWGP_B", "BOF", "RNPRIO", "ONL-DP", "SSE", "IMGT-ONTOLOGY", "InterNano", -# "OBI_BCGO", "suicideo", "CARD", "MISHA_TEST2", "TEST-ONT-0-0", "MSV", "MATO", "STATO", "ELIXHAUSER", -# "SNOMED_TEST", "BWT", "ZC", "AI", "NIFCELL", "NIFDYS", "MESH"] - -# acronyms = ["OBCS", "FLOPO", "HUPSON", "NMOSP_1_6", "NMOSP", "CCC", "DEMOGRAPH", "GLOB", "SNOMED_ANATOMY", "SNOMED_ORG", -# "SNOMED_CF", "ICO", "BWT2", "NGSONTO", "HIVO004", "OGG", "TESTING", "RCTOntology", "CEEROntology", -# "dikb-evidence", "ICDO3", "QIBO", "HOM-OSHPD-SC", "SRC-OSHPDSC", "test_pradip_purl", "NDF-RT", "envo_153", -# "HOM-ORTHOSURG", "eufut", "MCV", "OBI_IEDB_view", "HOM-I9I10MAPS", "MF", "VANDF", "GWAS_EFO_SKOS", "NatPrO", -# "HSDB_OCRe", "test-111", "OoEVV", "HOM-ICU", "CareLex", "DiagnosticOnt", "Phys_Med_Rehab", "PMR", -# "ICD9toICD10PCS", "HOM-DXandVCODES_OSHPD", "HOM_HARVARD", "HOM-PROCS_OSHPD", "HOM-ICD9CM-ECODES", -# "HOM-ICD9CM_PROCEDURES", "HOM-MDCDRG_OSHPD", "HOM_MDCs_DRGs", "HOM_EHS", "HOM-PCSTEST", "MESH-OWL", "PTSD", -# "HOM-UPENN-MEDS", "HOM-UPENN_MEDS", "SDO", "SOY", "SPTO", "CanCO", "CTX", "QUDT", "HOM-UPENNMEDS", "WHOFRE", -# "ICPCFRE", "MDRFRE", "thesaurus", "ontologia", "thealternativa", "SNMD_BDY", "SWO", "ICF-NoCodeLabel", -# "testabbr", "bccl", "bccl1", "HOM-MEDABBS", "HOM-TESTKM", "HOM-I9CM", "HOM-MDCDRG", "NonRCTOntology", -# "HOM-DEMOGR"] - - -# acronyms = ["uni-ece", "PFO", "PhenXTK", "HCPCS", "test.20230", "test.20930", "HOM-DATSRCTEST", "i2b2-patvisdims", -# "homv2", "HOM-EPICI2B2", "ICD9CM", "TAHH", "TAHE", "HOM-I9PCS", "CAO", "HOM-UCARE", "EpilepOnto", -# "HOM-DXPCS_MDCDRG", "HOM-PCS_OSHPD", "HOM-I9-ECODES", "HOM-VCODES_OSHPD", "HOM-SRCE_OSHPD", "UnitsOntology", -# "HOM-OSHPD_UseCas", "pharmgkb-owl", "phenomeblast-owl", "CAMRQ", "tJADNI2", "BIOA3", "TestHDB", "tJADNI", -# "BIOA", "UCBH", "BIOA2", "NeoMark", "MEO", "test-purl", "yipd", "BioModels", "CPO", "PhyMeRe", "onto", -# "TEO", "test-1", "ADW", "HOM-OSHPD", "test.13773", "test.16355", "profectus.test.installation.21838", -# "profectus.test.installation.21775", "profectus.test.installation.21934", -# "profectus.test.installation.22027", "profectus.test.installation.21975", -# "profectus.test.installation.22081", "profectus.test.installation.22611", -# "profectus.test.installation.22704", "profectus.test.installation.22770", -# "OntoDM-KDD"] - -# acronyms = ["PhenX", "HOMICD910PCS-150", "dsfs", "HOM-I910TESTPLUS", "DwC", "HOM-DATSRCTESTo", "HOM-DATASRCTESTn", -# "HOM-I910PCS-150", "HOM-ORTHOTEST", "test.8300", "HOM-OCHILDTEST", "OntoMA", "HOM-CLINIC", "DwC_test", -# "UCSF_15", "UCSF_41", "profectus.deid.installation.27982", "profectus.deid.installation.28036", -# "profectus.deid.installation.28409", "profectus.deid.installation.32434", -# "profectus.deid.installation.21442", "HOM-OCC", "profectus.deid.installation.7616", -# "profectus.deid.installation.6250", "DC_test", "CCONT", "profectus.deid.installation.14032", -# "profectus.deid.installation.14522", "profectus.deid.installation.19214", "BIOA3v", -# "profectus.deid.installation.3433", "profectus.deid.installation.16341", "RPO", -# "profectus.deid.installation.11714", "profectus.deid.installation.19037", -# "profectus.deid.installation.27298", "profectus.deid.installation.31807", "OBIws", "ooevv-tractTrace", -# "ooevv-vaccine", "pco", "VSO", "profectus.oshpd.installation.5931", "NIF-Subcell", "DwC_translations", -# "PabloTest", "ConsentOntology", "pablotest2", "prov-o", "oshpd.39537", "nhds.13469", "nhds.13896", -# "HOM-NHDS", "ONSTR", "miRNAO", "chi.58970", "chi.61020", "chi.76831", "HOM-CMS", "Clinical_Eval", -# "documentStatus", "geopolitical", "citation", "dcelements", "event", "FaBiO", "provenance", "skos", -# "chi.20896", "NTDO", "oshpd.33038", "OntoKBCF", "HCPCS-mod", "chi.63559", "VariO", "NIAID-GSC-BRC", -# "cms.11830", "HOM-CHICMS", "nhds.7622", "HOM-GLOB", "jnnn", "GlycO"] - -# acronyms = ["shrine.20839", "shrine.20676", "chi.50064", "MetaCT", "ThomCan", "Genomic-CDS", "OntoPneumo", "bd-test2", -# "avnguyen-test2", "Top-Menelas", "MCCV", "SemPhysKB-Human", "ZIP", "biocode", "PORO", "ATOL", "IDQA", -# "TRAK", "UCSD", "mixs", "bao_gpcr", "TrOn", "MTHMST", "DermaO", "rsa", "DermO", "ECGT", "UCSFI9I10ALL", -# "SBOLv", "DILIo", "Eligibility", "CHDWiki", "BOFrdf", "VTO", "PDO", "CSSO", "NHSQI", "SEDI", "SuicidO", -# "ONL-MSA", "EDDA", "ONL-MR-DA", "ADO", "OntoVIP", "CHMO", "BdOK", "BOFf", "SBOL", "RadLex_v3.91", -# "STNFRDRXDEMO", "OntoBioUSP", "Radlex3.9.1", "BNO", "DCO", "PROV", "BSAO", "HRDO", "SNMI", "FIX"] - -LinkedData::Models::Ontology.all.each do |ont| - ont.bring(:acronym) - acronym = ont.acronym - - if (purl_client.purl_exists(acronym)) - puts "#{acronym} exists" - purl_client.fix_purl(acronym) - else - puts "#{acronym} DOES NOT exist" - purl_client.create_purl(acronym) - end -end - - - - -# acronyms.each do |acronym| -# purl_client.fix_purl(acronym) -# end diff --git a/helpers/access_control_helper.rb b/helpers/access_control_helper.rb index 74416866..071d3afe 100644 --- a/helpers/access_control_helper.rb +++ b/helpers/access_control_helper.rb @@ -6,7 +6,8 @@ module AccessControlHelper ## # For a given object, check the access control settings. If they are restricted, handle appropriately. - # For a list, this will filter out results. For single objects, if will throw an error if access is denied. + # For a list, this will filter out results. + # For single objects, if will throw an error if access is denied. def check_access(obj) return obj unless LinkedData.settings.enable_security if obj.is_a?(Enumerable) @@ -24,7 +25,7 @@ def check_access(obj) # For a given object, check if the current user has permission to perform writes. def check_write_access(obj) return obj unless LinkedData.settings.enable_security - if obj.is_a?(LinkedData::Models::Base) && obj.write_restricted? + if obj.is_a?(LinkedData::Models::Base) writable = obj.writable?(env["REMOTE_USER"]) error 403, "Access denied for this resource" unless writable end diff --git a/helpers/application_helper.rb b/helpers/application_helper.rb index 24893eef..51bd4f08 100644 --- a/helpers/application_helper.rb +++ b/helpers/application_helper.rb @@ -139,10 +139,10 @@ def reply(*response) check_access(obj) if LinkedData.settings.enable_security # Slice or set check - filter_for_slice(obj) if LinkedData.settings.enable_slices + obj = filter_for_slice(obj) if LinkedData.settings.enable_slices # Check for custom ontologies set by user - filter_for_user_onts(obj) + obj = filter_for_user_onts(obj) LinkedData::Serializer.build_response(@env, status: status, ld_object: obj) end @@ -225,8 +225,8 @@ def restricted_ontologies(params=nil) found_onts = onts.length > 0 - filter_for_slice(onts) - filter_for_user_onts(onts) + onts = filter_for_slice(onts) + onts = filter_for_user_onts(onts) end onts = filter_access(onts) @@ -276,9 +276,10 @@ def month_param(params=nil) if params["month"] month = params["month"].strip if %r{(?^(0[1-9]|[1-9]|1[0-2])$)}x === month - month.to_i.to_s + return month.to_i.to_s end end + nil end # validates year for starting with 1 or 2 and containing 4 digits @@ -287,9 +288,10 @@ def year_param(params=nil) if params["year"] year = params["year"].strip if %r{(?^([1-2]\d{3})$)}x === year - year.to_i.to_s + return year.to_i.to_s end end + nil end ## @@ -395,19 +397,13 @@ def get_ontology_and_submission else submission = ont.latest_submission(status: [:RDF]) end - if submission.nil? - error 404, "Ontology #{@params["ontology"]} submission not found." - end + error 404, "Ontology #{@params["ontology"]} submission not found." if submission.nil? if !submission.ready?(status: [:RDF]) - error(404, - "Ontology #{@params["ontology"]} submission i"+ - "#{submission.submissionId} has not been parsed.") - end - if submission.nil? - if submission.nil? - error 404, "Ontology #{@params["acronym"]} does not have any submissions" - end + error 404, "Ontology #{@params["ontology"]} submission #{submission.submissionId} has not been parsed." end + + save_submission_language(submission) + return ont, submission end @@ -454,6 +450,22 @@ def naive_expiring_cache_read(key) return object[:object] end + + def save_submission_language(submission, language_property = :naturalLanguage) + request_lang = RequestStore.store[:requested_lang] + + return if submission.nil? || !request_lang.blank? + + submission.bring(language_property) if submission.bring?(language_property) + collection_natural_language = submission.send(language_property) rescue nil + return [] if collection_natural_language.blank? + + collection_natural_language = collection_natural_language.values.flatten if collection_natural_language.is_a?(Hash) + submissions_language = collection_natural_language.map { |natural_language| natural_language.to_s.split('/').last[0..1] }.compact.first + + RequestStore.store[:requested_lang] = submissions_language if submissions_language + end + end end end diff --git a/helpers/ontology_helper.rb b/helpers/ontology_helper.rb index 8ff1bada..5fb33178 100644 --- a/helpers/ontology_helper.rb +++ b/helpers/ontology_helper.rb @@ -63,8 +63,13 @@ def create_submission(ont) ont_submission.submissionId = submission_id # Get file info - add_file_to_submission(ont, ont_submission) - + filename, tmpfile = add_file_to_submission(ont, ont_submission) + # if no actual file was uploaded, we remove the file parameters + if filename.nil? && tmpfile.nil? + params.delete("uploadFilePath") + params.delete("diffFilePath") + end + # Add new format if it doesn't exist if ont_submission.hasOntologyLanguage.nil? error 422, "You must specify the ontology format using the `hasOntologyLanguage` parameter" if params["hasOntologyLanguage"].nil? || params["hasOntologyLanguage"].empty? diff --git a/helpers/search_helper.rb b/helpers/search_helper.rb index 1c8dc431..3805e650 100644 --- a/helpers/search_helper.rb +++ b/helpers/search_helper.rb @@ -30,51 +30,51 @@ module SearchHelper MATCH_TYPE_LABELGENERATED = "labelGenerated" MATCH_TYPE_MAP = { - "resource_id" => "id", - MATCH_TYPE_PREFLABEL => MATCH_TYPE_PREFLABEL, - "prefLabelExact" => MATCH_TYPE_PREFLABEL, - "prefLabelSuggestEdge" => MATCH_TYPE_PREFLABEL, - "prefLabelSuggestNgram" => MATCH_TYPE_PREFLABEL, - MATCH_TYPE_SYNONYM => MATCH_TYPE_SYNONYM, - "synonymExact" => MATCH_TYPE_SYNONYM, - "synonymSuggestEdge" => MATCH_TYPE_SYNONYM, - "synonymSuggestNgram" => MATCH_TYPE_SYNONYM, - MATCH_TYPE_PROPERTY => MATCH_TYPE_PROPERTY, - MATCH_TYPE_LABEL => MATCH_TYPE_LABEL, - "labelExact" => MATCH_TYPE_LABEL, - "labelSuggestEdge" => MATCH_TYPE_LABEL, - "labelSuggestNgram" => MATCH_TYPE_LABEL, - MATCH_TYPE_LABELGENERATED => MATCH_TYPE_LABELGENERATED, - "labelGeneratedExact" => MATCH_TYPE_LABELGENERATED, - "labellabelGeneratedSuggestEdge" => MATCH_TYPE_LABELGENERATED, - "labellabelGeneratedSuggestNgram" => MATCH_TYPE_LABELGENERATED, - "notation" => "notation", - "cui" => "cui", - "semanticType" => "semanticType" + "resource_id" => "id", + MATCH_TYPE_PREFLABEL => MATCH_TYPE_PREFLABEL, + "prefLabelExact" => MATCH_TYPE_PREFLABEL, + "prefLabelSuggestEdge" => MATCH_TYPE_PREFLABEL, + "prefLabelSuggestNgram" => MATCH_TYPE_PREFLABEL, + MATCH_TYPE_SYNONYM => MATCH_TYPE_SYNONYM, + "synonymExact" => MATCH_TYPE_SYNONYM, + "synonymSuggestEdge" => MATCH_TYPE_SYNONYM, + "synonymSuggestNgram" => MATCH_TYPE_SYNONYM, + MATCH_TYPE_PROPERTY => MATCH_TYPE_PROPERTY, + MATCH_TYPE_LABEL => MATCH_TYPE_LABEL, + "labelExact" => MATCH_TYPE_LABEL, + "labelSuggestEdge" => MATCH_TYPE_LABEL, + "labelSuggestNgram" => MATCH_TYPE_LABEL, + MATCH_TYPE_LABELGENERATED => MATCH_TYPE_LABELGENERATED, + "labelGeneratedExact" => MATCH_TYPE_LABELGENERATED, + "labellabelGeneratedSuggestEdge" => MATCH_TYPE_LABELGENERATED, + "labellabelGeneratedSuggestNgram" => MATCH_TYPE_LABELGENERATED, + "notation" => "notation", + "cui" => "cui", + "semanticType" => "semanticType" } # list of fields that allow empty query text QUERYLESS_FIELDS_PARAMS = { - "ontologies" => nil, - "notation" => "notation", - "cui" => "cui", - "semantic_types" => "semanticType", - ONTOLOGY_TYPES_PARAM => "ontologyType", - ALSO_SEARCH_PROVISIONAL_PARAM => nil, - SUBTREE_ID_PARAM => nil + "ontologies" => nil, + "notation" => "notation", + "cui" => "cui", + "semantic_types" => "semanticType", + ONTOLOGY_TYPES_PARAM => "ontologyType", + ALSO_SEARCH_PROVISIONAL_PARAM => nil, + SUBTREE_ID_PARAM => nil } QUERYLESS_FIELDS_STR = QUERYLESS_FIELDS_PARAMS.values.compact.join(" ") - def get_term_search_query(text, params={}) + def get_term_search_query(text, params = {}) validate_params_solr_population(ALLOWED_INCLUDES_PARAMS) sort = params.delete('sort') # raise error if text is empty AND (none of the QUERYLESS_FIELDS_PARAMS has been passed # OR either an exact match OR suggest search is being executed) if text.nil? || text.strip.empty? - if !QUERYLESS_FIELDS_PARAMS.keys.any? {|k| params.key?(k)} || - params[EXACT_MATCH_PARAM] == "true" || - params[SUGGEST_PARAM] == "true" + if !QUERYLESS_FIELDS_PARAMS.keys.any? { |k| params.key?(k) } || + params[EXACT_MATCH_PARAM] == "true" || + params[SUGGEST_PARAM] == "true" raise error 400, "The search query must be provided via /search?q=[&page=&pagesize=]" else text = '' @@ -82,10 +82,6 @@ def get_term_search_query(text, params={}) end end - lang = params["lang"] || params["language"] - lang_suffix = lang && !lang.eql?("all") ? "_#{lang}" : "" - - query = "" params["defType"] = "edismax" params["stopwords"] = "true" params["lowercaseOperators"] = "true" @@ -97,19 +93,33 @@ def get_term_search_query(text, params={}) params["hl.simple.pre"] = MATCH_HTML_PRE params["hl.simple.post"] = MATCH_HTML_POST - # text.gsub!(/\*+$/, '') - if params[EXACT_MATCH_PARAM] == "true" query = "\"#{solr_escape(text)}\"" - params["qf"] = "resource_id^20 prefLabel#{lang_suffix}^10 synonymExact#{lang_suffix} #{QUERYLESS_FIELDS_STR}" - params["hl.fl"] = "resource_id prefLabelExact#{lang_suffix} synonymExact#{lang_suffix} #{QUERYLESS_FIELDS_STR}" + params["qf"] = "resource_id^20 #{add_lang_suffix('prefLabel', '^10')} #{add_lang_suffix('synonymExact')} #{QUERYLESS_FIELDS_STR}" + params["hl.fl"] = "resource_id #{add_lang_suffix('prefLabelExact')} #{add_lang_suffix('synonymExact')} #{QUERYLESS_FIELDS_STR}" elsif params[SUGGEST_PARAM] == "true" || text[-1] == '*' text.gsub!(/\*+$/, '') query = "\"#{solr_escape(text)}\"" params["qt"] = "/suggest_ncbo" - params["qf"] = " prefLabelExact#{lang_suffix}^100 prefLabelSuggestEdge#{lang_suffix}^50 synonym#{lang_suffix}SuggestEdge^10 prefLabel#{lang_suffix}SuggestNgram synonym#{lang_suffix}SuggestNgram resource_id #{QUERYLESS_FIELDS_STR}" - params["pf"] = "prefLabelSuggest^50" - params["hl.fl"] = "prefLabelExact#{lang_suffix} prefLabelSuggestEdge#{lang_suffix} synonymSuggestEdge#{lang_suffix} prefLabelSuggestNgram#{lang_suffix} synonymSuggestNgram#{lang_suffix} resource_id #{QUERYLESS_FIELDS_STR}" + params["qf"] = [ + add_lang_suffix('prefLabelExact', '^100'), + add_lang_suffix('prefLabelSuggestEdge', '^50'), + add_lang_suffix('synonymSuggestEdge', '^10'), + add_lang_suffix('prefLabelSuggestNgram'), + add_lang_suffix('synonymSuggestNgram'), + "resource_id #{QUERYLESS_FIELDS_STR}" + ].join(' ') + + params["pf"] = add_lang_suffix('prefLabelSuggest', '^50') + + params["hl.fl"] = [ + add_lang_suffix('prefLabelExact'), + add_lang_suffix('prefLabelSuggestEdge'), + add_lang_suffix('synonymSuggestEdge'), + add_lang_suffix('prefLabelSuggestNgram'), + add_lang_suffix('synonymSuggestNgram'), + "resource_id #{QUERYLESS_FIELDS_STR}" + ].join(' ') else if text.strip.empty? query = '*' @@ -117,9 +127,19 @@ def get_term_search_query(text, params={}) query = solr_escape(text) end - params["qf"] = "resource_id^100 prefLabelExact#{lang_suffix}^90 prefLabel#{lang_suffix}^70 synonymExact#{lang_suffix}^50 synonym#{lang_suffix }^10 #{QUERYLESS_FIELDS_STR}" + params["qf"] = [ + "resource_id^100", + add_lang_suffix('prefLabelExact', '^90'), + add_lang_suffix('prefLabel', '^70'), + add_lang_suffix('synonymExact', '^50'), + add_lang_suffix('synonym', '^10'), + QUERYLESS_FIELDS_STR + ].join(' ') + params["qf"] << " property" if params[INCLUDE_PROPERTIES_PARAM] == "true" - params["hl.fl"] = "resource_id prefLabelExact#{lang_suffix} prefLabel#{lang_suffix } synonymExact#{lang_suffix} synonym#{lang_suffix } #{QUERYLESS_FIELDS_STR}" + + params["hl.fl"] = "resource_id #{add_lang_suffix('prefLabelExact')} #{ add_lang_suffix('prefLabel')} #{add_lang_suffix('synonymExact')} #{add_lang_suffix('synonym')} #{QUERYLESS_FIELDS_STR}" + params["hl.fl"] = "#{params["hl.fl"]} property" if params[INCLUDE_PROPERTIES_PARAM] == "true" end @@ -221,6 +241,73 @@ def add_matched_fields(solr_response, default_match) solr_response["match_types"] = all_matches end + def portal_language + Goo.main_languages.first + end + + def request_languages + lang = params['lang'] || params['languages'] + + return [portal_language] if lang.blank? + + lang.split(',') + end + + def request_multiple_languages? + request_languages.size > 1 || request_all_languages? + end + + def request_languages? + !(params['lang'] || params['language']).blank? + end + + def request_all_languages? + request_languages.first.eql?('all') + end + + def add_lang_suffix(attr, rank = "") + if request_languages? && !request_all_languages? + languages = request_languages + languages.map { |lang| "#{attr}_#{lang}#{rank} " }.join + else + "#{attr}#{rank}" + end + end + + def pref_label_by_language(doc) + Array(doc["prefLabel_#{request_languages.first}".to_sym]).first || Array(doc["prefLabel_none".to_sym]).first || Array(doc[:prefLabel]).first + end + + def filter_attrs_by_language(doc) + lang_values = {} + doc.each do |k, v| + attr, lang = k.to_s.split('_') + + next if [:ontology_rank, :resource_id, :resource_model].include?(k) + next if lang.blank? || attr.blank? + next if !(request_languages + %w[none]).include?(lang) && !request_all_languages? + + lang_values[attr.to_sym] ||= {} + lang_values[attr.to_sym][lang] ||= [] + lang_values[attr.to_sym][lang] += v + end + + if request_multiple_languages? + lang_values.each do |k, lang_vals| + doc[k] = lang_vals + end + else + lang_values.each do |k, lang_vals| + doc[k] = lang_vals.map { |l, v| l.eql?('none') ? nil : v }.compact.flatten + Array(lang_vals['none']) + end + + doc[:prefLabel] = pref_label_by_language(doc) + end + + doc + end + + # see https://github.com/rsolr/rsolr/issues/101 # and https://github.com/projecthydra/active_fedora/commit/75b4afb248ee61d9edb56911b2ef51f30f1ce17f # @@ -348,7 +435,7 @@ def populate_classes_from_search(classes, ontology_acronyms=nil) doc[:submission] = old_class.submission doc[:properties] = MultiJson.load(doc.delete(:propertyRaw)) if include_param_contains?(:properties) instance = LinkedData::Models::Class.read_only(doc) - instance.prefLabel = instance.prefLabel.first if instance.prefLabel.is_a?(Array) + instance.prefLabel = pref_label_by_language(doc) classes_hash[ont_uri_class_uri] = instance end diff --git a/helpers/slices_helper.rb b/helpers/slices_helper.rb index d17db53e..6f527f29 100644 --- a/helpers/slices_helper.rb +++ b/helpers/slices_helper.rb @@ -10,10 +10,8 @@ def filter_for_slice(obj) slice = current_slice() - if obj.is_a?(Enumerable) - if obj.first.is_a?(LinkedData::Models::Ontology) - obj.delete_if {|o| !slice.ontology_id_set.include?(o.id.to_s)} - end + if obj.is_a?(Enumerable) && obj.first.is_a?(LinkedData::Models::Ontology) + obj = obj.select { |o| slice.ontology_id_set.include?(o.id.to_s) } end obj end @@ -35,4 +33,4 @@ def current_slice_acronyms end end -helpers Sinatra::Helpers::SlicesHelper \ No newline at end of file +helpers Sinatra::Helpers::SlicesHelper diff --git a/helpers/submission_helper.rb b/helpers/submission_helper.rb index b79737d0..3c282416 100644 --- a/helpers/submission_helper.rb +++ b/helpers/submission_helper.rb @@ -51,6 +51,8 @@ def retrieve_submissions(options) submissions_query = submissions_query.where({ submissionStatus: [code: status] }) end + submissions_query = submissions_query.order_by(order_by) unless order_by.nil? + submissions_query = apply_submission_filters(submissions_query) submissions_query = submissions_query.filter(Goo::Filter.new(ontology: [:viewOf]).unbound) unless include_views submissions_query = submissions_query.filter(filter) if filter? @@ -72,4 +74,4 @@ def include_ready?(options) end end -helpers Sinatra::Helpers::SubmissionHelper \ No newline at end of file +helpers Sinatra::Helpers::SubmissionHelper diff --git a/helpers/users_helper.rb b/helpers/users_helper.rb index a9a14d30..fbb10d92 100644 --- a/helpers/users_helper.rb +++ b/helpers/users_helper.rb @@ -12,7 +12,7 @@ def filter_for_user_onts(obj) user = env["REMOTE_USER"] if obj.first.is_a?(LinkedData::Models::Ontology) - obj.delete_if {|o| !user.custom_ontology_id_set.include?(o.id.to_s)} + obj = obj.select {|o| user.custom_ontology_id_set.include?(o.id.to_s)} end obj @@ -23,7 +23,8 @@ def send_reset_token(email, username) error 404, "User not found" unless user reset_token = token(36) user.resetToken = reset_token - + user.resetTokenExpireTime = Time.now.to_i + 1.hours.to_i + user.save(override_security: true) LinkedData::Utils::Notifications.reset_password(user, reset_token) user @@ -41,9 +42,20 @@ def reset_password(email, username, token) error 404, "User not found" unless user + user.bring(:resetToken) + user.bring(:passwordHash) user.show_apikey = true + token_accepted = token.eql?(user.resetToken) + if token_accepted + error 401, "Invalid password reset token" if user.resetTokenExpireTime.nil? + error 401, "The password reset token expired" if user.resetTokenExpireTime < Time.now.to_i + user.resetToken = nil + user.resetTokenExpireTime = nil + user.save(override_security: true) if user.valid? + user.show_apikey = true + end - [user, token.eql?(user.resetToken)] + [user, token_accepted] end def oauth_authenticate(params) @@ -68,4 +80,4 @@ def login_password_authenticate(params) end end -helpers Sinatra::Helpers::UsersHelper \ No newline at end of file +helpers Sinatra::Helpers::UsersHelper diff --git a/run-unit-tests.sh b/run-unit-tests.sh index 43ff9fca..7734efa8 100755 --- a/run-unit-tests.sh +++ b/run-unit-tests.sh @@ -4,7 +4,6 @@ #docker-compose build #docker-compose up --exit-code-from unit-test -# wait-for-it is useful since solr container might not get ready quick enough for the unit tests -docker-compose run --rm api wait-for-it solr-ut:8983 -- bundle exec rake test TESTOPTS='-v' -#docker-compose run --rm api wait-for-it solr-ut:8983 -- bundle exec rake test TESTOPTS='-v' TEST='./test/controllers/test_annotator_controller.rb' -docker-compose down +docker-compose run --rm api bundle exec rake test TESTOPTS='-v' +#docker-compose run --rm apibundle exec rake test TESTOPTS='-v' TEST='./test/controllers/test_annotator_controller.rb' +docker-compose stop diff --git a/test/controllers/test_annotator_controller.rb b/test/controllers/test_annotator_controller.rb index 572c8750..717d80b5 100644 --- a/test/controllers/test_annotator_controller.rb +++ b/test/controllers/test_annotator_controller.rb @@ -2,7 +2,7 @@ class TestAnnotatorController < TestCase - def self.before_suite + def before_suite @@redis = Redis.new(:host => Annotator.settings.annotator_redis_host, :port => Annotator.settings.annotator_redis_port) db_size = @@redis.dbsize if db_size > MAX_TEST_REDIS_SIZE @@ -25,7 +25,7 @@ def self.before_suite annotator = Annotator::Models::NcboAnnotator.new annotator.init_redis_for_tests() annotator.create_term_cache_from_ontologies(@@ontologies, false) - mapping_test_set + self.class.mapping_test_set end def test_annotate @@ -267,14 +267,14 @@ def test_default_properties_output assert_equal 9, annotations.length annotations.sort! { |a,b| a["annotatedClass"]["prefLabel"].first.downcase <=> b["annotatedClass"]["prefLabel"].first.downcase } assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data", annotations.first["annotatedClass"]["@id"] - assert_equal "Aggregate Human Data", Array(annotations.first["annotatedClass"]["prefLabel"]).first + assert_equal "Aggregate Human Data", annotations.first["annotatedClass"]["prefLabel"] params = {text: text, include: "prefLabel,definition"} get "/annotator", params assert last_response.ok? annotations = MultiJson.load(last_response.body) assert_equal 9, annotations.length - annotations.sort! { |a,b| Array(a["annotatedClass"]["prefLabel"]).first.downcase <=> Array(b["annotatedClass"]["prefLabel"]).first.downcase } + annotations.sort! { |a,b| a["annotatedClass"]["prefLabel"].downcase <=> b["annotatedClass"]["prefLabel"].downcase } assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data", annotations.first["annotatedClass"]["@id"] assert_equal ["A resource that provides data from clinical care that comprises combined data from multiple individual human subjects."], annotations.first["annotatedClass"]["definition"] end @@ -354,7 +354,6 @@ def self.mapping_test_set class_id = terms_a[i] ont_acr = onts_a[i] sub = LinkedData::Models::Ontology.find(ont_acr).first.latest_submission(status: :any) - binding.pry if sub.nil? sub.bring(ontology: [:acronym]) c = LinkedData::Models::Class.find(RDF::URI.new(class_id)) .in(sub) diff --git a/test/controllers/test_batch_controller.rb b/test/controllers/test_batch_controller.rb index d1e9d144..ca37b156 100644 --- a/test/controllers/test_batch_controller.rb +++ b/test/controllers/test_batch_controller.rb @@ -1,7 +1,8 @@ require_relative '../test_case' class TestBatchController < TestCase - def self.before_suite + def before_suite + LinkedData::SampleData::Ontology.delete_ontologies_and_submissions @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true) end @@ -25,7 +26,7 @@ def test_class_batch_one_ontology assert last_response.ok? data = MultiJson.load(last_response.body) classes = data["http://www.w3.org/2002/07/owl#Class"] - assert classes.length == 4 + assert_equal 4, classes.length classes.each do |klass| assert_instance_of String, klass["prefLabel"] assert_instance_of Array, klass["synonym"] @@ -75,11 +76,11 @@ def test_class_batch_multiple assert last_response.ok? data = MultiJson.load(last_response.body) classes = data["http://www.w3.org/2002/07/owl#Class"] - assert classes.length == 6 + assert_equal 6, classes.length classes.each do |klass| assert_instance_of String, klass["prefLabel"] - assert !klass["synonym"] - assert klass["prefLabel"] == class_ids[klass["@id"]] + refute klass["synonym"] + assert_equal klass["prefLabel"], class_ids[klass["@id"]] end end @@ -87,6 +88,7 @@ def test_class_batch_multiple def test_class_all_bro mccl = @@ontologies.select { |y| y.id.to_s.include? "MCCL"}.first assert mccl, "mccl is not found to execute batch test." + # binding.pry classes = LinkedData::Models::Class.in(mccl.latest_submission).include(:prefLabel).page(1,500).read_only.all class_ids = {} classes.each do |klass| @@ -101,9 +103,10 @@ def test_class_all_bro } post "/batch/", call_params assert last_response.ok? +# refute last_response.ok? data = MultiJson.load(last_response.body) classes_response = data["http://www.w3.org/2002/07/owl#Class"] - assert classes_response.length == classes.length + assert_equal classes.length, classes_response.length classes_response.each do |klass| assert_instance_of String, klass["prefLabel"] assert klass["prefLabel"] == class_ids[klass["@id"]] diff --git a/test/controllers/test_categories_controller.rb b/test/controllers/test_categories_controller.rb index d7e07cd2..4cfa7a0b 100644 --- a/test/controllers/test_categories_controller.rb +++ b/test/controllers/test_categories_controller.rb @@ -117,4 +117,34 @@ def test_delete_category get "/categories/#{acronym}" assert last_response.status == 404 end -end \ No newline at end of file + + def test_parent_category + parent_category1 = LinkedData::Models::Category.new( + acronym: "PARENT1", + name: "Parent Category 1", + description: "Description for Parent Category 1." + ) + parent_category1.save + + parent_category2 = LinkedData::Models::Category.new( + acronym: "PARENT2", + name: "Parent Category 2", + description: "Description for Parent Category 2." + ) + parent_category2.save + + category_instance = LinkedData::Models::Category.new( + acronym: "CAT123", + name: "Sample Category", + description: "This is a sample category.", + parentCategory: [parent_category1, parent_category2] + ) + category_instance.save + + get '/categories/CAT123' + fetched_category = MultiJson.load(last_response.body) + + assert_equal fetched_category["parentCategory"].first , parent_category1.id.to_s + assert_equal fetched_category["parentCategory"].last , parent_category2.id.to_s + end +end diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb index fc5adb96..323d241d 100644 --- a/test/controllers/test_classes_controller.rb +++ b/test/controllers/test_classes_controller.rb @@ -2,13 +2,14 @@ class TestClassesController < TestCase - def self.before_suite + def before_suite options = {ont_count: 1, submission_count: 3, submissions_to_process: [1, 2], process_submission: true, random_submission_count: false, - process_options: {process_rdf: true, extract_metadata: false} + process_options: {process_rdf: true, extract_metadata: false}, + file_path: "./test/data/ontology_files/BRO_v3.2.owl", } return LinkedData::SampleData::Ontology.create_ontologies_and_submissions(options) end @@ -82,7 +83,6 @@ def test_notation_lookup assert response["@id"] == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Ontology_Development_and_Management" end - def test_all_class_pages ont = Ontology.find("TEST-ONT-0").include(:acronym).first @@ -99,7 +99,7 @@ def test_all_class_pages assert last_response.ok? page_response = MultiJson.load(last_response.body) page_response["collection"].each do |item| - assert_instance_of String, item["prefLabel"] + assert_instance_of String, item["prefLabel"], item["@id"] assert_instance_of String, item["@id"] assert_instance_of Hash, item["@context"] assert_instance_of Hash, item["links"] @@ -131,6 +131,7 @@ def test_single_cls_all ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] + clss_ids.each do |cls_id| escaped_cls= CGI.escape(cls_id) call = "/ontologies/#{ont.acronym}/classes/#{escaped_cls}?include=all" @@ -149,6 +150,7 @@ def test_single_cls_properties ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] + clss_ids.each do |cls_id| escaped_cls= CGI.escape(cls_id) call = "/ontologies/#{ont.acronym}/classes/#{escaped_cls}?include=properties" @@ -163,7 +165,6 @@ def test_single_cls_properties def test_single_cls ont = Ontology.find("TEST-ONT-0").include(:acronym).first - clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] @@ -182,13 +183,8 @@ def test_single_cls assert_instance_of(Array, cls["synonym"]) assert(cls["@id"] == cls_id) - if submission_id.nil? || submission_id == 2 - assert(cls["prefLabel"]["In version 3.2"]) - assert(cls["definition"][0]["In version 3.2"]) - else - assert(!cls["prefLabel"]["In version 3.2"]) - assert(!cls["definition"][0]["In version 3.2"]) - end + assert(cls["prefLabel"]["In version 3.2"]) + assert(cls["definition"][0]["In version 3.2"]) if cls["prefLabel"].include? "Electron" assert_equal(1, cls["synonym"].length) @@ -208,7 +204,7 @@ def test_roots_for_cls roots = MultiJson.load(last_response.body) assert_includes [9, 6, 5], roots.length roots.each do |r| - assert_instance_of String, r["prefLabel"] + assert_instance_of String, r["prefLabel"], r["@id"] assert_instance_of String, r["@id"] assert r.include?"hasChildren" #By definition roots have no parents @@ -221,7 +217,6 @@ def test_roots_for_cls end def test_classes_for_not_parsed_ontology - ont = Ontology.find("TEST-ONT-0").include(:acronym).first #first submission was not parsed @@ -232,7 +227,6 @@ def test_classes_for_not_parsed_ontology end def test_tree - ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', @@ -251,7 +245,6 @@ def test_tree end def test_path_to_root_for_cls - ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] @@ -264,7 +257,6 @@ def test_path_to_root_for_cls end def test_ancestors_for_cls - ont = Ontology.find("TEST-ONT-0").include(:acronym).first ancestors_data = {} ancestors_data['http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction'] =[ @@ -456,7 +448,6 @@ def test_calls_not_found end def test_children_for_cls_round_trip - clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_and_Cellular_Data', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Microscope" ] @@ -513,7 +504,7 @@ def test_class_page_with_metric_count assert last_response.ok? page_response = MultiJson.load(last_response.body) page_response["collection"].each do |item| - assert_instance_of String, item["prefLabel"] + assert_instance_of String, item["prefLabel"], item["@id"] assert_instance_of String, item["@id"] assert_instance_of Hash, item["@context"] assert_instance_of Hash, item["links"] @@ -533,4 +524,48 @@ def test_class_page_with_metric_count assert page_response["collection"].length == 0 end + def test_default_multilingual + ont = Ontology.find("TEST-ONT-0").include(:acronym).first + sub = ont.latest_submission + sub.bring_remaining + + # rdfs:label is NOT present and the prefLabel is NOT defined for the ontology or portal language + sub.naturalLanguage = [RDF::URI.new('http://lexvo.org/id/iso639-3/es')] + sub.save + + get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Community_Engagement')}" + assert last_response.ok? + page_response = MultiJson.load(last_response.body) + # does not contain a value in english show the generated one + assert_equal 'Community_Engagement', page_response["prefLabel"] + + # rdfs:label is present but NOT for either the ontology or portal language + get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}" + assert last_response.ok? + page_response = MultiJson.load(last_response.body) + # does not contain a value in english show the generated one + assert_equal 'Biospecimen_Management', page_response["prefLabel"] + + # prefLabel NOT present, rdfs:label is present but NOT for either the ontology or portal language + get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Gene_Therapy')}" + assert last_response.ok? + page_response = MultiJson.load(last_response.body) + # does not contain a value in english show the generated one + assert_equal 'Gene_Therapy', page_response["prefLabel"] + + # prefLabel is present in the ontology language + sub.naturalLanguage = [RDF::URI.new('http://lexvo.org/id/iso639-3/fr')] + sub.save + + + get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}" + assert last_response.ok? + page_response = MultiJson.load(last_response.body) + # show french value as specified in submission naturalLanguage + assert_equal 'Biospecimen Management', page_response["prefLabel"] + + sub.naturalLanguage = [] + sub.save + end + end diff --git a/test/controllers/test_collections_controller.rb b/test/controllers/test_collections_controller.rb index b7bc6f1b..11986f81 100644 --- a/test/controllers/test_collections_controller.rb +++ b/test/controllers/test_collections_controller.rb @@ -2,7 +2,7 @@ class TestCollectionsController < TestCase - def self.before_suite + def before_suite LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ process_submission: true, process_options: {process_rdf: true, extract_metadata: false}, @@ -19,7 +19,7 @@ def self.before_suite sub.save end - def self.after_suite + def after_suite LinkedData::SampleData::Ontology.delete_ontologies_and_submissions end diff --git a/test/controllers/test_dereference_resource_controller.rb b/test/controllers/test_dereference_resource_controller.rb index e828a5a1..03427c41 100644 --- a/test/controllers/test_dereference_resource_controller.rb +++ b/test/controllers/test_dereference_resource_controller.rb @@ -3,7 +3,7 @@ class TestDereferenceResourceController < TestCase - def self.before_suite + def before_suite LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ process_submission: true, process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false}, @@ -192,4 +192,4 @@ def sort_nested_hash(hash) sorted_hash.sort.to_h end -end \ No newline at end of file +end diff --git a/test/controllers/test_external_mappings_controller.rb b/test/controllers/test_external_mappings_controller.rb index cb1f255f..0a18bf63 100644 --- a/test/controllers/test_external_mappings_controller.rb +++ b/test/controllers/test_external_mappings_controller.rb @@ -2,7 +2,7 @@ class TestExternalMappingsController < TestCase - def self.before_suite + def before_suite ["BRO-TEST-MAP-0", "CNO-TEST-MAP-0", "FAKE-TEST-MAP-0"].each do |acr| LinkedData::Models::OntologySubmission.where(ontology: [acronym: acr]).to_a.each do |s| s.delete @@ -147,4 +147,3 @@ def delete_interportal_mappings end end - diff --git a/test/controllers/test_instances_controller.rb b/test/controllers/test_instances_controller.rb index e4b0460b..1ed2b330 100644 --- a/test/controllers/test_instances_controller.rb +++ b/test/controllers/test_instances_controller.rb @@ -2,7 +2,7 @@ class TestInstancesController < TestCase - def self.before_suite + def before_suite LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ process_submission: true, process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false}, diff --git a/test/controllers/test_mappings_controller.rb b/test/controllers/test_mappings_controller.rb index 736606de..2ab61261 100644 --- a/test/controllers/test_mappings_controller.rb +++ b/test/controllers/test_mappings_controller.rb @@ -2,9 +2,9 @@ class TestMappingsController < TestCase - def self.before_suite - - ["BRO-TEST-MAP-0", "CNO-TEST-MAP-0", "FAKE-TEST-MAP-0"].each do |acr| + def before_suite + self.backend_4s_delete + ["BRO-TEST-MAP-0","CNO-TEST-MAP-0","FAKE-TEST-MAP-0"].each do |acr| LinkedData::Models::OntologySubmission.where(ontology: [acronym: acr]).to_a.each do |s| s.delete end diff --git a/test/controllers/test_metrics_controller.rb b/test/controllers/test_metrics_controller.rb index f5e3d5f3..631edf4b 100644 --- a/test/controllers/test_metrics_controller.rb +++ b/test/controllers/test_metrics_controller.rb @@ -2,22 +2,22 @@ class TestMetricsController < TestCase - def self.before_suite + def before_suite if OntologySubmission.all.count > 100 puts "this test is going to wipe out all submission and ontologies. probably this is not a test env." return end - OntologySubmission.all.each { |s| s.delete } - Ontology.all.each { |o| o.delete } - @@data = { "classes" => [486, 481], # depending if owlapi imports SKOS - "averageChildCount" => 5, - "maxChildCount" => 65, - "classesWithOneChild" => [13, 14], - "classesWithMoreThan25Children" => 2, - "classesWithNoDefinition" => [11, 10], - "individuals" => 124, - "properties" => [63, 45], - "maxDepth" => 7 } + OntologySubmission.all.each {|s| s.delete } + Ontology.all.each {|o| o.delete } + @@data = {"classes"=>486, + "averageChildCount"=>5, + "maxChildCount"=>65, + "classesWithOneChild"=>14, + "classesWithMoreThan25Children"=>2, + "classesWithNoDefinition"=>11, + "individuals"=>124, + "properties"=>63, + "maxDepth"=> 7 } @@options = { ont_count: 2, submission_count: 3, submissions_to_process: [1, 2], diff --git a/test/controllers/test_notes_controller.rb b/test/controllers/test_notes_controller.rb index d9223669..83cb1045 100644 --- a/test/controllers/test_notes_controller.rb +++ b/test/controllers/test_notes_controller.rb @@ -3,9 +3,9 @@ class TestNotesController < TestCase - def self.before_suite - self.new("before_suite").delete_ontologies_and_submissions - @@ontology, @@cls = self.new("before_suite")._ontology_and_class + def before_suite + self.delete_ontologies_and_submissions + @@ontology, @@cls = self._ontology_and_class @@note_user = "test_note_user" @@user = LinkedData::Models::User.new( @@ -41,7 +41,7 @@ def test_all_notes get '/notes' assert last_response.ok? notes = MultiJson.load(last_response.body) - assert notes.length >= 5 + assert_operator 5, :<=, notes.length end def test_single_note @@ -62,21 +62,22 @@ def test_note_lifecycle relatedOntology: [@@ontology.id.to_s] } post "/notes", MultiJson.dump(note), "CONTENT_TYPE" => "application/json" - assert last_response.status == 201 + assert_equal 201, last_response.status new_note = MultiJson.load(last_response.body) get new_note["@id"] assert last_response.ok? + assert_equal 200, last_response.status note_changes = {body: "New testing body"} patch new_note["@id"], MultiJson.dump(note_changes), "CONTENT_TYPE" => "application/json" - assert last_response.status == 204 + assert_equal 204, last_response.status get new_note["@id"] patched_note = MultiJson.load(last_response.body) assert_equal patched_note["body"], note_changes[:body] delete new_note["@id"] - assert last_response.status == 204 + assert_equal 204, last_response.status end def test_proposal_lifecycle @@ -97,21 +98,23 @@ def test_proposal_lifecycle } post "/notes", MultiJson.dump(note), "CONTENT_TYPE" => "application/json" - assert last_response.status == 201 + assert_equal 201, last_response.status new_note = MultiJson.load(last_response.body) + # assert_equal 'blah', new_note get new_note["@id"] assert last_response.ok? note_changes = {proposal: {label: "New sleed study facility"}} patch new_note["@id"], MultiJson.dump(note_changes), "CONTENT_TYPE" => "application/json" - assert last_response.status == 204 + assert_equal 204, last_response.status get new_note["@id"] patched_note = MultiJson.load(last_response.body) - assert_equal patched_note["label"], note_changes[:label] + refute_nil patched_note['proposal']['label'] + assert_equal patched_note['proposal']['label'], note_changes[:proposal][:label] delete new_note["@id"] - assert last_response.status == 204 + assert_equal 204, last_response.status end def test_notes_for_ontology @@ -120,8 +123,8 @@ def test_notes_for_ontology get ont["links"]["notes"] notes = MultiJson.load(last_response.body) test_note = notes.select {|n| n["subject"].eql?("Test subject 1")} - assert test_note.length == 1 - assert notes.length >= 5 + assert_equal 1, test_note.length + assert_operator 5, :<=, notes.length end def test_notes_for_class @@ -130,7 +133,7 @@ def test_notes_for_class get cls["links"]["notes"] notes = MultiJson.load(last_response.body) test_note = notes.select {|n| n["subject"].eql?("Test subject 1")} - assert test_note.length == 1 - assert notes.length >= 5 + assert_equal 1, test_note.length + assert_operator 5, :<=, notes.length end end diff --git a/test/controllers/test_ontologies_controller.rb b/test/controllers/test_ontologies_controller.rb index ad062742..d05959e8 100644 --- a/test/controllers/test_ontologies_controller.rb +++ b/test/controllers/test_ontologies_controller.rb @@ -1,11 +1,12 @@ +require 'webrick' require_relative '../test_case' class TestOntologiesController < TestCase - def self.before_suite - _set_vars - _delete - _create_user - _create_onts + def before_suite + self.class._set_vars + self.class._delete + self.class._create_user + self.class._create_onts end def teardown @@ -29,6 +30,8 @@ def self._set_vars hasOntologyLanguage: "OWL", administeredBy: ["tom"] } + @@server_thread = nil + @@server_url = nil end def self._create_user @@ -255,6 +258,71 @@ def test_download_acl_only end end + def test_on_demand_ontology_pull + ont = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true)[2].first + ont.bring_remaining + acronym = ont.acronym + sub = ont.submissions.first + sub.bring(:pullLocation) if sub.bring?(:pullLocation) + assert_nil sub.pullLocation, msg = "Pull location should be nil at this point in the test" + + allowed_user = ont.administeredBy.first + allowed_user.bring(:apikey) if allowed_user.bring?(:apikey) + + post "/ontologies/#{acronym}/pull?apikey=#{allowed_user.apikey}" + assert_equal(404, last_response.status, msg="This ontology is NOT configured to be remotely pulled at this point in the test. It should return status 404") + + begin + start_server + sub.pullLocation = RDF::IRI.new(@@server_url) + sub.save + LinkedData.settings.enable_security = true + post "/ontologies/#{acronym}/pull?apikey=#{allowed_user.apikey}" + assert_equal(204, last_response.status, msg="The ontology admin was unable to execute the on-demand pull") + + blocked_user = User.new({ + username: "blocked", + email: "test@example.org", + password: "12345" + }) + blocked_user.save + post "/ontologies/#{acronym}/pull?apikey=#{blocked_user.apikey}" + assert_equal(403, last_response.status, msg="An unauthorized user was able to execute the on-demand pull") + ensure + del = User.find("blocked").first + del.delete if del + stop_server + LinkedData.settings.enable_security = false + del = User.find("blocked").first + del.delete if del + end + end + + def test_detach_a_view + view = Ontology.find(@@view_acronym).include(:viewOf).first + ont = view.viewOf + refute_nil view + refute_nil ont + + remove_view_of = {viewOf: ''} + patch "/ontologies/#{@@view_acronym}", MultiJson.dump(remove_view_of), "CONTENT_TYPE" => "application/json" + + assert last_response.status == 204 + + get "/ontologies/#{@@view_acronym}" + onto = MultiJson.load(last_response.body) + assert_nil onto["viewOf"] + + + add_view_of = {viewOf: @@acronym} + patch "/ontologies/#{@@view_acronym}", MultiJson.dump(add_view_of), "CONTENT_TYPE" => "application/json" + + assert last_response.status == 204 + + get "/ontologies/#{@@view_acronym}?include=all" + onto = MultiJson.load(last_response.body) + assert_equal onto["viewOf"], ont.id.to_s + end def test_detach_a_view view = Ontology.find(@@view_acronym).include(:viewOf).first @@ -282,11 +350,85 @@ def test_detach_a_view assert_equal onto["viewOf"], ont.id.to_s end + def test_ontology_agents + ontologies_and_submissions = create_ontologies_and_submissions(ont_count: 2, submission_count: 1, process_submission: true) + submission1 = ontologies_and_submissions[2].first.submissions.last + submission2 = ontologies_and_submissions[2].last.submissions.last + + ontology_acronym1 = ontologies_and_submissions[1].first + ontology_acronym2 = ontologies_and_submissions[1].last + + submission1.bring(*OntologySubmission.agents_attrs) + submission2.bring(*OntologySubmission.agents_attrs) + + # To insure that we don't have duplicated agents in the response + agent_syphax = _create_agent(name: 'Syphax', type: 'person') + + submission1.publisher = [_create_agent(name: 'Bilel', type: 'person'), agent_syphax] + submission1.hasContributor = [_create_agent(name: 'Clement', type: 'person'), agent_syphax] + + submission2.publisher = [_create_agent(name: 'Imad', type: 'person'), _create_agent(name: 'Serine', type: 'person')] + + submission1.save + submission2.save + + + get "/ontologies/#{ontology_acronym1}/agents" + + response = MultiJson.load(last_response.body) + assert_equal response.length, 3 + response.each do |r| + assert_includes ['Bilel', 'Syphax', 'Clement'], r["name"] + end + + get "/ontologies/#{ontology_acronym2}/agents" + + response = MultiJson.load(last_response.body) + assert_equal response.length, 2 + response.each do |r| + assert_includes ['Imad', 'Serine'], r["name"] + end + end + private + def start_server + ont_path = File.expand_path("../../data/ontology_files/BRO_v3.2.owl", __FILE__) + file = File.new(ont_path) + port = Random.rand(55000..65535) # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports + @@server_url = "http://localhost:#{port}/" + @@server_thread = Thread.new do + server = WEBrick::HTTPServer.new(Port: port) + server.mount_proc '/' do |req, res| + contents = file.read + file.rewind + res.body = contents + end + begin + server.start + ensure + server.shutdown + end + end + end + + def stop_server + Thread.kill(@@server_thread) if @@server_thread + end + def check400(response) assert response.status >= 400 assert MultiJson.load(response.body)["errors"] end + def _create_agent(name: 'name', type: 'person') + agent = LinkedData::Models::Agent.new({ + agentType: type, + name: name, + creator: User.find('tim').first + }) + agent.save + agent + end + end diff --git a/test/controllers/test_ontology_analytics_controller.rb b/test/controllers/test_ontology_analytics_controller.rb index 7f2df926..a37ffbc9 100644 --- a/test/controllers/test_ontology_analytics_controller.rb +++ b/test/controllers/test_ontology_analytics_controller.rb @@ -196,7 +196,7 @@ class TestOntologyAnalyticsController < TestCase } } - def self.before_suite + def before_suite @@redis = Redis.new(:host => Annotator.settings.annotator_redis_host, :port => Annotator.settings.annotator_redis_port) db_size = @@redis.dbsize if db_size > MAX_TEST_REDIS_SIZE @@ -220,32 +220,32 @@ def self.before_suite end def teardown - self.class._delete_onts - self.class._create_onts + self._delete_onts + self._create_onts end - def self._create_user + def _create_user username = "tim" test_user = LinkedData::Models::User.new(username: username, email: "#{username}@example.org", password: "password") test_user.save if test_user.valid? @@user = test_user.valid? ? test_user : LinkedData::Models::User.find(username).first end - def self._create_onts + def _create_onts @@onts.each do |acronym, name| ont = LinkedData::Models::Ontology.new(acronym: acronym, name: name, administeredBy: [@@user]) ont.save end end - def self._delete_onts + def _delete_onts @@onts.each do |acronym, _| ont = LinkedData::Models::Ontology.find(acronym).first ont.delete unless ont.nil? end end - def self._delete + def _delete _delete_onts test_user = LinkedData::Models::User.find("tim").first test_user.delete unless test_user.nil? diff --git a/test/controllers/test_ontology_submissions_controller.rb b/test/controllers/test_ontology_submissions_controller.rb index 33efe73f..d73e2a36 100644 --- a/test/controllers/test_ontology_submissions_controller.rb +++ b/test/controllers/test_ontology_submissions_controller.rb @@ -2,10 +2,11 @@ class TestOntologySubmissionsController < TestCase - def self.before_suite - _set_vars - _create_user - _create_onts + def before_suite + self.backend_4s_delete + self.class._set_vars + self.class._create_user + self.class._create_onts end def self._set_vars @@ -40,8 +41,7 @@ def self._create_onts end def setup - delete_ontologies_and_submissions - self.class.before_suite + before_suite end def test_submissions_for_given_ontology @@ -302,6 +302,49 @@ def test_upload_eco_portal_metadata end + def test_ontology_submissions_access_controller + count, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 2, submission_count: 1, process_submission: false) + # case first submission is private + acronym = created_ont_acronyms.first + ont = onts.first.bring_remaining + + begin + allowed_user = User.new({ + username: "allowed", + email: "test@example.org", + password: "12345" + }) + allowed_user.save + blocked_user = User.new({ + username: "blocked", + email: "test1254@example.org", + password: "12345" + }) + blocked_user.save + + ont.acl = [allowed_user] + ont.viewingRestriction = "private" + ont.save + + LinkedData.settings.enable_security = true + + get "/submissions?apikey=#{allowed_user.apikey}" + assert_equal 200, last_response.status + submissions = MultiJson.load(last_response.body) + assert_equal 2, submissions.size + + get "/submissions?apikey=#{blocked_user.apikey}" + assert_equal 200, last_response.status + submissions = MultiJson.load(last_response.body) + assert_equal 1, submissions.size + ensure + LinkedData.settings.enable_security = false + del = User.find("allowed").first + del.delete if del + del = User.find("blocked").first + del.delete if del + end + end def test_submissions_pagination num_onts_created, created_ont_acronyms, ontologies = create_ontologies_and_submissions(ont_count: 2, submission_count: 2) @@ -431,7 +474,7 @@ def test_submissions_pagination_filter assert last_response.ok? submissions = MultiJson.load(last_response.body) refute_empty submissions["collection"] - assert_equal ontologies.map{|x| x.latest_submission(status: :any).bring(:creationDate).creationDate}.sort.map(&:to_s), submissions["collection"].map{|x| x["creationDate"]}.reverse + assert_equal ontologies.map{|x| x.latest_submission(status: :any).bring(:creationDate).creationDate}.sort, submissions["collection"].map{|x| DateTime.parse(x["creationDate"])}.reverse # test search with format get "/submissions?page=1&pagesize=100&acronym=tes&name=tes&hasOntologyLanguage=SKOS" @@ -575,6 +618,16 @@ def test_submissions_param_include test_submissions_custom_includes end + def test_submission_diff + num_onts_created, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 2, + process_submission: true, + process_options: { process_rdf: true, extract_metadata: false, diff: true} ) + + ont = onts.first + sub = ont.latest_submission(status: :any) + + get "/ontologies/#{ont.acronym}/submissions/#{sub.submissionId}/diff" + end private def submission_keys(sub) sub.to_hash.keys - %w[@id @type id] diff --git a/test/controllers/test_properties_controller.rb b/test/controllers/test_properties_controller.rb index 96879083..c364a236 100644 --- a/test/controllers/test_properties_controller.rb +++ b/test/controllers/test_properties_controller.rb @@ -2,7 +2,7 @@ class TestPropertiesController < TestCase - def self.before_suite + def before_suite count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ process_submission: true, process_options:{process_rdf: true, extract_metadata: false}, @@ -27,7 +27,7 @@ def self.before_suite @@acronyms = @@ontologies.map { |ont| ont.bring_remaining; ont.acronym } end - def self.after_suite + def after_suite LinkedData::SampleData::Ontology.delete_ontologies_and_submissions end @@ -47,14 +47,33 @@ def test_single_property get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Originator" assert last_response.ok? results = MultiJson.load(last_response.body) + assert results.is_a?(Hash) assert_equal ["Originator"], results["label"] assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Originator", results["@id"] + assert results.key?('range') + assert results.key?('domain') get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23DummyProp" assert_equal 404, last_response.status end + def test_single_property_all_attributes + get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Originator?display=all" + assert last_response.ok? + results = MultiJson.load(last_response.body) + assert_equal ["Originator"], results["label"] + assert results.key?('range') + assert results.key?('domain') + + assert_equal results["properties"]["http://www.w3.org/2000/01/rdf-schema#comment"], ["Originator of a class"] + assert_equal results["properties"]["http://www.w3.org/2004/02/skos/core#prefLabel"], ["Originator"] + assert_equal results["properties"]["http://www.w3.org/1999/02/22-rdf-syntax-ns#type"], ["http://www.w3.org/2002/07/owl#DatatypeProperty"] + assert_equal results["properties"]["http://www.w3.org/2000/01/rdf-schema#domain"], ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Algorithm"] + assert_equal results["properties"]["http://www.w3.org/2000/01/rdf-schema#label"], ["Originator"] + + end + def test_property_roots get "/ontologies/#{@@acronyms.first}/properties/roots" assert last_response.ok? @@ -66,10 +85,10 @@ def test_property_roots assert_includes [18, 13], opr.length # count datatype properties dpr = pr.select { |p| p["@type"] == "http://www.w3.org/2002/07/owl#DatatypeProperty" } - assert_includes [32,31], dpr.length + assert_includes [32, 31], dpr.length # count annotation properties apr = pr.select { |p| p["@type"] == "http://www.w3.org/2002/07/owl#AnnotationProperty" } - assert_includes [12,8], apr.length + assert_includes [12, 8], apr.length # check for non-root properties assert_empty pr.select { |p| ["http://www.w3.org/2004/02/skos/core#broaderTransitive", @@ -174,7 +193,7 @@ def test_property_descendants dn = MultiJson.load(last_response.body) assert_equal 2, dn.length assert_equal ["http://www.semanticweb.org/ontologies/2009/9/12/Ontology1255323704656.owl#overExpress", - "http://www.semanticweb.org/ontologies/2009/9/12/Ontology1255323704656.owl#underExpress"].sort, dn.map { |d| d["@id"] }.sort + "http://www.semanticweb.org/ontologies/2009/9/12/Ontology1255323704656.owl#underExpress"].sort, dn.map { |d| d["@id"] }.sort end def test_property_parents @@ -207,7 +226,7 @@ def test_property_children assert_empty ch get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23semanticRelation" - return unless last_response.ok? #depending if owlapi import SKOS + return unless last_response.ok? # depending if owlapi import SKOS get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23semanticRelation/children" assert last_response.ok? diff --git a/test/controllers/test_properties_search_controller.rb b/test/controllers/test_properties_search_controller.rb index 6c99fc40..b989cd1a 100644 --- a/test/controllers/test_properties_search_controller.rb +++ b/test/controllers/test_properties_search_controller.rb @@ -2,7 +2,9 @@ class TestPropertiesSearchController < TestCase - def self.before_suite + def before_suite + self.backend_4s_delete + count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ process_submission: true, process_options:{process_rdf: true, extract_metadata: false, index_properties: true}, @@ -26,7 +28,7 @@ def self.before_suite @@ontologies = bro.concat(mccl) end - def self.after_suite + def after_suite LinkedData::SampleData::Ontology.delete_ontologies_and_submissions LinkedData::Models::OntologyProperty.indexClear LinkedData::Models::OntologyProperty.indexCommit diff --git a/test/controllers/test_provisional_classes_controller.rb b/test/controllers/test_provisional_classes_controller.rb index 7225d772..e54c7805 100644 --- a/test/controllers/test_provisional_classes_controller.rb +++ b/test/controllers/test_provisional_classes_controller.rb @@ -1,9 +1,9 @@ require_relative '../test_case' class TestProvisionalClassesController < TestCase - def self.before_suite - self.new("before_suite").delete_ontologies_and_submissions - @@ontology, classes = self.new("before_suite")._ontology_and_classes + def before_suite + self.delete_ontologies_and_submissions + @@ontology, classes = self._ontology_and_classes @@cls = classes[0] @@cls1 = classes[1] @@ -32,7 +32,7 @@ def self.before_suite end end - def self.after_suite + def after_suite 3.times do |i| @@pcs[i].delete end diff --git a/test/controllers/test_provisional_relations_controller.rb b/test/controllers/test_provisional_relations_controller.rb index 83f2761d..f097dde9 100644 --- a/test/controllers/test_provisional_relations_controller.rb +++ b/test/controllers/test_provisional_relations_controller.rb @@ -1,9 +1,9 @@ require_relative '../test_case' class TestProvisionalRelationsController < TestCase - def self.before_suite - self.new("before_suite").delete_ontologies_and_submissions - @@ontology, classes = self.new("before_suite")._ontology_and_classes + def before_suite + self.delete_ontologies_and_submissions + @@ontology, classes = self._ontology_and_classes @@cls1 = classes[0] @@cls2 = classes[1] @@ -39,7 +39,7 @@ def self.before_suite @@test_rel.save end - def self.after_suite + def after_suite @@test_pc.delete @@test_user.delete end diff --git a/test/controllers/test_recommender_controller.rb b/test/controllers/test_recommender_controller.rb index 58d6d942..c46255fc 100644 --- a/test/controllers/test_recommender_controller.rb +++ b/test/controllers/test_recommender_controller.rb @@ -2,7 +2,7 @@ class TestRecommenderController < TestCase - def self.before_suite + def before_suite @@redis = Redis.new(:host => Annotator.settings.annotator_redis_host, :port => Annotator.settings.annotator_redis_port) db_size = @@redis.dbsize if db_size > MAX_TEST_REDIS_SIZE diff --git a/test/controllers/test_recommender_v1_controller.rb b/test/controllers/test_recommender_v1_controller.rb index 3ac4862d..fe67ffa7 100644 --- a/test/controllers/test_recommender_v1_controller.rb +++ b/test/controllers/test_recommender_v1_controller.rb @@ -1,40 +1,12 @@ require_relative '../test_case' - +# recommender_v1 is deprecated as of 2024-10-27 +# TODO: remove completely after 2025-10-27 class TestRecommenderV1Controller < TestCase - - def self.before_suite - LinkedData::SampleData::Ontology.delete_ontologies_and_submissions - @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true) - @@text = < @@text + :text => 'recommender v1 is deprecated' } get "/recommender_v1", params - assert last_response.ok? - recommendations = MultiJson.load(last_response.body) - assert_instance_of(Array, recommendations) - assert_equal(3, recommendations.length, msg='Failed to return 3 recommendations') - rec = recommendations.first - assert_instance_of(Hash, rec) - ont_acronyms = @@ontologies.map {|o| o.bring(:acronym); o.acronym } - assert ont_acronyms.include? rec['ontology']['acronym'] - assert rec['annotatedClasses'].length == 0 # no classes requested - assert rec['numTermsMatched'] > 0 - assert rec['numTermsTotal'] > 0 - assert rec['numTermsTotal'] >= rec['numTermsMatched'] - assert recommendations[0]['score'].to_i >= recommendations[1]['score'].to_i - assert recommendations[1]['score'].to_i >= recommendations[2]['score'].to_i + assert_equal 410, last_response.status end - end diff --git a/test/controllers/test_replies_controller.rb b/test/controllers/test_replies_controller.rb index 41b15e2e..19a6ddd0 100644 --- a/test/controllers/test_replies_controller.rb +++ b/test/controllers/test_replies_controller.rb @@ -2,8 +2,8 @@ class TestRepliesController < TestCase - def self.before_suite - ontologies = self.new("before_suite").create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: false)[2] + def before_suite + ontologies = self.create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: false)[2] @@ontology = ontologies.first @@reply_user = "test_reply_user" diff --git a/test/controllers/test_schemes_controller.rb b/test/controllers/test_schemes_controller.rb index d4504aa3..b8c6893f 100644 --- a/test/controllers/test_schemes_controller.rb +++ b/test/controllers/test_schemes_controller.rb @@ -2,7 +2,7 @@ class TestSchemesController < TestCase - def self.before_suite + def before_suite LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ process_submission: true, acronym: 'INRAETHES', @@ -13,7 +13,7 @@ def self.before_suite }) end - def self.after_suite + def after_suite LinkedData::SampleData::Ontology.delete_ontologies_and_submissions end diff --git a/test/controllers/test_search_controller.rb b/test/controllers/test_search_controller.rb index 7549ca3e..86e01cc3 100644 --- a/test/controllers/test_search_controller.rb +++ b/test/controllers/test_search_controller.rb @@ -2,7 +2,7 @@ class TestSearchController < TestCase - def self.before_suite + def before_suite LinkedData::Models::Ontology.indexClear LinkedData::Models::Agent.indexClear LinkedData::Models::Class.indexClear @@ -59,7 +59,7 @@ def self.before_suite @@test_pc_child.save end - def self.after_suite + def after_suite @@test_pc_root.delete @@test_pc_child.delete LinkedData::SampleData::Ontology.delete_ontologies_and_submissions @@ -92,7 +92,7 @@ def test_search_ontology_filter assert last_response.ok? results = MultiJson.load(last_response.body) doc = results["collection"][0] - assert_equal "cell line", doc["prefLabel"].first + assert_equal "cell line", doc["prefLabel"] assert doc["links"]["ontology"].include? acronym results["collection"].each do |doc| acr = doc["links"]["ontology"].split('/')[-1] @@ -153,7 +153,7 @@ def test_search_other_filters .join(' ') .include?("Funding Resource") end - assert_equal "Funding Resource", results["collection"][0]["prefLabel"].first + assert_equal "Funding Resource", results["collection"][0]["prefLabel"] assert_equal "T028", results["collection"][0]["semanticType"][0] assert_equal "X123456", results["collection"][0]["cui"][0] @@ -208,7 +208,7 @@ def test_search_provisional_class assert_includes [10, 6], results["collection"].length # depending if owlapi import SKOS concepts provisional = results["collection"].select {|res| assert_equal ontology_type, res["ontologyType"]; res["provisional"]} assert_equal 1, provisional.length - assert_equal @@test_pc_root.label, provisional[0]["prefLabel"].first + assert_equal @@test_pc_root.label, provisional[0]["prefLabel"] # subtree root with provisional class test get "search?ontology=#{acronym}&subtree_root_id=#{CGI::escape(@@cls_uri.to_s)}&also_search_provisional=true" @@ -217,32 +217,60 @@ def test_search_provisional_class provisional = results["collection"].select {|res| res["provisional"]} assert_equal 1, provisional.length - assert_equal @@test_pc_child.label, provisional[0]["prefLabel"].first + assert_equal @@test_pc_child.label, provisional[0]["prefLabel"] end def test_multilingual_search get "/search?q=Activity&ontologies=BROSEARCHTEST-0" - res = MultiJson.load(last_response.body) + res = MultiJson.load(last_response.body) + refute_equal 0, res["totalCount"] doc = res["collection"].select{|doc| doc["@id"].to_s.eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first refute_nil doc + assert_equal "ActivityEnglish", doc["prefLabel"] res = LinkedData::Models::Class.search("prefLabel_none:Activity", {:fq => "submissionAcronym:BROSEARCHTEST-0", :start => 0, :rows => 80}) refute_equal 0, res["response"]["numFound"] refute_nil res["response"]["docs"].select{|doc| doc["resource_id"].eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first + get "/search?q=Activit%C3%A9&ontologies=BROSEARCHTEST-0&lang=fr" res = MultiJson.load(last_response.body) refute_equal 0, res["totalCount"] - refute_nil res["collection"].select{|doc| doc["@id"].eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first - + doc = res["collection"].select{|doc| doc["@id"].eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first + refute_nil doc + assert_equal "Activité", doc["prefLabel"] get "/search?q=ActivityEnglish&ontologies=BROSEARCHTEST-0&lang=en" res = MultiJson.load(last_response.body) refute_equal 0, res["totalCount"] - refute_nil res["collection"].select{|doc| doc["@id"].eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first + doc = res["collection"].select{|doc| doc["@id"].eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first + refute_nil doc + assert_equal "ActivityEnglish", doc["prefLabel"] + + + get "/search?q=ActivityEnglish&ontologies=BROSEARCHTEST-0&lang=fr,es" + res = MultiJson.load(last_response.body) + assert_equal 0, res["totalCount"] + + get "/search?q=ActivityEnglish&ontologies=BROSEARCHTEST-0&lang=en,es" + res = MultiJson.load(last_response.body) + refute_equal 0, res["totalCount"] + doc = res["collection"].select{|doc| doc["@id"].eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first + refute_nil doc + expected_pref_label = {"none"=>["Activity"], "en"=>["ActivityEnglish"]} + assert_equal expected_pref_label, doc["prefLabel"] + + get "/search?q=ActivityEnglish&ontologies=BROSEARCHTEST-0&lang=all" + res = MultiJson.load(last_response.body) + refute_equal 0, res["totalCount"] + doc = res["collection"].select{|doc| doc["@id"].eql?('http://bioontology.org/ontologies/Activity.owl#Activity')}.first + refute_nil doc + expected_pref_label = {"none"=>["Activity"], "en"=>["ActivityEnglish"], "fr"=>["Activité"]} + assert_equal expected_pref_label, doc["prefLabel"] + get "/search?q=ActivityEnglish&ontologies=BROSEARCHTEST-0&lang=fr&require_exact_match=true" @@ -264,5 +292,229 @@ def test_multilingual_search end + def test_search_obo_id + skip 'need to be fixed in the futur to be aligned with bioportal' + + ncit_acronym = 'NCIT' + ogms_acronym = 'OGMS' + cno_acronym = 'CNO' + + begin + LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ + process_submission: true, + acronym: ncit_acronym, + acronym_suffix: '', + name: "NCIT Search Test", + pref_label_property: "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P108", + synonym_property: "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90", + definition_property: "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P97", + file_path: "./test/data/ontology_files/ncit_test.owl", + ontology_format: 'OWL', + ont_count: 1, + submission_count: 1 + }) + LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ + process_submission: true, + acronym: ogms_acronym, + acronym_suffix: '', + name: "OGMS Search Test", + file_path: "./test/data/ontology_files/ogms_test.owl", + ontology_format: 'OWL', + ont_count: 1, + submission_count: 1 + }) + LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ + process_submission: true, + acronym: cno_acronym, + acronym_suffix: '', + name: "CNO Search Test", + file_path: "./test/data/ontology_files/CNO_05.owl", + ontology_format: 'OWL', + ont_count: 1, + submission_count: 1 + }) + + # mdorf, 3/2/2024, when the : is followed by a LETTER, as in NCIT:C20480, + # then Solr does not split the query on the tokens, + # but when the : is followed by a number, as in OGMS:0000071, + # then Solr does split this on tokens and shows the other resuluts + get "/search?q=OGMS:0000071" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + assert_equal 6, docs.size + assert_equal ogms_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[0]["links"]["ontology"]) + assert_equal cno_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[1]["links"]["ontology"]) + assert_equal ncit_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[2]["links"]["ontology"]) + + label1 = docs[1]["prefLabel"].kind_of?(Array) ? docs[1]["prefLabel"].first : docs[1]["prefLabel"] + label2 = docs[2]["prefLabel"].kind_of?(Array) ? docs[2]["prefLabel"].first : docs[2]["prefLabel"] + label3 = docs[3]["prefLabel"].kind_of?(Array) ? docs[3]["prefLabel"].first : docs[3]["prefLabel"] + label4 = docs[4]["prefLabel"].kind_of?(Array) ? docs[4]["prefLabel"].first : docs[4]["prefLabel"] + label5 = docs[5]["prefLabel"].kind_of?(Array) ? docs[5]["prefLabel"].first : docs[5]["prefLabel"] + + assert_equal 'realization', label1 + assert_equal 'realization', label2 + assert label3.upcase.include?('OGMS ') + assert label4.upcase.include?('OGMS ') + assert label5.upcase.include?('OGMS ') + + get "/search?q=CNO:0000002" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + assert_equal 7, docs.size + assert_equal cno_acronym, LinkedData::Utils::Triples.last_iri_fragment(docs[0]["links"]["ontology"]) + acr_1 = LinkedData::Utils::Triples.last_iri_fragment(docs[1]["links"]["ontology"]) + assert_includes [ncit_acronym, ogms_acronym], acr_1 + acr_2= LinkedData::Utils::Triples.last_iri_fragment(docs[2]["links"]["ontology"]) + + assert acr_2 === ncit_acronym || acr_2 === ogms_acronym + + label3 = docs[3]["prefLabel"].kind_of?(Array) ? docs[3]["prefLabel"].first : docs[3]["prefLabel"] + label4 = docs[4]["prefLabel"].kind_of?(Array) ? docs[4]["prefLabel"].first : docs[4]["prefLabel"] + label5 = docs[5]["prefLabel"].kind_of?(Array) ? docs[5]["prefLabel"].first : docs[5]["prefLabel"] + label6 = docs[6]["prefLabel"].kind_of?(Array) ? docs[6]["prefLabel"].first : docs[6]["prefLabel"] + + assert label3.upcase.include?('CNO ') + assert label4.upcase.include?('CNO ') + assert label5.upcase.include?('CNO ') + assert label6.upcase.include?('CNO ') + + # mdorf, 3/2/2024, when the : is followed by a LETTER, as in NCIT:C20480, + # then Solr does not split the query on the tokens, + # but when the : is followed by a number, as in OGMS:0000071, + # then Solr does split this on tokens and shows the other resuluts + get "/search?q=Thesaurus:C20480" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + assert_equal 1, docs.size + + label0 = docs[0]["prefLabel"].kind_of?(Array) ? docs[0]["prefLabel"].first : docs[0]["prefLabel"] + assert_equal 'Cellular Process', label0 + + get "/search?q=NCIT:C20480" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + assert_equal 1, docs.size + + label0 = docs[0]["prefLabel"].kind_of?(Array) ? docs[0]["prefLabel"].first : docs[0]["prefLabel"] + assert_equal 'Cellular Process', label0 + + get "/search?q=Leukocyte Apoptotic Process&ontologies=#{ncit_acronym}" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + + label0 = docs[0]["prefLabel"].kind_of?(Array) ? docs[0]["prefLabel"].first : docs[0]["prefLabel"] + label1 = docs[1]["prefLabel"].kind_of?(Array) ? docs[1]["prefLabel"].first : docs[1]["prefLabel"] + label2 = docs[2]["prefLabel"].kind_of?(Array) ? docs[2]["prefLabel"].first : docs[2]["prefLabel"] + + assert_equal 'Leukocyte Apoptotic Process', label0 + assert_equal 'Leukocyte Apoptotic Test Class', label1 + assert_equal 'Lymphocyte Apoptotic Process', label2 + ensure + ont = LinkedData::Models::Ontology.find(ncit_acronym).first + ont.delete if ont + ont = LinkedData::Models::Ontology.find(ncit_acronym).first + assert_nil ont + + ont = LinkedData::Models::Ontology.find(ogms_acronym).first + ont.delete if ont + ont = LinkedData::Models::Ontology.find(ogms_acronym).first + assert_nil ont + + ont = LinkedData::Models::Ontology.find(cno_acronym).first + ont.delete if ont + ont = LinkedData::Models::Ontology.find(cno_acronym).first + assert_nil ont + end + end + + def test_search_short_id + skip 'need to be fixed in the futur to be aligned with bioportal' + vario_acronym = 'VARIO' + + begin + LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ + process_submission: true, + acronym: vario_acronym, + acronym_suffix: "", + name: "VARIO OBO Search Test", + file_path: "./test/data/ontology_files/vario_test.obo", + ontology_format: 'OBO', + ont_count: 1, + submission_count: 1 + }) + get "/search?q=VariO:0012&ontologies=#{vario_acronym}" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + assert_equal 1, docs.size + + get "/search?q=Blah:0012&ontologies=#{vario_acronym}" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + assert_equal 0, docs.size + + get "/search?q=Vario:12345&ontologies=#{vario_acronym}" + assert last_response.ok? + results = MultiJson.load(last_response.body) + docs = results["collection"] + assert_equal 0, docs.size + ensure + ont = LinkedData::Models::Ontology.find(vario_acronym).first + ont.delete if ont + ont = LinkedData::Models::Ontology.find(vario_acronym).first + assert ont.nil? + end + end + + def test_language_attribute_filter + get "/search?q=Activit%C3%A9&ontologies=BROSEARCHTEST-0&lang=fr" + results = MultiJson.load(last_response.body) + assert last_response.ok? + assert_equal 1, results["collection"].size + doc = results["collection"][0] + pref_label = doc["prefLabel"].kind_of?(Array) ? doc["prefLabel"].first : doc["prefLabel"] + assert_equal "Activité", pref_label + assert_equal 1, doc["definition"].size + assert 1, doc["definition"][0].include?("d’intérêt pouvant") + + get "/search?q=ActivityEnglish&ontologies=BROSEARCHTEST-0&lang=en" + results = MultiJson.load(last_response.body) + assert last_response.ok? + assert_equal 1, results["collection"].size + doc = results["collection"][0] + pref_label = doc["prefLabel"].kind_of?(Array) ? doc["prefLabel"].first : doc["prefLabel"] + assert_equal "ActivityEnglish", pref_label + assert_equal 1, doc["definition"].size + assert 1, doc["definition"][0].include?("Activity of interest that may be related to") + + get "/search?q=ActivityEnglish&ontologies=BROSEARCHTEST-0" + results = MultiJson.load(last_response.body) + assert last_response.ok? + assert_equal 1, results["collection"].size + doc = results["collection"][0] + pref_label = doc["prefLabel"].kind_of?(Array) ? doc["prefLabel"].first : doc["prefLabel"] + assert_equal "ActivityEnglish", pref_label + assert_equal 1, doc["definition"].size + assert 1, doc["definition"][0].include?("Activity of interest that may be related to") + + get "/search?q=Activit%C3%A9&ontologies=BROSEARCHTEST-0&lang=all" + results = MultiJson.load(last_response.body) + assert last_response.ok? + assert_equal 1, results["collection"].size + doc = results["collection"][0] + assert doc["prefLabel"].kind_of?(Hash) + assert_equal 3, doc["prefLabel"].size + assert doc["synonym"].kind_of?(Hash) + assert_equal 1, doc["synonym"].size + assert doc["definition"].kind_of?(Hash) + assert_equal 2, doc["definition"].size + end end diff --git a/test/controllers/test_search_models_controller.rb b/test/controllers/test_search_models_controller.rb index 233c7bc4..0585318d 100644 --- a/test/controllers/test_search_models_controller.rb +++ b/test/controllers/test_search_models_controller.rb @@ -2,7 +2,7 @@ class TestSearchModelsController < TestCase - def self.after_suite + def after_suite LinkedData::SampleData::Ontology.delete_ontologies_and_submissions LinkedData::Models::Ontology.indexClear LinkedData::Models::Agent.indexClear @@ -12,7 +12,7 @@ def self.after_suite end def setup - self.class.after_suite + after_suite end def test_show_all_collection diff --git a/test/controllers/test_skos_xl_label_controller.rb b/test/controllers/test_skos_xl_label_controller.rb index 4c929e2d..e848f294 100644 --- a/test/controllers/test_skos_xl_label_controller.rb +++ b/test/controllers/test_skos_xl_label_controller.rb @@ -2,7 +2,7 @@ class TestSkosXlLabelController < TestCase - def self.before_suite + def before_suite LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ process_submission: true, acronym: 'INRAETHES', @@ -18,7 +18,7 @@ def self.before_suite sub.save end - def self.after_suite + def after_suite LinkedData::SampleData::Ontology.delete_ontologies_and_submissions end diff --git a/test/controllers/test_slices_controller.rb b/test/controllers/test_slices_controller.rb index 601b15a7..27efce1c 100644 --- a/test/controllers/test_slices_controller.rb +++ b/test/controllers/test_slices_controller.rb @@ -2,12 +2,11 @@ class TestSlicesController < TestCase - def self.before_suite + def before_suite ont_count, ont_acronyms, @@onts = LinkedData::SampleData::Ontology.create_ontologies_and_submissions(ont_count: 1, submission_count: 0) - @@slice_acronyms = ["tst-a", "tst-b"].sort - _create_slice(@@slice_acronyms[0], "Test Slice A", @@onts) - _create_slice(@@slice_acronyms[1], "Test Slice B", @@onts) + self.class._create_slice(@@slice_acronyms[0], "Test Slice A", @@onts) + self.class._create_slice(@@slice_acronyms[1], "Test Slice B", @@onts) @@user = User.new({ username: "test-slice", @@ -15,17 +14,17 @@ def self.before_suite password: "12345" }).save @@new_slice_data = { acronym: 'tst-c', name: "Test Slice C", ontologies: ont_acronyms} - @@old_security_setting = LinkedData.settings.enable_security + self.class.enable_security end - def self.after_suite + def after_suite LinkedData::Models::Slice.all.each(&:delete) @@user.delete - reset_security(@@old_security_setting) + self.class.reset_security end def setup - self.class.reset_security(@@old_security_setting) + self.class.reset_security self.class.reset_to_not_admin(@@user) LinkedData::Models::Slice.find(@@new_slice_data[:acronym]).first&.delete end diff --git a/test/controllers/test_users_controller.rb b/test/controllers/test_users_controller.rb index a165a5d7..c924d975 100644 --- a/test/controllers/test_users_controller.rb +++ b/test/controllers/test_users_controller.rb @@ -1,7 +1,7 @@ require_relative '../test_case' class TestUsersController < TestCase - def self.before_suite + def before_suite # Create a bunch of test users @@usernames = %w(fred goerge henry ben mark matt charlie) @@ -29,7 +29,7 @@ def test_admin_creation existent_user = self.class.make_admin(existent_user) assert _create_admin_user(apikey: existent_user.apikey), "Admin can create an admin user or update it to be an admin" self.class.reset_to_not_admin(existent_user) - delete "/users/#{@@username}" + _delete_user(@@username) end def test_all_users @@ -59,16 +59,66 @@ def test_create_new_user assert last_response.ok? assert MultiJson.load(last_response.body)["username"].eql?(@@username) - delete created_user["@id"] + _delete_user(created_user["username"]) + post "/users", MultiJson.dump(user.merge(username: @@username)), "CONTENT_TYPE" => "application/json" assert last_response.status == 201 assert MultiJson.load(last_response.body)["username"].eql?(@@username) get "/users/#{@@username}" assert last_response.ok? - assert MultiJson.load(last_response.body)["username"].eql?(@@username) + assert MultiJson.load(last_response.body)["username"].eql?(@@username) + assert_equal "test_user@example.org", MultiJson.load(last_response.body)["email"] + end + + def test_reset_password + username = 'resetpswd' + user = {email: "#{username}@example.org", password: "resetme"} + put "/users/#{username}", MultiJson.dump(user), "CONTENT_TYPE" => "application/json" + assert last_response.status == 201 + user = User.find(username).include(User.attributes).first + assert_nil user.resetToken + post "/users/create_reset_password_token", {username: username, email: "bademail@example.org"} + user = User.find(username).include(User.attributes).first + assert_nil user.resetToken + assert_equal 404, last_response.status + post "/users/reset_password", {username: 'badusername', email: "#{username}@example.org", token: 'badtoken'} + post "/users/create_reset_password_token", {username: username, email: "#{username}@example.org"} + assert_equal 204, last_response.status + user = User.find(username).include(User.attributes).first + refute_nil user.resetToken + post "/users/reset_password", {username: username, email: "#{username}@example.org", token: 'badtoken'} + assert_equal 401, last_response.status + post "/users/reset_password", {username: 'badusername', email: "#{username}@example.org", token: 'badtoken'} + assert_equal 404, last_response.status + post "/users/reset_password", {username: username, token: user.resetToken} + assert_equal 404, last_response.status + post "/users/reset_password", {email: "#{username}@example.org", token: user.resetToken} + assert_equal 404, last_response.status + post "/users/reset_password", {username: username, email: "badexampe@example.org", token: user.resetToken} + assert_equal 404, last_response.status + post "/users/reset_password", {username: username, email: "#{username}@example.org", token: user.resetToken} + assert_equal 200, last_response.status + assert_equal "#{username}@example.org", MultiJson.load(last_response.body)["email"] + user = User.find(username).include(User.attributes).first + assert_nil user.resetToken + end + + def test_reset_password_expired_token + username = 'resetexpired' + user = {email: "#{username}@example.org", password: "resetme"} + put "/users/#{username}", MultiJson.dump(user), "CONTENT_TYPE" => "application/json" + assert last_response.status == 201 + post "/users/create_reset_password_token", {username: username, email: "#{username}@example.org"} + assert_equal 204, last_response.status + user = User.find(username).include(User.attributes).first + user.resetTokenExpireTime = Time.now.to_i - 2.hours.to_i + user.save + post "/users/reset_password", {username: username, email: "#{username}@example.org", token: user.resetToken} + assert_equal 401, last_response.status end + def test_create_new_invalid_user put "/users/totally_new_user" assert last_response.status == 422 @@ -90,13 +140,21 @@ def test_update_patch_user end def test_delete_user - delete "/users/ben" - assert last_response.status == 204 + self.class.enable_security + + delete "/users/ben?apikey=#{@@users.first.apikey}" + assert_equal 403, last_response.status + + self.class.make_admin(@@users.first) + delete "/users/ben?apikey=#{@@users.first.apikey}" + assert_equal 204, last_response.status @@usernames.delete("ben") + self.class.reset_security + self.class.reset_to_not_admin(@@users.first) get "/users/ben" - assert last_response.status == 404 + assert_equal 404, last_response.status end def test_user_not_found @@ -148,6 +206,18 @@ def test_oauth_authentication end end + def test_hide_sensitive_data + user = @@users[0] + reset_token = "reset_password_token" + user.resetToken = reset_token + user.save + username = user.username + get "/users/#{username}?display=resetToken,passwordHash" + assert last_response.ok? + refute_includes MultiJson.load(last_response.body), 'resetToken', "resetToken should NOT be included in the response" + refute_includes MultiJson.load(last_response.body), 'passwordHash', "passwordHash should NOT be included in the response" + end + private def _create_admin_user(apikey: nil) user = {email: "#{@@username}@example.org", password: "pass_the_word", role: ['ADMINISTRATOR']} @@ -173,6 +243,37 @@ def _create_admin_user(apikey: nil) user = MultiJson.load(last_response.body) assert user["username"].eql?(@@username) + true if user["role"].eql?(['ADMINISTRATOR']) + end + private + + def _delete_user(username) + LinkedData::Models::User.find(@@username).first&.delete + end + def _create_admin_user(apikey: nil) + user = {email: "#{@@username}@example.org", password: "pass_the_word", role: ['ADMINISTRATOR']} + _delete_user(@@username) + + put "/users/#{@@username}", MultiJson.dump(user), "CONTENT_TYPE" => "application/json", "Authorization" => "apikey token=#{apikey}" + assert last_response.status == 201 + created_user = MultiJson.load(last_response.body) + assert created_user["username"].eql?(@@username) + + get "/users/#{@@username}?apikey=#{apikey}" + assert last_response.ok? + user = MultiJson.load(last_response.body) + assert user["username"].eql?(@@username) + + return true if user["role"].eql?(['ADMINISTRATOR']) + + patch "/users/#{@@username}", MultiJson.dump(role: ['ADMINISTRATOR']), "CONTENT_TYPE" => "application/json", "Authorization" => "apikey token=#{apikey}" + assert last_response.status == 204 + + get "/users/#{@@username}?apikey=#{apikey}" + assert last_response.ok? + user = MultiJson.load(last_response.body) + assert user["username"].eql?(@@username) + true if user["role"].eql?(['ADMINISTRATOR']) end end diff --git a/test/data/ontology_files/BRO_v3.2.owl b/test/data/ontology_files/BRO_v3.2.owl index b2aeccf5..de4a5186 100644 --- a/test/data/ontology_files/BRO_v3.2.owl +++ b/test/data/ontology_files/BRO_v3.2.owl @@ -634,7 +634,8 @@ Activity ActivityEnglish Activité - Activity of interest that may be related to a BRO:Resource. + Activity of interest that may be related to a BRO:Resource. + Activité d’intérêt pouvant être liée à un BRO:Resource. activities @@ -645,7 +646,9 @@ Activity related to the creation, use, or maintenance of a biorepository (http://en.wikipedia.org/wiki/Biorepository) - Biospecimen Management + Biospecimen Management + Activity related to the creation, use, or maintenance of a biorepository (http://en.wikipedia.org/wiki/Biorepository) + Activité liée à la création, à l'utilisation ou à la maintenance d'un bioréférentiel (http://en.wikipedia.org/wiki/Biorepository) @@ -655,7 +658,6 @@ As defined in http://en.wikipedia.org/wiki/Community_engagement - Community Engagement @@ -675,7 +677,7 @@ As defined in http://en.wikipedia.org/wiki/Gene_therapy - Gene Therapy + Gene Therapy @@ -6328,4 +6330,3 @@ radionuclide (tracer), which is introduced into the body on a biologically activ - diff --git a/test/data/ontology_files/CNO_05.owl b/test/data/ontology_files/CNO_05.owl index 8c36234b..c6b61ab1 100644 --- a/test/data/ontology_files/CNO_05.owl +++ b/test/data/ontology_files/CNO_05.owl @@ -1,61 +1,43 @@ - - - - - - - - - - - - - - - - - -]> - - + xmlns:Thesaurus="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#" + xmlns:terms="http://purl.org/dc/terms/" + xmlns:xml="http://www.w3.org/XML/1998/namespace" + xmlns:obo_annot="http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#" + xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" + xmlns:obo="http://purl.obolibrary.org/obo/" + xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#" + xmlns:dc="http://purl.org/dc/elements/1.1/"> - 13/03/2012 - An ontology to describe the field of Computational Neurosciences - Birgit Kriener - Computational Neuroscience Ontology - Erik De Schutter - Fahim T. Imam - INCF MultiScale Modeling Task Force - Lars Schwabe - Padraig Gleeson - Sean Hill - Stephen D. Larson - Subhasis Ray - This ontology is used to add the Definition class of annotation as in NIF. -The source of the definition can be defined with class from OBO-annotation - This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. - Yann Le Franc - version 0.5 + An ontology to describe the field of Computational Neurosciences + Computational Neuroscience Ontology + Erik De Schutter + Stephen D. Larson + Sean Hill + Yann Le Franc + This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. + 13/03/2012 + Lars Schwabe + This ontology is used to add the Definition class of annotation as in NIF. +The source of the definition can be defined with class from OBO-annotation + version 0.5 + Birgit Kriener + Subhasis Ray + INCF MultiScale Modeling Task Force + Fahim T. Imam + Padraig Gleeson @@ -68,19 +50,111 @@ The source of the definition can be defined with class from OBO-annotation - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -88,6 +162,18 @@ The source of the definition can be defined with class from OBO-annotation + + + + + + + + + + + - name - - + + + name @@ -112,9 +198,9 @@ The source of the definition can be defined with class from OBO-annotation - numerical value - - + + + numerical value @@ -130,9 +216,25 @@ The source of the definition can be defined with class from OBO-annotation + + + + C40918 + Physiologic Function + Bone Formation Stimulation + C1371285 + Bone_Formation_Stimulation + Bone Formation Stimulation + Bone Formation Stimulation involves initiation of synthesis by osteoblasts of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate. + Bone Formation Stimulation + + + + - + @@ -142,46 +244,108 @@ The source of the definition can be defined with class from OBO-annotation - - - - + + + + + + + + + + - + - + - + + + + + + + + realization + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + + + + + + + - defined model type - - - - - This general class includes the most common types of models classified based on the level of description of the nervous system. - a generically_dependent_continuant that is a category of models regarded as sharing particular characteristics, qualities, and/or defined similarities. - defined type of model - definition based on the following NCI thesaurus entry: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Type_of_Event + + + + + This general class includes the most common types of models classified based on the level of description of the nervous system. + definition based on the following NCI thesaurus entry: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Type_of_Event + defined model type + defined type of model + a generically_dependent_continuant that is a category of models regarded as sharing particular characteristics, qualities, and/or defined similarities. @@ -189,15 +353,15 @@ The source of the definition can be defined with class from OBO-annotation - model component - - - - - This class is based on the assumption that models can represented as particular assemblies of components that can be either specific to the different level of description (cellular, synaptic and network) or generic. - a generically dependent continuant that is a constituent part of a model - definition based on element from NCI Thesaurus: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Element_Part - model element + + + + + This class is based on the assumption that models can represented as particular assemblies of components that can be either specific to the different level of description (cellular, synaptic and network) or generic. + definition based on element from NCI Thesaurus: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Element_Part + model component + model element + a generically dependent continuant that is a constituent part of a model @@ -205,13 +369,13 @@ The source of the definition can be defined with class from OBO-annotation - parameter - - - - - elementary model component role that defines an elementary model component as constant value determining the characteristics or behaviour of the model + + + + + parameter + elementary model component role that defines an elementary model component as constant value determining the characteristics or behaviour of the model @@ -219,13 +383,13 @@ The source of the definition can be defined with class from OBO-annotation - reset potential - - - - - - value of the membrane potential at which the model is maintained after the emission of a spike. + + + + + + reset potential + value of the membrane potential at which the model is maintained after the emission of a spike. @@ -233,10 +397,10 @@ The source of the definition can be defined with class from OBO-annotation - physical constant SBO:0000565 http://en.wikipedia.org/wiki/Physical_constant + physical constant A physical constant that is required in the calculation of a system parameter @@ -245,11 +409,11 @@ The source of the definition can be defined with class from OBO-annotation - phenomenological plasticity model - http://www.scholarpedia.org/article/Models_of_synaptic_plasticity - http://www.scholarpedia.org/article/Models_of_synaptic_plasticity - long term plasticity model that is based on an input-output relationship between neuronal activity and synaptic plasticity. This type of model does not explicitly account for the biochemistry and physiology leading to synaptic plasticity. + http://www.scholarpedia.org/article/Models_of_synaptic_plasticity + http://www.scholarpedia.org/article/Models_of_synaptic_plasticity + phenomenological plasticity model + long term plasticity model that is based on an input-output relationship between neuronal activity and synaptic plasticity. This type of model does not explicitly account for the biochemistry and physiology leading to synaptic plasticity. @@ -257,10 +421,10 @@ The source of the definition can be defined with class from OBO-annotation - cellular model - The distinction between the different subclasses is based on the different "spiking mechanisms". - a defined type of model that represent the biological activities of a cell. + The distinction between the different subclasses is based on the different "spiking mechanisms". + cellular model + a defined type of model that represent the biological activities of a cell. @@ -268,9 +432,9 @@ The source of the definition can be defined with class from OBO-annotation - synapse model - a defined type of model that represents the biological processes involved in synaptic transmission + synapse model + a defined type of model that represents the biological processes involved in synaptic transmission @@ -278,9 +442,9 @@ The source of the definition can be defined with class from OBO-annotation - network model - a defined type of model that represents biological neural networks. + network model + a defined type of model that represents biological neural networks. @@ -288,9 +452,9 @@ The source of the definition can be defined with class from OBO-annotation - plasticity model - a defined type of model that describes the mechanisms underlying the plasticity of the nervous system. + plasticity model + a defined type of model that describes the mechanisms underlying the plasticity of the nervous system. @@ -298,10 +462,10 @@ The source of the definition can be defined with class from OBO-annotation - artificial neuron model - This class can be further subdivided into binary neuron, McCullogh neurons and all variants of the artificial neuron models. - a cellular model that represents the electrical activity of a nerve cell with simplified function + This class can be further subdivided into binary neuron, McCullogh neurons and all variants of the artificial neuron models. + artificial neuron model + a cellular model that represents the electrical activity of a nerve cell with simplified function @@ -309,10 +473,10 @@ The source of the definition can be defined with class from OBO-annotation - point process model - - a cellular model that reproduce particular features of real neuron spiking patterns with statistical point process models. + + point process model + a cellular model that reproduce particular features of real neuron spiking patterns with statistical point process models. @@ -320,9 +484,9 @@ The source of the definition can be defined with class from OBO-annotation - spiking model - a cellular model that describes the mechanism of action potential emission in biological nerve cell. + spiking model + a cellular model that describes the mechanism of action potential emission in biological nerve cell. @@ -330,10 +494,10 @@ The source of the definition can be defined with class from OBO-annotation - balanced random network - PMID: 10809012 - defined model that corresponds to a network of sparsely connected excitatory and inhibitory neurons which can switch between firing states depending on the balance between excitation and inhibition. + PMID: 10809012 + balanced random network + defined model that corresponds to a network of sparsely connected excitatory and inhibitory neurons which can switch between firing states depending on the balance between excitation and inhibition. @@ -341,10 +505,10 @@ The source of the definition can be defined with class from OBO-annotation - Hopfield network - defined model that is a form of recurrent artificial neural network invented by John Hopfield. - http://en.wikipedia.org/wiki/Hopfield_network + http://en.wikipedia.org/wiki/Hopfield_network + Hopfield network + defined model that is a form of recurrent artificial neural network invented by John Hopfield. @@ -352,10 +516,10 @@ The source of the definition can be defined with class from OBO-annotation - biophysical spiking model - a spiking model that describe the interactions between the ionic conductances that participates to the generation of an action potential + biophysical spiking model + a spiking model that describe the interactions between the ionic conductances that participates to the generation of an action potential @@ -363,9 +527,9 @@ The source of the definition can be defined with class from OBO-annotation - threshold-based spiking model - a spiking model that represents the spiking mechanism as the result of a threshold crossing. + threshold-based spiking model + a spiking model that represents the spiking mechanism as the result of a threshold crossing. @@ -373,11 +537,11 @@ The source of the definition can be defined with class from OBO-annotation - reduced model - This class could become a superclass called dynamical models or dynamical system models in contrast with biophysical and threshold based models. + This class could become a superclass called dynamical models or dynamical system models in contrast with biophysical and threshold based models. It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - biophysical model that is obtained by dimensionality reduction of a detailed model. + reduced model + biophysical model that is obtained by dimensionality reduction of a detailed model. @@ -385,9 +549,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - detailed model - biophysical model that describes in detail the conductance variations of the ionic currents responsible of the generation of an action potential + detailed model + biophysical model that describes in detail the conductance variations of the ionic currents responsible of the generation of an action potential @@ -395,11 +559,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - pulse-based model - This classe refers to detailed integrate-and-fire models as described in Destexhe A. (1997, PMID: 9097470) and Hill S. and Tononi G. (2005, PMID: 15537811) - a threshold based spiking neuron model that is an hybrid between Hodgkin and Huxley and integrate-and-fire models. The model describes the impact of fast sodium and delayed rectifier potassium conductances on the subthreshold membrane voltage dynamic and considers action potentials as pulses during which the sodium and potassium conductances are set to particular values representing their participation to the generation and repolarization of the action potential. - conductance-based model + conductance-based model + This classe refers to detailed integrate-and-fire models as described in Destexhe A. (1997, PMID: 9097470) and Hill S. and Tononi G. (2005, PMID: 15537811) + pulse-based model + a threshold based spiking neuron model that is an hybrid between Hodgkin and Huxley and integrate-and-fire models. The model describes the impact of fast sodium and delayed rectifier potassium conductances on the subthreshold membrane voltage dynamic and considers action potentials as pulses during which the sodium and potassium conductances are set to particular values representing their participation to the generation and repolarization of the action potential. @@ -407,10 +571,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - one variable model - - a threshold-based model that uses only one variable to describe the nerve cells behavior. + + one variable model + a threshold-based model that uses only one variable to describe the nerve cells behavior. @@ -418,9 +582,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - two variable model - a threshold-based model that uses two variables to describe the nerve cells behavior. + two variable model + a threshold-based model that uses two variables to describe the nerve cells behavior. @@ -428,9 +592,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - three variable model - a threshold-based model that uses three variables to describe the nerve cells behavior + three variable model + a threshold-based model that uses three variables to describe the nerve cells behavior @@ -438,9 +602,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spike response model - a threshold-based model that correspond to a generalization of the leaky integrate-and-fire model and give a simple description of action potential generation in neurons + spike response model + a threshold-based model that correspond to a generalization of the leaky integrate-and-fire model and give a simple description of action potential generation in neurons @@ -448,11 +612,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - current-based model - - a model of chemical synapse that consider the impact of the chemical release as a current source in the post-synaptic model with the postsynaptic membrane voltage considered to be constant. + + current-based model + a model of chemical synapse that consider the impact of the chemical release as a current source in the post-synaptic model with the postsynaptic membrane voltage considered to be constant. @@ -460,10 +624,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - conductance-based model - - a model of chemical synapse that consider the impact of the chemical release as a modification of conductance in the post-synaptic model with the post-synaptic potential varying over time. + + conductance-based model + a model of chemical synapse that consider the impact of the chemical release as a modification of conductance in the post-synaptic model with the post-synaptic potential varying over time. @@ -471,9 +635,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - rate model - network model composed of rate-based neuron models + rate model + network model composed of rate-based neuron models @@ -481,10 +645,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - artificial neural network model - corresponds to Kohonen maps, Multiple Layer perceptron, ... - network model composed of artificial neuron models. + corresponds to Kohonen maps, Multiple Layer perceptron, ... + artificial neural network model + network model composed of artificial neuron models. @@ -492,9 +656,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spiking network model - network model that is composed of spiking neuron models. + spiking network model + network model that is composed of spiking neuron models. @@ -502,10 +666,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - chemical synapse model - a synapse model that describes the impact of chemical compounds released by the synapse + chemical synapse model + a synapse model that describes the impact of chemical compounds released by the synapse @@ -513,9 +677,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - electrical synapse model - a synapse model that describe synapses transmitting directly ionic currents. + electrical synapse model + a synapse model that describe synapses transmitting directly ionic currents. @@ -523,10 +687,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - cellular plasticity model - This class would contains models that describes the link between potassium channels and NMDA activation as described in hippocampus for instance. - plasticity model that describes the variations of the cellular intrinsic excitability due to regulation of ionic conductances depending on the network activity. + This class would contains models that describes the link between potassium channels and NMDA activation as described in hippocampus for instance. + cellular plasticity model + plasticity model that describes the variations of the cellular intrinsic excitability due to regulation of ionic conductances depending on the network activity. @@ -534,10 +698,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic plasticity model - model of plasticity that represents the mechanisms underlying changes in synaptic transmission, depending on the network or cellular activity. - synaptic plasticity rule + synaptic plasticity model + synaptic plasticity rule + model of plasticity that represents the mechanisms underlying changes in synaptic transmission, depending on the network or cellular activity. @@ -545,9 +709,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - short term facilitation model - a model of short term synaptic plasticity that represents the increase of the synaptic efficacy for a short period of time. + short term facilitation model + a model of short term synaptic plasticity that represents the increase of the synaptic efficacy for a short period of time. @@ -555,9 +719,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - cellular model component - aggregated model composed that is used to build cellular models + cellular model component + aggregated model composed that is used to build cellular models @@ -565,9 +729,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synapse model component - aggregated model component that is used to build synaptic models. + synapse model component + aggregated model component that is used to build synaptic models. @@ -575,10 +739,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - resting membrane potential - - - value of the neuronal membrane potential at rest + + + resting membrane potential + value of the neuronal membrane potential at rest @@ -586,10 +750,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - refractory mechanism - This is a general term that encompass the refractory period usually defined with a time constant and the resetting of the membrane potential during the refractory period. - a cellular model component that represents the mechanism by which the model is kept unresponsive to any stimulus after the emission of an action potential. + This is a general term that encompass the refractory period usually defined with a time constant and the resetting of the membrane potential during the refractory period. + refractory mechanism + a cellular model component that represents the mechanism by which the model is kept unresponsive to any stimulus after the emission of an action potential. @@ -597,12 +761,12 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - model quality - - - - - quality that represents a qualitative feature of the model that can be either independent of the model specification or a property resulting of the particular model specification + + + + + model quality + quality that represents a qualitative feature of the model that can be either independent of the model specification or a property resulting of the particular model specification @@ -610,9 +774,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spiking mechanism - a cellular model component that represents the mechanisms generating action potential in a cellular model type. + spiking mechanism + a cellular model component that represents the mechanisms generating action potential in a cellular model type. @@ -620,9 +784,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - morphology - a cellular model component that represents the morphology of the model + morphology + a cellular model component that represents the morphology of the model @@ -630,9 +794,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - intracellular dynamic - a cellular model component that represents a chemical signaling occuring inside the nerve cell + intracellular dynamic + a cellular model component that represents a chemical signaling occuring inside the nerve cell @@ -640,9 +804,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - stimulation current - current model that represents input currents provided to the model via an electrode (intracellular or extracellular). + stimulation current + current model that represents input currents provided to the model via an electrode (intracellular or extracellular). @@ -650,8 +814,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - generic model component + generic model component @@ -659,9 +823,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - probabilistic component - a generic model component that represents the probabilistic variations of any model component. + probabilistic component + a generic model component that represents the probabilistic variations of any model component. @@ -669,9 +833,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - ionic current model - a current model that describes the flow of ions through cellular membrane. + ionic current model + a current model that describes the flow of ions through cellular membrane. @@ -679,9 +843,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic current - current model that represents the flow of ions triggered by the activation of a chemical or electrical synapse model. + synaptic current + current model that represents the flow of ions triggered by the activation of a chemical or electrical synapse model. @@ -689,9 +853,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - abstract current model - a current model that is an abtraction of complex current interactions and which is used to reproduce a particular cellular behavior such as rebound or adaptation. + abstract current model + a current model that is an abtraction of complex current interactions and which is used to reproduce a particular cellular behavior such as rebound or adaptation. @@ -699,10 +863,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - continuous - - a spiking mechanism that considers the action potential initiation as a continuous process often based on the non linearity of the conductance changes supporting the initiation of an action potential. This mechanism is the opposite of a threshold-based mechanisms. + + continuous + a spiking mechanism that considers the action potential initiation as a continuous process often based on the non linearity of the conductance changes supporting the initiation of an action potential. This mechanism is the opposite of a threshold-based mechanisms. @@ -710,9 +874,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - threshold-based - a spiking mechanism that considers the action potential initiation as a result of a thresholding operation. + threshold-based + a spiking mechanism that considers the action potential initiation as a result of a thresholding operation. @@ -720,9 +884,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - point - a morphology that is used to represents the models without specified geometry. + point + a morphology that is used to represents the models without specified geometry. @@ -730,9 +894,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - single compartment - a morphology that consider the cellular morphology as a unique compartment + single compartment + a morphology that consider the cellular morphology as a unique compartment @@ -740,9 +904,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - multiple compartment - a morphology that represents the modeled cell with multiple compartments. This morphology spans the models called the Ball-and-stick model and the models based on reconstructed morphologies. + multiple compartment + a morphology that represents the modeled cell with multiple compartments. This morphology spans the models called the Ball-and-stick model and the models based on reconstructed morphologies. @@ -750,10 +914,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - reconstructed - - morphological quality that represents model morphologies build upon the reconstruction of a real nerve cell morphology using imaging techniques such as camera lucida or two-photon imaging. + + reconstructed + morphological quality that represents model morphologies build upon the reconstruction of a real nerve cell morphology using imaging techniques such as camera lucida or two-photon imaging. @@ -761,9 +925,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - calcium dynamic - an intracellular dynamic model component that represents the variation of the intracellular calcium concentration over time. + calcium dynamic + an intracellular dynamic model component that represents the variation of the intracellular calcium concentration over time. @@ -771,10 +935,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - biochemical dynamic - NOTE: Shouldn't be separated from calcium dynamic as calcium is also a molecular participant. One possible solution would be to change into: reduced calcium dynamic to represent the simplification of buffering and detailed biochemical reactions that details the calcium buffering!!! - an intracellular dynamic model component that represents the dynamic of the intracellular biochemical reactions and molecular participant concentrations over time. + NOTE: Shouldn't be separated from calcium dynamic as calcium is also a molecular participant. One possible solution would be to change into: reduced calcium dynamic to represent the simplification of buffering and detailed biochemical reactions that details the calcium buffering!!! + biochemical dynamic + an intracellular dynamic model component that represents the dynamic of the intracellular biochemical reactions and molecular participant concentrations over time. @@ -782,9 +946,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - network model component - a model component that is used to build network model types. + network model component + a model component that is used to build network model types. @@ -792,9 +956,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - non linear spike generation current - abstract current model that represents an additional non-linear current ψ which leads to a divergence of the potential toward infinity in a finite time during the emission of an action potential. + non linear spike generation current + abstract current model that represents an additional non-linear current ψ which leads to a divergence of the potential toward infinity in a finite time during the emission of an action potential. @@ -802,18 +966,18 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - defined model - + - - - - - a generically_dependent_continuant that represent the set of models commonly used to build other models. + + + + + defined model + a generically_dependent_continuant that represent the set of models commonly used to build other models. @@ -821,10 +985,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - integrate-and-fire - a defined model that represent the evolution of voltage as the derivative of the law of capacitance. The action potential is emitted when the value of the voltage reaches a threshold and is considered as Dirac function. After the emission the voltage is resetted to the resting potential value. - http://en.wikipedia.org/wiki/Biological_neuron_model#Integrate-and-fire + http://en.wikipedia.org/wiki/Biological_neuron_model#Integrate-and-fire + integrate-and-fire + a defined model that represent the evolution of voltage as the derivative of the law of capacitance. The action potential is emitted when the value of the voltage reaches a threshold and is considered as Dirac function. After the emission the voltage is resetted to the resting potential value. @@ -832,11 +996,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - adaptive exponential integrate-and-fire - AdEx - a defined model that is a spiking neuron model with two variables. The first equation describes the dynamics of the membrane potential and includes an activation ter with an exponential voltage dependence. Voltage is coupled to a second equation which describes adaptation. Both variables are reset if an action potential has been triggered. This model has been introduced by Brette and Gerstner in 2005. - http://www.scholarpedia.org/article/Adaptive_exponential_integrate-and-fire_model + http://www.scholarpedia.org/article/Adaptive_exponential_integrate-and-fire_model + AdEx + adaptive exponential integrate-and-fire + a defined model that is a spiking neuron model with two variables. The first equation describes the dynamics of the membrane potential and includes an activation ter with an exponential voltage dependence. Voltage is coupled to a second equation which describes adaptation. Both variables are reset if an action potential has been triggered. This model has been introduced by Brette and Gerstner in 2005. @@ -844,10 +1008,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - independent variable - http://en.wikipedia.org/wiki/Variable_(mathematics) - variable regarded as inputs to a system and may take on different values freely + http://en.wikipedia.org/wiki/Variable_(mathematics) + independent variable + variable regarded as inputs to a system and may take on different values freely @@ -855,10 +1019,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - dependent variable - http://en.wikipedia.org/wiki/Variable_(mathematics) - variable regarded as values that change as a consequence of changes in other values in the system. + http://en.wikipedia.org/wiki/Variable_(mathematics) + dependent variable + variable regarded as values that change as a consequence of changes in other values in the system. @@ -866,11 +1030,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - exponential integrate-and-fire - EIF - a defined model that is an integrate-and-fire model in which the action potentials are generated by an exponential current instead of a fixed threshold. The exponential integrate-and-fire model is defined in Fourcaud-Trocme and al. 2003 - w.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001056 + w.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001056 + EIF + exponential integrate-and-fire + a defined model that is an integrate-and-fire model in which the action potentials are generated by an exponential current instead of a fixed threshold. The exponential integrate-and-fire model is defined in Fourcaud-Trocme and al. 2003 @@ -878,11 +1042,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - leaky integrate-and-fire - LIF, Lapicque's model - a defined model that is an integrate-and-fire model with a leak component added to the membrane potential, reflecting the diffusion of ions that occurs through the membrane when some equilibrium is not reached in the cell. - http://en.wikipedia.org/wiki/Biological_neuron_model#Leaky_integrate-and-fire + http://en.wikipedia.org/wiki/Biological_neuron_model#Leaky_integrate-and-fire + LIF, Lapicque's model + leaky integrate-and-fire + a defined model that is an integrate-and-fire model with a leak component added to the membrane potential, reflecting the diffusion of ions that occurs through the membrane when some equilibrium is not reached in the cell. @@ -890,10 +1054,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - quadratic integrate-and-fire - QIF - a defined model that is an integrate-and-fire model in which the action potentials are generated by a quadratic current instead of a fixed threshold. The quadratic integrate-and-fire model is defined in Latham and al. 2000. This model is identical to the Theta neuron proposed by Ermentrout and Kopell (1986) with a variable change. + QIF + quadratic integrate-and-fire + a defined model that is an integrate-and-fire model in which the action potentials are generated by a quadratic current instead of a fixed threshold. The quadratic integrate-and-fire model is defined in Latham and al. 2000. This model is identical to the Theta neuron proposed by Ermentrout and Kopell (1986) with a variable change. @@ -901,10 +1065,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - theta neuron model - a defined model that is well suited to describe the processes involving rapid changes in membrane potential, known as bursts. The theta model describes parabolic bursting and has been defined in Ermentrout and Kopell, SIAM journal of Applied Mathematics 1986. - http://en.wikipedia.org/wiki/Theta_model + http://en.wikipedia.org/wiki/Theta_model + theta neuron model + a defined model that is well suited to describe the processes involving rapid changes in membrane potential, known as bursts. The theta model describes parabolic bursting and has been defined in Ermentrout and Kopell, SIAM journal of Applied Mathematics 1986. @@ -912,10 +1076,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - adaptive integrate-and-fire - ALIF - a defined model that is a two-variable integrate-and-fire model. The second variable accounts for the currents involved in spike frequency adaptation. This variable increase transiently during action potentials and decay between action potential. + ALIF + adaptive integrate-and-fire + a defined model that is a two-variable integrate-and-fire model. The second variable accounts for the currents involved in spike frequency adaptation. This variable increase transiently during action potentials and decay between action potential. @@ -923,11 +1087,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - generalized integrate-and-fire - GIF - PMID: 12611957 - a defined model that is a two variable integrate-and-fire model with a threshold for spike generation and a reset as in the leaky integrate-and-fire model. The two variables represent subthreshold resonance behavior and result from the linearization of the Hodgkin and Huxley equation around a subthreshold holding potential. This model is similar to the resonate-and-fire model proposed by Izhikevich (2001) + PMID: 12611957 + GIF + generalized integrate-and-fire + a defined model that is a two variable integrate-and-fire model with a threshold for spike generation and a reset as in the leaky integrate-and-fire model. The two variables represent subthreshold resonance behavior and result from the linearization of the Hodgkin and Huxley equation around a subthreshold holding potential. This model is similar to the resonate-and-fire model proposed by Izhikevich (2001) @@ -935,10 +1099,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - integrate-and-fire-or-burst - IFB - a defined model that is a two-variable integrate-and-fire model. The second variable is a slow variable that represents the inactivation of the low-threshold calcium current. This model reproduces the features of the bursting behavior of thalamo-cortical relay neurons and has been proposed by Smith and al., 2000 + IFB + integrate-and-fire-or-burst + a defined model that is a two-variable integrate-and-fire model. The second variable is a slow variable that represents the inactivation of the low-threshold calcium current. This model reproduces the features of the bursting behavior of thalamo-cortical relay neurons and has been proposed by Smith and al., 2000 @@ -946,10 +1110,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - Izhikevich model - PMID: 18244602 - a defined model that is a minimal two-variable integrate-and-fire model that reproduces different features depending on the value of 4 parameters. The second variable represents the adaptation. This model has been proposed in Izhikevich, 2003. + PMID: 18244602 + Izhikevich model + a defined model that is a minimal two-variable integrate-and-fire model that reproduces different features depending on the value of 4 parameters. The second variable represents the adaptation. This model has been proposed in Izhikevich, 2003. @@ -957,10 +1121,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - resonate-and-fire - PMID: 11665779 - a defined model that is a two variable integrate-and-fire model proposed by Izhikevich in Izhikevich, 2001. + PMID: 11665779 + resonate-and-fire + a defined model that is a two variable integrate-and-fire model proposed by Izhikevich in Izhikevich, 2001. @@ -968,11 +1132,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - HindMarch and Rose model - PMID: 6144106 - a defined model that is a three-variable model: the membrane potential written in dimensionless unit, the spiking variable that represent the fast transport of sodium and potassium ions and the bursting variable that represent the slow transport of other ions. This model aims to study the spiking-bursting behavior of the membrane potential observed in experiments. - http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model + PMID: 6144106 + http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model + HindMarch and Rose model + a defined model that is a three-variable model: the membrane potential written in dimensionless unit, the spiking variable that represent the fast transport of sodium and potassium ions and the bursting variable that represent the slow transport of other ions. This model aims to study the spiking-bursting behavior of the membrane potential observed in experiments. @@ -980,10 +1144,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - Rotstein model - PMID: 16927211 - a defined model that is three variable reduced model defined in Rotstein and al. 2006 in J. Comp. Neurosci. + PMID: 16927211 + Rotstein model + a defined model that is three variable reduced model defined in Rotstein and al. 2006 in J. Comp. Neurosci. @@ -991,10 +1155,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - Shinomoto model - PMID: 20478693 - a defined model that is a multi-timescale adaptive threshold model of neuronal spiking incorporated into the stochastic framework of the linear-nonlinear Poisson model in the form of a generalized linear model. + PMID: 20478693 + Shinomoto model + a defined model that is a multi-timescale adaptive threshold model of neuronal spiking incorporated into the stochastic framework of the linear-nonlinear Poisson model in the form of a generalized linear model. @@ -1002,12 +1166,12 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spike response model - a defined model that is a generalization of the leaky integrate-and-fire model. As in the leaky integrate-and-fire model, action potentials are generated when the voltage passes a threshold. Leaky integrate-and-fire models are formulated using differential equations for the voltage, whereas the Spike Response Model is formulated using filters. - doi:10.1162/neco.1997.9.5.1015 - http://icwww.epfl.ch/~gerstner/SPNM/node27.html - http://www.scholarpedia.org/article/Spike-response_model + doi:10.1162/neco.1997.9.5.1015 + http://icwww.epfl.ch/~gerstner/SPNM/node27.html + http://www.scholarpedia.org/article/Spike-response_model + spike response model + a defined model that is a generalization of the leaky integrate-and-fire model. As in the leaky integrate-and-fire model, action potentials are generated when the voltage passes a threshold. Leaky integrate-and-fire models are formulated using differential equations for the voltage, whereas the Spike Response Model is formulated using filters. @@ -1015,12 +1179,12 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spike response model SRM0 - PMID: 16633938 - a defined model that is a simplified version of the Spike Response Model and does not include a dependence of the response kernel κ upon the time since the last spike. - http://icwww.epfl.ch/~gerstner/SPNM/node27.html#SECTION02323000000000000000 - http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_SRM.5C.28_0.5C.29 + PMID: 16633938 + http://icwww.epfl.ch/~gerstner/SPNM/node27.html#SECTION02323000000000000000 + http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_SRM.5C.28_0.5C.29 + spike response model SRM0 + a defined model that is a simplified version of the Spike Response Model and does not include a dependence of the response kernel κ upon the time since the last spike. @@ -1028,11 +1192,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - cumulative spike response model - PMID: 8888612 - a defined model that is a spike response model where refractoriness and adaptation were modeled by the combined effects of the spike after potentials of several previous spikes, rather than only the most recent spike. - http://www.scholarpedia.org/article/Spike-response_model#Cumulative_Spike_Response_Model:_bursting_and_adaptation + PMID: 8888612 + http://www.scholarpedia.org/article/Spike-response_model#Cumulative_Spike_Response_Model:_bursting_and_adaptation + cumulative spike response model + a defined model that is a spike response model where refractoriness and adaptation were modeled by the combined effects of the spike after potentials of several previous spikes, rather than only the most recent spike. @@ -1040,10 +1204,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spike response model with cumulative dynamic threshold - a defined model that is a spike response model in which the value of the threshold depends on all previous spikes not only the most recent one. - http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_with_a_cumulative_dynamic_threshold + http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_with_a_cumulative_dynamic_threshold + spike response model with cumulative dynamic threshold + a defined model that is a spike response model in which the value of the threshold depends on all previous spikes not only the most recent one. @@ -1051,9 +1215,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - dynamic threshold - a threshold-based spiking mechanism that represent the variation of the spiking threshold over time based on particular criterions. + dynamic threshold + a threshold-based spiking mechanism that represent the variation of the spiking threshold over time based on particular criterions. @@ -1061,9 +1225,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - fixed threshold - a threshold-based spiking mechanism that considers the threshold as constant over time. + fixed threshold + a threshold-based spiking mechanism that considers the threshold as constant over time. @@ -1071,10 +1235,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spike shape kernel - a cellular model component that is used to build spike response model and which describes the form of the action potential and its spike after-potential. This kernel is a function of the time since the last action potential. It can describe a depolarizing, hyperpolarizing or resonating spike after-potential. - http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation + http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation + spike shape kernel + a cellular model component that is used to build spike response model and which describes the form of the action potential and its spike after-potential. This kernel is a function of the time since the last action potential. It can describe a depolarizing, hyperpolarizing or resonating spike after-potential. @@ -1082,11 +1246,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - responsiveness kernel - a cellular model component that is used to build spike response model and which describes the linear response to an incoming short pulse. The responsiveness kernel to an input pulse depends on the time since the last spike. - http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation - linear filter of the membrane + http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation + linear filter of the membrane + responsiveness kernel + a cellular model component that is used to build spike response model and which describes the linear response to an incoming short pulse. The responsiveness kernel to an input pulse depends on the time since the last spike. @@ -1094,9 +1258,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - adaptation current - an abstract current model that represents the mechanism of spiking frequency adaptation. + adaptation current + an abstract current model that represents the mechanism of spiking frequency adaptation. @@ -1104,9 +1268,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - rebound current - abstract current model that represents the mechanisms of rebound. + rebound current + abstract current model that represents the mechanisms of rebound. @@ -1114,12 +1278,12 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spiking current - - abstract current model that represents the mechanisms involved in the action potential and which is used to build HindMarch and Rose models - http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model - spiking variable, y + http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model + spiking variable, y + + spiking current + abstract current model that represents the mechanisms involved in the action potential and which is used to build HindMarch and Rose models @@ -1127,12 +1291,12 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - bursting current - - abstract current model that represents the mechanisms of bursting and used to build HindMarch and Rose models. - bursting variable, z - http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model + http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model + bursting variable, z + + bursting current + abstract current model that represents the mechanisms of bursting and used to build HindMarch and Rose models. @@ -1140,11 +1304,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - membrane recovery variable - - PMID: 18244602 - abstract current model which accounts for the activation of potassium ionic currents and inactivation of sodium ionic currents and provides negative feedback to the membrane voltage + PMID: 18244602 + + membrane recovery variable + abstract current model which accounts for the activation of potassium ionic currents and inactivation of sodium ionic currents and provides negative feedback to the membrane voltage @@ -1152,11 +1316,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - Connor-Stevens model - PMID: 5575343 - a defined model that is an extended action potential generating model using gastropod somas. This model is similar to the Hodgkin and Huxley model and contains a sodium, potassium and leak current with faster dynamics for the sodium and potassium currents. In addition, a transient potassium current, called, A-current, has been included. - http://www.scholarpedia.org/article/Conductance-based_models#Examples_and_Variants + PMID: 5575343 + http://www.scholarpedia.org/article/Conductance-based_models#Examples_and_Variants + Connor-Stevens model + a defined model that is an extended action potential generating model using gastropod somas. This model is similar to the Hodgkin and Huxley model and contains a sodium, potassium and leak current with faster dynamics for the sodium and potassium currents. In addition, a transient potassium current, called, A-current, has been included. @@ -1164,10 +1328,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - Wang-Buzsaki model - PMID: 8815919 - a defined model that is a network model composed of single compartment models, derived from the original Hodgkin-Huxley model. This network model represents a network of hippocampal interneurons. + PMID: 8815919 + Wang-Buzsaki model + a defined model that is a network model composed of single compartment models, derived from the original Hodgkin-Huxley model. This network model represents a network of hippocampal interneurons. @@ -1175,12 +1339,12 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - Fitzhugh-Nagumo model - Bonhoeffer-van der Pol model - PMID: 19431309 - a defined model that is a two-dimensional simplification of the Hodgkin-Huxley model of spike generation in squid giant axons. The model consist of a voltage-like variable having cubic nonlinearity that allows regenerative self-excitation via positive feedback and a recovery variable having a linear dynamics that provides a slower negative feedback. - http://www.scholarpedia.org/article/FitzHugh-Nagumo_model + PMID: 19431309 + http://www.scholarpedia.org/article/FitzHugh-Nagumo_model + Bonhoeffer-van der Pol model + Fitzhugh-Nagumo model + a defined model that is a two-dimensional simplification of the Hodgkin-Huxley model of spike generation in squid giant axons. The model consist of a voltage-like variable having cubic nonlinearity that allows regenerative self-excitation via positive feedback and a recovery variable having a linear dynamics that provides a slower negative feedback. @@ -1188,11 +1352,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - Morris-Lecar model - PMID: 7260316 - a defined model that is a two-dimensional reduced excitation model applicable to systems having two non-inactivating voltage-sensitive conductances. The original form of the model employed an instantaneously responding voltage-sensitive calcium conductance for excitation and a delayed voltage-dependent potassium conductance for recovery. - http://www.scholarpedia.org/article/Morris-Lecar_model + PMID: 7260316 + http://www.scholarpedia.org/article/Morris-Lecar_model + Morris-Lecar model + a defined model that is a two-dimensional reduced excitation model applicable to systems having two non-inactivating voltage-sensitive conductances. The original form of the model employed an instantaneously responding voltage-sensitive calcium conductance for excitation and a delayed voltage-dependent potassium conductance for recovery. @@ -1200,9 +1364,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic action - a synapse model component that describes the impact of synaptic model on the post-synaptic model. + synaptic action + a synapse model component that describes the impact of synaptic model on the post-synaptic model. @@ -1210,9 +1374,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - connection element - a synapse model component that describe how the synapse is connected between two neuron models + connection element + a synapse model component that describe how the synapse is connected between two neuron models @@ -1220,10 +1384,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic weight - a synapse model component that refers to the strength or amplitude of a connection between two nodes, corresponding in biology to the amount of influence the firing of one neuron has on another. - http://en.wikipedia.org/wiki/Synaptic_weight + http://en.wikipedia.org/wiki/Synaptic_weight + synaptic weight + a synapse model component that refers to the strength or amplitude of a connection between two nodes, corresponding in biology to the amount of influence the firing of one neuron has on another. @@ -1231,10 +1395,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - plasticity mechanism - - a synapse model component that relates to plasticity models. + + plasticity mechanism + a synapse model component that relates to plasticity models. @@ -1242,9 +1406,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic conductance dynamic - a synaptic model component that describes the dynamic of the synaptic conductance in the post-synaptic model + synaptic conductance dynamic + a synaptic model component that describes the dynamic of the synaptic conductance in the post-synaptic model @@ -1252,9 +1416,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic delay - - delay between the activation of the synapse and its impact on the post-synaptic model. + + synaptic delay + delay between the activation of the synapse and its impact on the post-synaptic model. @@ -1262,9 +1426,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - voltage dependent receptor activation - a synapse model component that describes the voltage dependent activation of receptor such as NMDA receptor that will participate in the total synaptic current. + voltage dependent receptor activation + a synapse model component that describes the voltage dependent activation of receptor such as NMDA receptor that will participate in the total synaptic current. @@ -1272,9 +1436,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - release mechanism - a synapse model component that describes the neurotrasmitter release. + release mechanism + a synapse model component that describes the neurotrasmitter release. @@ -1282,9 +1446,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - neurotransmittor diffusion - a synapse model component that describes the diffusion of neurotransmitter in the extracellular space. + neurotransmittor diffusion + a synapse model component that describes the diffusion of neurotransmitter in the extracellular space. @@ -1292,9 +1456,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - post-synaptic element - a connection element which points to the model elements of the post-synaptic model that are used in the equations of the synapse model. + post-synaptic element + a connection element which points to the model elements of the post-synaptic model that are used in the equations of the synapse model. @@ -1302,9 +1466,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - pre-synaptic element - a connection element which points to the model elements of the pre-synaptic model that are used in the equations of the synapse model. + pre-synaptic element + a connection element which points to the model elements of the pre-synaptic model that are used in the equations of the synapse model. @@ -1312,10 +1476,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - voltage-dependent current model - - an ionic current model that represents the current flowing through ionic channel triggered by the change in voltage. + + voltage-dependent current model + an ionic current model that represents the current flowing through ionic channel triggered by the change in voltage. @@ -1323,9 +1487,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - voltage and ionic dependent current model - an ionic current model that represents the current flowing through ionic channel triggered by the change of voltage and the binding of a particular ion. + voltage and ionic dependent current model + an ionic current model that represents the current flowing through ionic channel triggered by the change of voltage and the binding of a particular ion. @@ -1333,10 +1497,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - supervised learning - http://en.wikipedia.org/wiki/Supervised_learning - learning rule that produces an infered function to predict correct output value for any valid input object, based on an error function estimated through the training period with the presentation of input/output pairs. + http://en.wikipedia.org/wiki/Supervised_learning + supervised learning + learning rule that produces an infered function to predict correct output value for any valid input object, based on an error function estimated through the training period with the presentation of input/output pairs. @@ -1344,9 +1508,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - ionic dependent current model - a biochemically activated current model that represents the current flowing through ionic channel triggered by the binding of a particular ion. + ionic dependent current model + a biochemically activated current model that represents the current flowing through ionic channel triggered by the binding of a particular ion. @@ -1354,9 +1518,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - biochemically activated current - an ionic current model that represents the current flowing through ionic channels triggered by action of biochemical components. + biochemically activated current + an ionic current model that represents the current flowing through ionic channels triggered by action of biochemical components. @@ -1364,9 +1528,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - unsupervised learning - learning rule that produces an infered function based on unlabeled data without any feedback to evaluate the potential solution. + unsupervised learning + learning rule that produces an infered function based on unlabeled data without any feedback to evaluate the potential solution. @@ -1374,9 +1538,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - excitatory action - a synaptic action that increases the post-synaptic model activity and/or voltage + excitatory action + a synaptic action that increases the post-synaptic model activity and/or voltage @@ -1384,9 +1548,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - inhibitory action - a synaptic action that decreases the post-synaptic activity and/or voltage + inhibitory action + a synaptic action that decreases the post-synaptic activity and/or voltage @@ -1394,9 +1558,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - shunting action - a synaptic action that modifies the global conductance of the post-synaptic model + shunting action + a synaptic action that modifies the global conductance of the post-synaptic model @@ -1404,9 +1568,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - instantaneous rise and monexponential decay - a synaptic conductance dynamic which assumes an instanteanous rise of the conductance followed by an exponential decay with a time constant. + instantaneous rise and monexponential decay + a synaptic conductance dynamic which assumes an instanteanous rise of the conductance followed by an exponential decay with a time constant. @@ -1414,9 +1578,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - difference of two exponentials - a synaptic conductance dynamic that is described as the difference of two exponential functions which represent the rising and the decay phase with two distinct time constants. + difference of two exponentials + a synaptic conductance dynamic that is described as the difference of two exponential functions which represent the rising and the decay phase with two distinct time constants. @@ -1424,9 +1588,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - alpha function - a synaptic conductance dynamic describing a conductance that has a rising phase with a certain rise time. As it has just a single time constant, the time course of the rise and decay are correlated. + alpha function + a synaptic conductance dynamic describing a conductance that has a rising phase with a certain rise time. As it has just a single time constant, the time course of the rise and decay are correlated. @@ -1434,10 +1598,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - cellular elements - - a network model component that refers to the cellular model type used to build the network model + + cellular elements + a network model component that refers to the cellular model type used to build the network model @@ -1445,10 +1609,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic element - - a network model component that refers to the synapse model type used to build the network model + + synaptic element + a network model component that refers to the synapse model type used to build the network model @@ -1456,10 +1620,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - connectivity pattern - - a model component quality that represents a connectivity pattern obtained with specific connectivity rule + + connectivity pattern + a model component quality that represents a connectivity pattern obtained with specific connectivity rule @@ -1467,9 +1631,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - rate function - a cellular model component that describes the dynamic of the cellular model firing rate. + rate function + a cellular model component that describes the dynamic of the cellular model firing rate. @@ -1477,10 +1641,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - recurrent - a connectivity pattern in which connections between units form a directed cycle. - http://en.wikipedia.org/wiki/Recurrent_neural_network#Fully_recurrent_network + http://en.wikipedia.org/wiki/Recurrent_neural_network#Fully_recurrent_network + recurrent + a connectivity pattern in which connections between units form a directed cycle. @@ -1488,10 +1652,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - feedforward - a connectivity pattern in which connections between units do not form a directed cycle. - http://en.wikipedia.org/wiki/Feedforward_neural_networks + http://en.wikipedia.org/wiki/Feedforward_neural_networks + feedforward + a connectivity pattern in which connections between units do not form a directed cycle. @@ -1499,10 +1663,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - small world - a connectivity pattern in which most nodes are not neighbors of one another, but most node can be reached from every other by a small number of hops or steps. - http://en.wikipedia.org/wiki/Small-world_network + http://en.wikipedia.org/wiki/Small-world_network + small world + a connectivity pattern in which most nodes are not neighbors of one another, but most node can be reached from every other by a small number of hops or steps. @@ -1510,9 +1674,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - functional grouping - cellular grouping quality that represents cellular grouping defined by common functional criterons. + functional grouping + cellular grouping quality that represents cellular grouping defined by common functional criterons. @@ -1520,9 +1684,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - anatomical grouping - cellular grouping quality that represents cellular grouping based on anatomical information + anatomical grouping + cellular grouping quality that represents cellular grouping based on anatomical information @@ -1530,9 +1694,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - current model - a cellular model component that represents the different types of modeled currents that can influence the trajectory of the membrane voltage + current model + a cellular model component that represents the different types of modeled currents that can influence the trajectory of the membrane voltage @@ -1540,9 +1704,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - current localization - current model quality that represents the location of the current source on a neuronal model (somatic, primary dendrite, ...) + current localization + current model quality that represents the location of the current source on a neuronal model (somatic, primary dendrite, ...) @@ -1550,9 +1714,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - current distribution - current model quality that represents the spatial distribution of current sources (ionic channels, synaptic channels, stimulation electrode) on a compartment + current distribution + current model quality that represents the spatial distribution of current sources (ionic channels, synaptic channels, stimulation electrode) on a compartment @@ -1560,9 +1724,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - connectivity rule - a network layout component that describe the rules used to establish connections between the cellular elements of the network model + connectivity rule + a network layout component that describe the rules used to establish connections between the cellular elements of the network model @@ -1570,9 +1734,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - voltage - http://www.ebi.ac.uk/sbo/main/SBO:0000259 + http://www.ebi.ac.uk/sbo/main/SBO:0000259 + voltage @@ -1580,8 +1744,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - capacitance + capacitance @@ -1589,8 +1753,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - current + current @@ -1598,8 +1762,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - diameter - + + diameter @@ -1607,8 +1771,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - length + length @@ -1616,8 +1780,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - synaptic plasticity element + synaptic plasticity element @@ -1625,8 +1789,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - frequency + frequency @@ -1634,8 +1798,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - maximal conductance - + + maximal conductance @@ -1643,9 +1807,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - random - cellular grouping quality that represents probabilistic grouping of cellular models within network models. + random + cellular grouping quality that represents probabilistic grouping of cellular models within network models. @@ -1653,8 +1817,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spike time - + + spike time @@ -1662,8 +1826,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - time constant - + + time constant @@ -1671,8 +1835,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - volume + volume @@ -1680,8 +1844,8 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - indices + indices @@ -1689,9 +1853,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - cellular grouping quality - a model component quality that represent the properties of cellular grouping in network models + cellular grouping quality + a model component quality that represent the properties of cellular grouping in network models @@ -1699,9 +1863,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - rate-based neuron model - a cellular model that describe the firing activity of neuron using a rate function. + rate-based neuron model + a cellular model that describe the firing activity of neuron using a rate function. @@ -1709,9 +1873,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - refractory period - - a duration that represent the duration during which the model cannot emit a subsequent spike following an initial spike. + + refractory period + a duration that represent the duration during which the model cannot emit a subsequent spike following an initial spike. @@ -1719,9 +1883,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spiking threshold - - voltage above which the model emits a spike + + spiking threshold + voltage above which the model emits a spike @@ -1729,10 +1893,10 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - elementary model component role + + elementary model component role - - role played by the model elements + role played by the model elements @@ -1740,9 +1904,9 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - cellular grouping - a network layout component that defines the common attribute or property used to create arbitrary groups of cellular model type. + cellular grouping + a network layout component that defines the common attribute or property used to create arbitrary groups of cellular model type. @@ -1750,11 +1914,11 @@ It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. - spatial embedding - Models can be defined without any mention of space. + Models can be defined without any mention of space. The model can be enriched with particular spatial embedding. - a generic model component that add spatial information to the model + spatial embedding + a generic model component that add spatial information to the model @@ -1762,9 +1926,9 @@ The model can be enriched with particular spatial embedding. - two dimensional layout - relates to http://neurolex.org/wiki/Category:Two_dimensional_region + relates to http://neurolex.org/wiki/Category:Two_dimensional_region + two dimensional layout @@ -1772,9 +1936,9 @@ The model can be enriched with particular spatial embedding. - three dimensional layout - http://neurolex.org/wiki/Category:Three_dimensional_region + http://neurolex.org/wiki/Category:Three_dimensional_region + three dimensional layout @@ -1782,8 +1946,8 @@ The model can be enriched with particular spatial embedding. - spatial coordinates + spatial coordinates @@ -1791,8 +1955,8 @@ The model can be enriched with particular spatial embedding. - 2D coordinates + 2D coordinates @@ -1800,8 +1964,8 @@ The model can be enriched with particular spatial embedding. - 3D coordinates + 3D coordinates @@ -1809,8 +1973,8 @@ The model can be enriched with particular spatial embedding. - polar coordinates + polar coordinates @@ -1818,10 +1982,10 @@ The model can be enriched with particular spatial embedding. - pre-synaptic indice - This term should be transformed into a datatype. - a pre-synaptic element that specifies the indices of the pre-synaptic neuron model + This term should be transformed into a datatype. + pre-synaptic indice + a pre-synaptic element that specifies the indices of the pre-synaptic neuron model @@ -1829,10 +1993,10 @@ The model can be enriched with particular spatial embedding. - user-defined - cellular distribution quality that represents the distribution of cellular models in network models arranged based on user-defined criterions that are not based on anatomical information. - is a quality + is a quality + user-defined + cellular distribution quality that represents the distribution of cellular models in network models arranged based on user-defined criterions that are not based on anatomical information. @@ -1840,9 +2004,9 @@ The model can be enriched with particular spatial embedding. - abstract morphology - a morphological quality that describe abstract representation of the morphology. Often cellular compartment are represented as iso-potential cylindrical compartments. + abstract morphology + a morphological quality that describe abstract representation of the morphology. Often cellular compartment are represented as iso-potential cylindrical compartments. @@ -1850,10 +2014,10 @@ The model can be enriched with particular spatial embedding. - uniform - cellular distribution quality that represents a cellular distribution in network models where cellular models are uniformly distributed in the abstract space. - is a quality + is a quality + uniform + cellular distribution quality that represents a cellular distribution in network models where cellular models are uniformly distributed in the abstract space. @@ -1861,10 +2025,10 @@ The model can be enriched with particular spatial embedding. - pre-synaptic variable - elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model. 0123456789 + pre-synaptic variable + elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model. @@ -1872,10 +2036,10 @@ The model can be enriched with particular spatial embedding. - developmental plasticity model - - model of network plasticity based on developmental rules that will change the structure of the network. + + developmental plasticity model + model of network plasticity based on developmental rules that will change the structure of the network. @@ -1883,11 +2047,11 @@ The model can be enriched with particular spatial embedding. - Hodgkin and Huxley model - PMID: 12991237 - defined model that describes how action potentials in neurons are initiated and propagated in squid giant axon. - http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model + PMID: 12991237 + http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model + Hodgkin and Huxley model + defined model that describes how action potentials in neurons are initiated and propagated in squid giant axon. @@ -1895,9 +2059,9 @@ The model can be enriched with particular spatial embedding. - post-synaptic indice - a post-synaptic element that specifies the indices of the post-synaptic neuron model + post-synaptic indice + a post-synaptic element that specifies the indices of the post-synaptic neuron model @@ -1905,10 +2069,10 @@ The model can be enriched with particular spatial embedding. - anatomically defined - cellular distribution quality that represents the cellular distribution in the network model based on criterions derived from anatomical information - is a quality + is a quality + anatomically defined + cellular distribution quality that represents the cellular distribution in the network model based on criterions derived from anatomical information @@ -1916,10 +2080,10 @@ The model can be enriched with particular spatial embedding. - morphological quality - Similar to sao1057800815 - a model component quality that described the kind of morphology used in the neuron models. + Similar to sao1057800815 + morphological quality + a model component quality that described the kind of morphology used in the neuron models. @@ -1927,10 +2091,10 @@ The model can be enriched with particular spatial embedding. - functional quality - Example: oscillatory, bursting, synchronization, ... - a model quality that describes the intrinsic functional quality of the models + Example: oscillatory, bursting, synchronization, ... + functional quality + a model quality that describes the intrinsic functional quality of the models @@ -1938,9 +2102,9 @@ The model can be enriched with particular spatial embedding. - post-synaptic variable - elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model. + post-synaptic variable + elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model. @@ -1948,9 +2112,9 @@ The model can be enriched with particular spatial embedding. - uniform - a current distribution where current models are uniformly distributed. + uniform + a current distribution where current models are uniformly distributed. @@ -1958,10 +2122,10 @@ The model can be enriched with particular spatial embedding. - learning rule - http://en.wikipedia.org/wiki/Learning_rule - network model component that is a method which improves the neural network's performance. It is done by updating the weights and bias level of a network after a network is stimulated in an environment. + http://en.wikipedia.org/wiki/Learning_rule + learning rule + network model component that is a method which improves the neural network's performance. It is done by updating the weights and bias level of a network after a network is stimulated in an environment. @@ -1969,9 +2133,9 @@ The model can be enriched with particular spatial embedding. - random - a current distribution where current models are distributed according to a particular probability distribution. + random + a current distribution where current models are distributed according to a particular probability distribution. @@ -1979,9 +2143,9 @@ The model can be enriched with particular spatial embedding. - non-linear - a current distribution where current models are distributed according to a non-linear function of space. + non-linear + a current distribution where current models are distributed according to a non-linear function of space. @@ -1989,9 +2153,9 @@ The model can be enriched with particular spatial embedding. - linear - a current distribution where current models are distributed according to a linear function of space. + linear + a current distribution where current models are distributed according to a linear function of space. @@ -1999,8 +2163,8 @@ The model can be enriched with particular spatial embedding. - concentration + concentration @@ -2008,13 +2172,13 @@ The model can be enriched with particular spatial embedding. - current model quality - - - - - model component quality that represent specific properties attached to current models + + + + + current model quality + model component quality that represent specific properties attached to current models @@ -2022,13 +2186,13 @@ The model can be enriched with particular spatial embedding. - model description - - - - - - an information content entity that represents the differents types of formats which can exist for describing a model (scientific paper, database entry, XML format, ...) + + + + + + model description + an information content entity that represents the differents types of formats which can exist for describing a model (scientific paper, database entry, XML format, ...) @@ -2036,13 +2200,13 @@ The model can be enriched with particular spatial embedding. - mathematical concept - - - - a thing that represents the differents mathematical concepts used to represent models. - link to SBO, Kisao, Teddy + + + + link to SBO, Kisao, Teddy + mathematical concept + a thing that represents the differents mathematical concepts used to represent models. @@ -2050,9 +2214,9 @@ The model can be enriched with particular spatial embedding. - network layout component - a network model component that describe the different level of organization of the network model + network layout component + a network model component that describe the different level of organization of the network model @@ -2060,9 +2224,9 @@ The model can be enriched with particular spatial embedding. - cellular distribution - a network layout component that represents the distribution of the cellular model type in euclidian or non euclidean space. + cellular distribution + a network layout component that represents the distribution of the cellular model type in euclidian or non euclidean space. @@ -2070,9 +2234,9 @@ The model can be enriched with particular spatial embedding. - one dimensional layout - related to definition in NIF: http://neurolex.org/wiki/Category:One_dimensional_region + related to definition in NIF: http://neurolex.org/wiki/Category:One_dimensional_region + one dimensional layout @@ -2080,15 +2244,15 @@ The model can be enriched with particular spatial embedding. - model - + - - a generically_dependent_continuant that is a placeholder for any model + + model + a generically_dependent_continuant that is a placeholder for any model @@ -2096,10 +2260,10 @@ The model can be enriched with particular spatial embedding. - elementary model component - an elementary model component is the smallest model component on which aggregated component are built. These elements can have either the role of parameter or the role of variable. - http://www.thefreedictionary.com/elementary + http://www.thefreedictionary.com/elementary + elementary model component + an elementary model component is the smallest model component on which aggregated component are built. These elements can have either the role of parameter or the role of variable. @@ -2107,10 +2271,10 @@ The model can be enriched with particular spatial embedding. - short term plasticity model - model of synaptic plasticity that describes the short term changes in the synaptic activity. - short term plasticity rule + short term plasticity model + short term plasticity rule + model of synaptic plasticity that describes the short term changes in the synaptic activity. @@ -2118,10 +2282,10 @@ The model can be enriched with particular spatial embedding. - long term plasticity model - long term plasticity rule - model of synaptic plasticity that describes the long term changes in the synaptic activity. + long term plasticity model + long term plasticity rule + model of synaptic plasticity that describes the long term changes in the synaptic activity. @@ -2129,9 +2293,9 @@ The model can be enriched with particular spatial embedding. - rate-based plasticity model - a phenomenological model of long term synaptic plasticity that represent the variation of synaptic impact depending on the firing rate of the models. + rate-based plasticity model + a phenomenological model of long term synaptic plasticity that represent the variation of synaptic impact depending on the firing rate of the models. @@ -2139,9 +2303,9 @@ The model can be enriched with particular spatial embedding. - spike timing dependent plasticity model - a phenomenological model of long term synaptic plasticity that represent the variation of synaptic efficacy depending on the relative spike timing of the pre- and post-synaptic models. + spike timing dependent plasticity model + a phenomenological model of long term synaptic plasticity that represent the variation of synaptic efficacy depending on the relative spike timing of the pre- and post-synaptic models. @@ -2149,9 +2313,9 @@ The model can be enriched with particular spatial embedding. - biophysical model - a model of long term synaptic plasticity that represents the biophysical mechanisms involved in the changes of synaptic efficacy. + biophysical model + a model of long term synaptic plasticity that represents the biophysical mechanisms involved in the changes of synaptic efficacy. @@ -2159,11 +2323,11 @@ The model can be enriched with particular spatial embedding. - homeostatic plasticity model - homeostatic plasticity rule - http://en.wikipedia.org/wiki/Homeostatic_plasticity - synaptic plasticity model that account for the capacity of neurons to regulate their own excitability relative to network activity. + http://en.wikipedia.org/wiki/Homeostatic_plasticity + homeostatic plasticity model + homeostatic plasticity rule + synaptic plasticity model that account for the capacity of neurons to regulate their own excitability relative to network activity. @@ -2171,10 +2335,10 @@ The model can be enriched with particular spatial embedding. - Markram and Tsodyks model - PMID: 9012851 - defined model that describes the impact of neurotransmitter release and synaptic depression. + PMID: 9012851 + Markram and Tsodyks model + defined model that describes the impact of neurotransmitter release and synaptic depression. @@ -2182,11 +2346,11 @@ The model can be enriched with particular spatial embedding. - Song and Abbott model - PMID: 10966623 - defined model that is a phenomenological model of spike timing dependent plasticity - http://www.scholarpedia.org/article/Models_of_synaptic_plasticity#Spike_timing_based_models + PMID: 10966623 + http://www.scholarpedia.org/article/Models_of_synaptic_plasticity#Spike_timing_based_models + Song and Abbott model + defined model that is a phenomenological model of spike timing dependent plasticity @@ -2194,9 +2358,9 @@ The model can be enriched with particular spatial embedding. - zero dimensional layout - relates to http://neurolex.org/wiki/Category:Zero_dimensional_region + relates to http://neurolex.org/wiki/Category:Zero_dimensional_region + zero dimensional layout @@ -2204,9 +2368,9 @@ The model can be enriched with particular spatial embedding. - resistance - http://www.ebi.ac.uk/sbo/main/SBO:0000254 + http://www.ebi.ac.uk/sbo/main/SBO:0000254 + resistance @@ -2214,8 +2378,8 @@ The model can be enriched with particular spatial embedding. - time + time @@ -2223,9 +2387,9 @@ The model can be enriched with particular spatial embedding. - rate 0987654321 + rate @@ -2233,9 +2397,9 @@ The model can be enriched with particular spatial embedding. - developmental learning - learning rule based on the mechanisms taking place during the development of the nervous system. + developmental learning + learning rule based on the mechanisms taking place during the development of the nervous system. @@ -2243,11 +2407,11 @@ The model can be enriched with particular spatial embedding. - reinforcement learning - a learning rule that allow to learn by interacting with an environment through a trial and error process during which the reward is maximized. - http://www.scholarpedia.org/article/Reinforcement_learning - reward-based learning + http://www.scholarpedia.org/article/Reinforcement_learning + reward-based learning + reinforcement learning + a learning rule that allow to learn by interacting with an environment through a trial and error process during which the reward is maximized. @@ -2255,10 +2419,10 @@ The model can be enriched with particular spatial embedding. - synaptic plasticity model component - - a component of plasticity models that describes the rules governing the changes in synaptic efficacy. + + synaptic plasticity model component + a component of plasticity models that describes the rules governing the changes in synaptic efficacy. @@ -2266,9 +2430,9 @@ The model can be enriched with particular spatial embedding. - pair-based rule - timing dependency that modifies the synaptic weight depending on the time difference between pairs of action potentials. + pair-based rule + timing dependency that modifies the synaptic weight depending on the time difference between pairs of action potentials. @@ -2276,9 +2440,9 @@ The model can be enriched with particular spatial embedding. - triplet-based rule - timing dependency that modifies the synaptic weight depending on the time difference between triplets of action potentials. + triplet-based rule + timing dependency that modifies the synaptic weight depending on the time difference between triplets of action potentials. @@ -2286,10 +2450,10 @@ The model can be enriched with particular spatial embedding. - suppression model - reference the model from Froemke and Dan, 2002 described in Morrisson, 2008 - timing dependency that accounts for the suppression of NMDA receptor during spike timing dependent long term depression + reference the model from Froemke and Dan, 2002 described in Morrisson, 2008 + suppression model + timing dependency that accounts for the suppression of NMDA receptor during spike timing dependent long term depression @@ -2297,9 +2461,9 @@ The model can be enriched with particular spatial embedding. - short term depression model - a model of short term synaptic plasticity that represent the decrease of the synaptic efficacy for a short period of time + short term depression model + a model of short term synaptic plasticity that represent the decrease of the synaptic efficacy for a short period of time @@ -2307,9 +2471,9 @@ The model can be enriched with particular spatial embedding. - model component quality - - quality exhibited by model components + + model component quality + quality exhibited by model components @@ -2317,9 +2481,9 @@ The model can be enriched with particular spatial embedding. - cellular distribution quality - model component quality that describes the distribution of cellular model in abstract space + cellular distribution quality + model component quality that describes the distribution of cellular model in abstract space @@ -2327,15 +2491,15 @@ The model can be enriched with particular spatial embedding. - ModelDB accession number - + - A CRID symbol that is sufficient to look up a model from ModelDB + ModelDB accession number + A CRID symbol that is sufficient to look up a model from ModelDB @@ -2343,9 +2507,9 @@ The model can be enriched with particular spatial embedding. - mixed grouping - cellular grouping quality that represents the grouping of cellular model based on two criterions: anatomical and functional + mixed grouping + cellular grouping quality that represents the grouping of cellular model based on two criterions: anatomical and functional @@ -2353,9 +2517,9 @@ The model can be enriched with particular spatial embedding. - delay - http://www.ebi.ac.uk/sbo/main/SBO:0000225 + http://www.ebi.ac.uk/sbo/main/SBO:0000225 + delay @@ -2363,9 +2527,9 @@ The model can be enriched with particular spatial embedding. - duration - http://www.ebi.ac.uk/sbo/main/SBO:0000347 + http://www.ebi.ac.uk/sbo/main/SBO:0000347 + duration @@ -2373,7 +2537,7 @@ The model can be enriched with particular spatial embedding. - obsolete + obsolete @@ -2381,9 +2545,9 @@ The model can be enriched with particular spatial embedding. - plasticity model component - a model component that is used to build a plasticity model type + plasticity model component + a model component that is used to build a plasticity model type @@ -2391,9 +2555,9 @@ The model can be enriched with particular spatial embedding. - timing dependency - a component of a synaptic plasticity rule that describes the dependency of synaptic changes on the relative spike timing in the pre- and post-synaptic models + timing dependency + a component of a synaptic plasticity rule that describes the dependency of synaptic changes on the relative spike timing in the pre- and post-synaptic models @@ -2401,9 +2565,9 @@ The model can be enriched with particular spatial embedding. - weight update component - a component of a synaptic plasticity rule that describes the changes in synaptic weight. + weight update component + a component of a synaptic plasticity rule that describes the changes in synaptic weight. @@ -2411,9 +2575,9 @@ The model can be enriched with particular spatial embedding. - voltage dependency - a component of a synaptic plasticity rule that describes the relation between the post-synaptic voltage and the change in synaptic efficacy. + voltage dependency + a component of a synaptic plasticity rule that describes the relation between the post-synaptic voltage and the change in synaptic efficacy. @@ -2421,10 +2585,10 @@ The model can be enriched with particular spatial embedding. - weight independent - a weight update component that updates the weight with additive increment - additive + weight independent + additive + a weight update component that updates the weight with additive increment @@ -2432,10 +2596,10 @@ The model can be enriched with particular spatial embedding. - weight dependent - http://www.scholarpedia.org/article/Spike-timing_dependent_plasticity#Weight_dependence:_hard_bounds_and_soft_bounds - weight update component that updates the weight within bounded range by multiplying the changes by constants called soft bounds or multiplicative weight dependence. + http://www.scholarpedia.org/article/Spike-timing_dependent_plasticity#Weight_dependence:_hard_bounds_and_soft_bounds + weight dependent + weight update component that updates the weight within bounded range by multiplying the changes by constants called soft bounds or multiplicative weight dependence. @@ -2443,9 +2607,9 @@ The model can be enriched with particular spatial embedding. - learning rate - elementary model component that set the amount by which synaptic weight are updated + learning rate + elementary model component that set the amount by which synaptic weight are updated @@ -2453,10 +2617,10 @@ The model can be enriched with particular spatial embedding. - leakage current - abstract current model that approximates the passive properties of biological neurons. - http://www.scholarpedia.org/article/Conductance-based_models + http://www.scholarpedia.org/article/Conductance-based_models + leakage current + abstract current model that approximates the passive properties of biological neurons. @@ -2464,9 +2628,9 @@ The model can be enriched with particular spatial embedding. - aggregated model component - a model component that results from the aggregation of parameters and/or variable and/or mathematical operators + aggregated model component + a model component that results from the aggregation of parameters and/or variable and/or mathematical operators @@ -2474,10 +2638,10 @@ The model can be enriched with particular spatial embedding. - variable - elementary model component role that defines an elementary model component as a value that may change within the scope of a given problem or set of operations. - http://en.wikipedia.org/wiki/Variable_(mathematics) + http://en.wikipedia.org/wiki/Variable_(mathematics) + variable + elementary model component role that defines an elementary model component as a value that may change within the scope of a given problem or set of operations. @@ -2485,9 +2649,9 @@ The model can be enriched with particular spatial embedding. - membrane capacitance - - Measure of the amount of electric charge stored (or separated) by the cellular membrane for a given electric potential. The unit of capacitance is the Farad. + + membrane capacitance + Measure of the amount of electric charge stored (or separated) by the cellular membrane for a given electric potential. The unit of capacitance is the Farad. @@ -2495,9 +2659,9 @@ The model can be enriched with particular spatial embedding. - membrane resistance - - Measure of the degree to which the cellular membrane opposes the passage of an electric current. The SI unit of electrical resistance is the ohm. + + membrane resistance + Measure of the degree to which the cellular membrane opposes the passage of an electric current. The SI unit of electrical resistance is the ohm. @@ -2505,8 +2669,16 @@ The model can be enriched with particular spatial embedding. - membrane time constante + membrane time constante + + + + + + + + cno test value @@ -2514,35 +2686,77 @@ The model can be enriched with particular spatial embedding. - Federal Funding Resource 0123456789 + Federal Funding Resource + + + + + + + + ncit test value + + + + ogms test value + + + + + + + + thesaurus test value + + + + + + + + + + + + + + + + + + + + + + - - - + + + - - + + - + - + diff --git a/test/data/ontology_files/ncit_test.owl b/test/data/ontology_files/ncit_test.owl new file mode 100644 index 00000000..608a9d96 --- /dev/null +++ b/test/data/ontology_files/ncit_test.owl @@ -0,0 +1,23197 @@ + + + + 23.12d + en + NCI Thesaurus, a controlled vocabulary in support of NCI administrative and scientific activities. Produced by the Enterprise Vocabulary System (EVS), a project by the NCI Center for Biomedical Informatics and Information Technology. National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U.S.A. + December 26, 2023 + + + + + + + + + + + + + A1 + Conceptual Entity + Role Has Domain + Role_Has_Domain + Role_Has_Domain + An association that specifies the parent of the branch encompassing a role's domain. + Role_Has_Domain + + + + + + Role_Has_Domain + PT + NCI + + + + + An association that specifies the parent of the branch encompassing a role's domain. + NCI + + + + + + + + A10 + Conceptual Entity + Has CDRH Parent + Has_CDRH_Parent + Has_CDRH_Parent + An association created to allow the source CDRH to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. + Has_CDRH_Parent + + + + + + Has_CDRH_Parent + PT + NCI + + + + + An association created to allow the source CDRH to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. + NCI + + + + + + + + A11 + Conceptual Entity + Has_NICHD_Parent + Has_NICHD_Parent + An association created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are a contributing source. + Has_NICHD_Parent + + + + + + Has_NICHD_Parent + PT + NCI + + + + + An association created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are a contributing source. + NCI + + + + + + + + A12 + Conceptual Entity + Has Data Element + Has_Data_Element + Has_Data_Element + An association created to relate a data element concept to the codelist term that is used to bundle its subset of valid value concepts. + Has_Data_Element + + + + + + Has_Data_Element + PT + NCI + + + + + An association created to relate a data element concept to the codelist term that is used to bundle its subset of valid value concepts. + NCI + + + + + + + + A13 + Conceptual Entity + Related_To_Genetic_Biomarker + Related_To_Genetic_Biomarker + An association that indicates that a finding or lab test is related to a gene, possibly through a variant or product. + Related_To_Genetic_Biomarker + + + + + + An association that indicates that a finding or lab test is related to a gene, possibly through a variant or product. + NCI + + + + + Related_To_Genetic_Biomarker + PT + NCI + + + + + + + + A14 + Conceptual Entity + Neoplasm_Has_Special_Category + Neoplasm_Has_Special_Category + An association that indicates that a neoplastic disease can have the characteristics defined by a Neoplasm by Special Category concept. + Neoplasm_Has_Special_Category + + + + + + Neoplasm_Has_Special_Category + PT + NCI + + + + + An association that indicates that a neoplastic disease can have the characteristics defined by a Neoplasm by Special Category concept. + NCI + + + + + + + + A15 + Conceptual Entity + Has_CTCAE_5_Parent + Has_CTCAE_5_Parent + An association created to allow the source CTCAE 5.0 to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which CTCAE is the contributing source. + Has_CTCAE_5_Parent + + + + + + Has_CTCAE_5_Parent + PT + NCI + + + + + An association created to allow the source CTCAE 5.0 to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which CTCAE is the contributing source. + NCI + + + + + + + + A16 + Conceptual Entity + Has_INC_Parent + Has_INC_Parent + An association created to allow the source INC to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. + Has_INC_Parent + + + + + + Has_INC_Parent + PT + NCI + + + + + An association created to allow the source INC to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. + NCI + + + + + + + + A17 + Conceptual Entity + Has_Pharmaceutical_State_Of_Matter + Has_Pharmaceutical_State_Of_Matter + State of Matter + An association that specifies the physical conditions describing the molecular form of a product. The target value should belong to the EDQM-HC State of Matter Terminology. + Has_Pharmaceutical_State_Of_Matter + + + + + + Has_Pharmaceutical_State_Of_Matter + PT + NCI + + + + + State of Matter + PT + EDQM-HC + + + + + An association that specifies the physical conditions describing the molecular form of a product. The target value should belong to the EDQM-HC State of Matter Terminology. + NCI + + + + + + + + A18 + Conceptual Entity + Has_Pharmaceutical_Basic_Dose_Form + Basic Dose Form + Has_Pharmaceutical_Basic_Dose_Form + An association that specifies the category of the pharmaceutical dose form, used to group together related pharmaceutical dose forms. The target value should belong to the EDQM-HC Basic Dose Form Terminology. + Has_Pharmaceutical_Basic_Dose_Form + + + + + + Basic Dose Form + PT + EDQM-HC + + + + + Has_Pharmaceutical_Basic_Dose_Form + PT + NCI + + + + + An association that specifies the category of the pharmaceutical dose form, used to group together related pharmaceutical dose forms. The target value should belong to the EDQM-HC Basic Dose Form Terminology. + NCI + + + + + + + + A19 + Conceptual Entity + Has_Pharmaceutical_Administration_Method + Administration Method + Has_Pharmaceutical_Administration_Method + An association that specifies the methods by which a pharmaceutical product is intended to be administered to the patient. The target value should belong to the EDQM-HC Administration Method Terminology. + Has_Pharmaceutical_Administration_Method + + + + + + Administration Method + PT + EDQM-HC + + + + + Has_Pharmaceutical_Administration_Method + PT + NCI + + + + + An association that specifies the methods by which a pharmaceutical product is intended to be administered to the patient. The target value should belong to the EDQM-HC Administration Method Terminology. + NCI + + + + + + + + A2 + Conceptual Entity + Role Has Range + Role_Has_Range + Role_Has_Range + An association that specifies the parent of the branch encompassing the role's range. + Role_Has_Range + + + + + + Role_Has_Range + PT + NCI + + + + + An association that specifies the parent of the branch encompassing the role's range. + NCI + + + + + + + + A20 + Conceptual Entity + Has_Pharmaceutical_Intended_Site + Has_Pharmaceutical_Intended_Site + Intended Site + An association that specifies the general body sites at which a pharmaceutical product is intended to be administered. The target value should belong to the EDQM-HC Intended Site of Administration Terminology. + Has_Pharmaceutical_Intended_Site + + + + + + Has_Pharmaceutical_Intended_Site + PT + NCI + + + + + Intended Site + EDQM-HC + PT + + + + + An association that specifies the general body sites at which a pharmaceutical product is intended to be administered. The target value should belong to the EDQM-HC Intended Site of Administration Terminology. + NCI + + + + + + + + A21 + Conceptual Entity + Has_Pharmaceutical_Release_Characteristics + Has_Pharmaceutical_Release_Characteristics + Release Characteristics + An association that specifies the timing by which an active ingredient is made available in the body after administration of the pharmaceutical product, in comparison with a conventional, direct release of the active ingredient. The target value should belong to the EDQM-HC Release Characteristics Terminology. + Has_Pharmaceutical_Release_Characteristics + + + + + + Has_Pharmaceutical_Release_Characteristics + PT + NCI + + + + + Release Characteristics + PT + EDQM-HC + + + + + An association that specifies the timing by which an active ingredient is made available in the body after administration of the pharmaceutical product, in comparison with a conventional, direct release of the active ingredient. The target value should belong to the EDQM-HC Release Characteristics Terminology. + NCI + + + + + + + + A22 + Conceptual Entity + Has_Pharmaceutical_Transformation + Has_Pharmaceutical_Transformation + Transformation + An association that specifies the procedures that are carried out in order to convert a manufactured item that requires such a procedure into a pharmaceutical product. The target value should belong to the EDQM-HC Transformation Terminology. + Has_Pharmaceutical_Transformation + + + + + + Has_Pharmaceutical_Transformation + PT + NCI + + + + + Transformation + PT + EDQM-HC + + + + + An association that specifies the procedures that are carried out in order to convert a manufactured item that requires such a procedure into a pharmaceutical product. The target value should belong to the EDQM-HC Transformation Terminology. + NCI + + + + + + + + A23 + Conceptual Entity + Has_PCDC_Data_Type + Has_PCDC_Data_Type + An association that specifies one of three data types for a particular variable, String, Code or Number. + Has_PCDC_Data_Type + + + + + + Has_PCDC_Data_Type + PT + NCI + + + + + An association that specifies one of three data types for a particular variable, String, Code or Number. + NCI + + + + + + + + A24 + Conceptual Entity + Is_PCDC_AML_Authorized_Value_For_Variable + Is_PCDC_AML_Authorized_Value_For_Variable + An association that indicates a PCDC AML concept is a Authorized Value for a PCDC AML Variable concept. + Is_PCDC_AML_Authorized_Value_For_Variable + + + + + + Is_PCDC_AML_Authorized_Value_For_Variable + PT + NCI + + + + + An association that indicates a PCDC AML concept is a Authorized Value for a PCDC AML Variable concept. + NCI + + + + + + + + A25 + Conceptual Entity + Value_Set_Is_Paired_With + Value_Set_Is_Paired_With + An association that specifies the paired ‘Test or Parameter Name’ codelist that goes with the ‘Test or Parameter Code’ codelist. This association uni-directionally points from a Test/Parameter Code Codelist to the Test/Parameter Name Codelist. + Value_Set_Is_Paired_With + + + + + + Value_Set_Is_Paired_With + PT + NCI + + + + + An association that specifies the paired ‘Test or Parameter Name’ codelist that goes with the ‘Test or Parameter Code’ codelist. This association uni-directionally points from a Test/Parameter Code Codelist to the Test/Parameter Name Codelist. + NCI + + + + + + + + A26 + Conceptual Entity + Has_PCDC_AML_Authorized_Value + Has_PCDC_AML_Authorized_Value + An association that shows which PCDC AML Authorized Values are possible for a specific Variable. + Has_PCDC_AML_Authorized_Value + + + + + + Has_PCDC_AML_Authorized_Value + PT + NCI + + + + + An association that shows which PCDC AML Authorized Values are possible for a specific Variable. + NCI + + + + + + + + A27 + Conceptual Entity + Has_CTDC_Value + Has_CTDC_Value + An association connecting a CTDC Property concept to its dedicated value concept(s). + Has_CTDC_Value + + + + + + Has_CTDC_Value + PT + NCI + + + + + An association connecting a CTDC Property concept to its dedicated value concept(s). + NCI + + + + + + + + A28 + Conceptual Entity + Is_PCDC_EWS_Authorized_Value_For_Variable + Is_PCDC_EWS_Authorized_Value_For_Variable + An association that indicates a PCDC EWS concept is a Authorized Value for a specific PCDC EWS Variable concept. + Is_PCDC_EWS_Authorized_Value_For_Variable + + + + + + Is_PCDC_EWS_Authorized_Value_For_Variable + PT + NCI + + + + + An association that indicates a PCDC EWS concept is a Authorized Value for a specific PCDC EWS Variable concept. + NCI + + + + + + + + A29 + Conceptual Entity + Has_PCDC_EWS_Authorized_Value + Has_PCDC_EWS_Authorized_Value + An association that shows which Authorized Values are possible for a specific PCDC EWS Variable concept. + Has_PCDC_EWS_Authorized_Value + + + + + + Has_PCDC_EWS_Authorized_Value + PT + NCI + + + + + An association that shows which Authorized Values are possible for a specific PCDC EWS Variable concept. + NCI + + + + + + + + A3 + Conceptual Entity + Role Has Parent + Role_Has_Parent + Role_Has_Parent + An association that specifies that a role exists as part of a role hierarchy and specifies the role's parent, the role that this role specializes. + Role_Has_Parent + + + + + + Role_Has_Parent + PT + NCI + + + + + An association that specifies that a role exists as part of a role hierarchy and specifies the role's parent, the role that this role specializes. + NCI + + + + + + + + A30 + Conceptual Entity + Has_ICDC_Value + Has_ICDC_Value + An association connecting an ICDC Property concept to its dedicated value concept(s). + Has_ICDC_Value + + + + + + Has_ICDC_Value + PT + NCI + + + + + An association connecting an ICDC Property concept to its dedicated value concept(s). + NCI + + + + + + + + A31 + Conceptual Entity + Has_GDC_Value + Has_GDC_Value + An association that connects a concept representing a GDC property to its dedicated value concept(s). + Has_GDC_Value + + + + + + Has_GDC_Value + PT + NCI + + + + + An association that connects a concept representing a GDC property to its dedicated value concept(s). + NCI + + + + + + + + A32 + Conceptual Entity + Is_Value_For_GDC_Property + Is_Value_For_GDC_Property + An association that that connects a concept representing a GDC value to any associated GDC property concept(s). + Is_Value_For_GDC_Property + + + + + + Is_Value_For_GDC_Property + PT + NCI + + + + + An association that that connects a concept representing a GDC value to any associated GDC property concept(s). + NCI + + + + + + + + A33 + Conceptual Entity + Is_PCDC_GCT_Authorized_Value_For_Variable + Is_PCDC_GCT_Authorized_Value_For_Variable + An association that indicates a concept is a dedicated Authorized Value concept for a specific PCDC GCT Variable. + Is_PCDC_GCT_Authorized_Value_For_Variable + + + + + + Is_PCDC_GCT_Authorized_Value_For_Variable + PT + NCI + + + + + An association that indicates a concept is a dedicated Authorized Value concept for a specific PCDC GCT Variable. + NCI + + + + + + + + A34 + Conceptual Entity + Has_PCDC_GCT_Authorized_Value + Has_PCDC_GCT_Authorized_Value + An association that shows which Authorized Values are possible for a specific PCDC GCT Variable. + Has_PCDC_GCT_Authorized_Value + + + + + + Has_PCDC_GCT_Authorized_Value + PT + NCI + + + + + An association that shows which Authorized Values are possible for a specific PCDC GCT Variable. + NCI + + + + + + + + A35 + Conceptual Entity + Is_PCDC_ALL_Authorized_Value_For_Variable + Is_PCDC_ALL_Authorized_Value_For_Variable + An association that indicates a PCDC ALL concept is a Authorized Value for a PCDC ALL Variable concept. + Is_PCDC_ALL_Authorized_Value_For_Variable + + + + + + Is_PCDC_ALL_Authorized_Value_For_Variable + PT + NCI + + + + + An association that indicates a PCDC ALL concept is a Authorized Value for a PCDC ALL Variable concept. + NCI + + + + + + + + A36 + Conceptual Entity + Has_PCDC_ALL_Authorized_Value + Has_PCDC_ALL_Authorized_Value + An association that shows which PCDC ALL Authorized Values are possible for a specific Variable. + Has_PCDC_ALL_Authorized_Value + + + + + + Has_PCDC_ALL_Authorized_Value + PT + NCI + + + + + An association that shows which PCDC ALL Authorized Values are possible for a specific Variable. + NCI + + + + + + + + A37 + Conceptual Entity + Has_SeroNet_Authorized_Value + Has_SeroNet_Authorized_Value + An association that shows which Authorized Values are possible for a specific SeroNet Variable. + Has_SeroNet_Authorized_Value + + + + + + Has_SeroNet_Authorized_Value + PT + NCI + + + + + An association that shows which Authorized Values are possible for a specific SeroNet Variable. + NCI + + + + + + + + A38 + Conceptual Entity + Has_PCDC_OS_Authorized_Value + Has_PCDC_OS_Authorized_Value + An association that shows which Authorized Values are possible for a specific PCDC OS Variable. + Has_PCDC_OS_Authorized_Value + + + + + + Has_PCDC_OS_Authorized_Value + PT + NCI + + + + + An association that shows which Authorized Values are possible for a specific PCDC OS Variable. + NCI + + + + + + + + A39 + Conceptual Entity + Has_PCDC_HL_Authorized_Value + Has_PCDC_HL_Authorized_Value + An association that shows which Authorized Values are possible for a specific PCDC HL Variable. + Has_PCDC_HL_Authorized_Value + + + + + + Has_PCDC_HL_Authorized_Value + PT + NCI + + + + + An association that shows which Authorized Values are possible for a specific PCDC HL Variable. + NCI + + + + + + + + A4 + Conceptual Entity + Qualifier Applies To + Qualifier_Applies_To + Qualifier_Applies_To + An association that indicates the property or association that the qualifier is to be used with. + Qualifier_Applies_To + + + + + + Qualifier_Applies_To + PT + NCI + + + + + An association that indicates the property or association that the qualifier is to be used with. + NCI + + + + + + + + A40 + Conceptual Entity + Has_DIPG_DMG_Authorized_Value + Has_DIPG_DMG_Authorized_Value + An association that shows which Authorized Values are possible for a specific DIPG/DMG Variable. + Has_DIPG_DMG_Authorized_Value + + + + + + Has_DIPG_DMG_Authorized_Value + PT + NCI + + + + + An association that shows which Authorized Values are possible for a specific DIPG/DMG Variable. + NCI + + + + + + + + A41 + Conceptual Entity + Has_Pharmaceutical_Basic_Administrable_Dose_Form + Has_Pharmaceutical_Basic_Administrable_Dose_Form + An association that specifies the physical form of the medication when the drug is administered to the patient. + The Administrable Dosage Form assignation is in status of Pending Approval by European Directorate for the Quality of Medicines (EDQM). + Has_Pharmaceutical_Basic_Administrable_Dose_Form + + + + + + Has_Pharmaceutical_Basic_Administrable_Dose_Form + PT + NCI + + + + + An association that specifies the physical form of the medication when the drug is administered to the patient. + NCI + + + + + + + + A42 + Conceptual Entity + Has_OORO_PC_Value + Has_OORO_PC_Value + An association specifying the Values for a specific OORO Prostate Cancer (PC) Attribute. + Has_OORO_PC_Value + + + + + + Has_OORO_PC_Value + PT + NCI + + + + + An association specifying the Values for a specific OORO Prostate Cancer (PC) Attribute. + NCI + George Chang + + + + + + + + A43 + Conceptual Entity + Has_OORO_HNC_Value + Has_OORO_HNC_Value + An association specifying the Values for a specific OORO Head and Neck Cancer (HNC) Attribute. + Has_OORO_HNC_Value + + + + + + Has_OORO_HNC_Value + PT + NCI + + + + + An association specifying the Values for a specific OORO Head and Neck Cancer (HNC) Attribute. + NCI + + + + + + + + A44 + Conceptual Entity + Has_OORO_BC_Value + Has_OORO_BC_Value + An association specifying the Values for a specific OORO Breast Cancer (BC) Attribute. + Has_OORO_BC_Value + + + + + + Has_OORO_BC_Value + PT + NCI + + + + + An association specifying the Values for a specific OORO Breast Cancer (BC) Attribute. + NCI + + + + + + + + A45 + Conceptual Entity + Has_OORO_LC_Value + Has_OORO_LC_Value + An association specifying the Values for a specific OORO Lung Cancer (LC) Attribute + Has_OORO_LC_Value + + + + + + Has_OORO_LC_Value + SY + NCI + + + + + An association specifying the Values for a specific OORO Lung Cancer (LC) Attribute + NCI + + + + + + + + A46 + Conceptual Entity + Has_OORO_Data_Type + Has_OORO_Data_Type + An association that specifies one of three data types for a particular variable, String, Code or Number. + Has_OORO_Data_Type + + + + + + Has_OORO_Data_Type + NCI + PT + + + + + + + + A48 + Conceptual Entity + Has_ACC-AHA_SARS2_Authorized_Value + Has_ACC-AHA_SARS2_Authorized_Value + An association that shows which Authorized Values are possible for a specific ACC/AHA SARS2 Variable. + Has_ACC-AHA_SARS2_Authorized_Value + + + + + + Has_ACC-AHA_SARS2_Authorized_Value + PT + NCI + + + + + An association that shows which Authorized Values are possible for a specific ACC/AHA SARS2 Variable. + NCI + + + + + + + + A5 + Conceptual Entity + Has Salt Form + Has_Salt_Form + Has_Salt_Form + An association that connects the salt form of a drug with its free acid or free base. + USAGE NOTE: A salt form of a drug consists of 2 parts, one acidic and one basic group that are readily disassociated in liquid phase. Salt forms are either salts of strong acids and basic drugs (e.g. Atropine Sulfate, Cetirizine Hydrochloride) or salts of strong bases and acidic drugs (Allopurinol Sodium). This association is usually used in conjunction with Has_Free_Acid_Or_Base_Form. + Has_Salt_Form + + + + + + Has_Salt_Form + PT + NCI + + + + + An association that connects the salt form of a drug with its free acid or free base. + NCI + + + + + + + + A6 + Conceptual Entity + Has Free Acid Or Base Form + Has_Free_Acid_Or_Base_Form + Has_Free_Acid_Or_Base_Form + An association that connects the salt form of a drug with its free acid or free base. + The free acid or base is responsible for the drug's therapeutic effect. Hence, the salt form of a drug has the same mechanism of action as the free acid or base form. + Has_Free_Acid_Or_Base_Form + + + + + + Has_Free_Acid_Or_Base_Form + PT + NCI + + + + + An association that connects the salt form of a drug with its free acid or free base. + NCI + + + + + + + + A7 + Conceptual Entity + Has Target + Has_Target + Has_Target + An association that connects a drug or other agent to a clinically intended, molecular-scale target. The target value may be a gene, gene product, anatomic structure, cell, biological process, or other concept, where the effect of the agent on the target is thought to be of therapeutic, diagnostic, or other clinical relevance to a disease process. The effect is most often direct, as defined at a molecular scale, but may also be indirect and/or defined at a larger scale. + Has_Target + + + + + + Has_Target + PT + NCI + + + + + An association that connects a drug or other agent to a clinically intended, molecular-scale target. The target value may be a gene, gene product, anatomic structure, cell, biological process, or other concept, where the effect of the agent on the target is thought to be of therapeutic, diagnostic, or other clinical relevance to a disease process. The effect is most often direct, as defined at a molecular scale, but may also be indirect and/or defined at a larger scale. + NCI + + + + + + + + A8 + Conceptual Entity + Concept Is In Subset + Concept_In_Subset + Concept_In_Subset + An association that connects the concept defining a particular terminology subset with concepts that belong to this subset. + Concept_In_Subset + + + + + + Concept_In_Subset + PT + NCI + + + + + An association that connects the concept defining a particular terminology subset with concepts that belong to this subset. + NCI + + + + + + + + A9 + Conceptual Entity + Is Related To Endogenous Product + Is_Related_To_Endogenous_Product + Is_Related_To_Endogenous_Product + An association that is asserted when there is a relationship or association between the therapeutic moiety and the endogenous gene product. + Is_Related_To_Endogenous_Product + + + + + + Is_Related_To_Endogenous_Product + PT + NCI + + + + + An association that is asserted when there is a relationship or association between the therapeutic moiety and the endogenous gene product. + NCI + + + + + + + + NHC0 + Conceptual Entity + code + code + A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus. + true + code + + + + + + code + PT + NCI + + + + + A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus. + NCI + + + + + + + + P100 + Conceptual Entity + OMIM Number + OMIM_Number + OMIM_Number + A property representing the accession number for a Protein or Gene within the OMIM database. + OMIM_Number + + + + + + OMIM_Number + PT + NCI + + + + + A property representing the accession number for a Protein or Gene within the OMIM database. + NCI + + + + + + + + P101 + Conceptual Entity + Homologous Gene + Homologous_Gene + Homologous_Gene + A property representing genes from other organisms that are similar in sequence and provide insight to the gene's function. + Homologous_Gene + + + + + + Homologous_Gene + PT + NCI + + + + + A property representing genes from other organisms that are similar in sequence and provide insight to the gene's function. + NCI + + + + + + + + P102 + Conceptual Entity + GenBank Accession Number + GenBank_Accession_Number + GenBank_Accession_Number + A property representing the accession number for a Gene within the GenBank database. + GenBank_Accession_Number + + + + + + GenBank_Accession_Number + PT + NCI + + + + + A property representing the accession number for a Gene within the GenBank database. + NCI + + + + + + + + P106 + Conceptual Entity + Semantic Type + Semantic_Type + Semantic_Type + A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. + In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. + Semantic_Type + + + + + + Semantic_Type + PT + NCI + + + + + A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. + NCI + + + + + + + + P107 + Conceptual Entity + Display Name + Display_Name + Display Name + Display_Name + A property representing an alternative Preferred Name for use in some NCI systems. + Display_Name + + + + + + Display Name + SY + NCI + + + + + Display_Name + PT + NCI + + + + + A property representing an alternative Preferred Name for use in some NCI systems. + NCI + + + + + + + + P108 + Conceptual Entity + Preferred Name + Preferred_Name + Preferred Name + Preferred Term + Preferred_Name + A property representing the word or phrase that NCI uses by preference to refer to the concept. + Preferred_Name + + + + + + Preferred Name + SY + NCI + + + + + Preferred Term + SY + NCI + + + + + Preferred_Name + PT + NCI + + + + + A property representing the word or phrase that NCI uses by preference to refer to the concept. + NCI + + + + + + + + P167 + Conceptual Entity + Image Link + Image_Link + Image_Link + A property representing a link to an image in an external database. + Image_Link + + + + + + Image_Link + PT + NCI + + + + + A property representing a link to an image in an external database. + NCI + + + + + + + + P171 + Conceptual Entity + PubMedID Primary Reference + PubMedID_Primary_Reference + PubMedID_Primary_Reference + A property used to provide a primary reference for descriptions of an NCI Thesaurus concept. + PubMedID_Primary_Reference + + + + + + PubMedID_Primary_Reference + PT + NCI + + + + + A property used to provide a primary reference for descriptions of an NCI Thesaurus concept. + NCI + + + + + + + + P175 + Conceptual Entity + NSC Number + NSC Number + NSC Number + NSC_Code + NSC_Number + NSC_Number_Property + A property representing a numeric identifier for substances submitted to the National Cancer Institute (NCI) for testing and evaluation. It is named after the Cancer Chemotherapy National Service Center (CCNSC), created in 1955, which originally ran the testing program and assigned these numbers. The testing program and repository is now run by the NCI Developmental Therapeutics Program (DTP). Assignment of NSC numbers was never done in a way that would guarantee one and only one NSC number would be assigned to a particular substance. + NSC Number + + + + + + NSC Number + PT + NCI + + + + + NSC_Code + SY + NCI + + + + + NSC_Number + SY + NCI + + + + + NSC_Number_Property + SY + NCI + + + + + A property representing a numeric identifier for substances submitted to the National Cancer Institute (NCI) for testing and evaluation. It is named after the Cancer Chemotherapy National Service Center (CCNSC), created in 1955, which originally ran the testing program and assigned these numbers. The testing program and repository is now run by the NCI Developmental Therapeutics Program (DTP). Assignment of NSC numbers was never done in a way that would guarantee one and only one NSC number would be assigned to a particular substance. + NCI + + + + + + + + P200 + Conceptual Entity + OLD PARENT + OLD_PARENT + OLD_PARENT + A property used to store the name of parent concepts present at the time a concept was retired. + OLD_PARENT + + + + + + OLD_PARENT + PT + NCI + + + + + A property used to store the name of parent concepts present at the time a concept was retired. + NCI + + + + + + + + P201 + Conceptual Entity + OLD CHILD + OLD_CHILD + OLD_CHILD + A property used to store the name of children concepts present at the time a concept was retired. + OLD_CHILD + + + + + + OLD_CHILD + PT + NCI + + + + + A property used to store the name of children concepts present at the time a concept was retired. + NCI + + + + + + + + P203 + Conceptual Entity + OLD KIND + OLD_KIND + OLD_KIND + Used to store the name of the concept's kind at the time a concept was retired. + OLD_KIND + + + + + + OLD_KIND + PT + NCI + + + + + Used to store the name of the concept's kind at the time a concept was retired. + NCI + + + + + + + + P204 + Conceptual Entity + OLD ROLE + OLD_ROLE + OLD_ROLE + A property used to store the name and value of asserted roles present at the time a concept was retired. + OLD_ROLE + + + + + + OLD_ROLE + PT + NCI + + + + + A property used to store the name and value of asserted roles present at the time a concept was retired. + NCI + + + + + + + + P205 + Conceptual Entity + OLD STATE + OLD_STATE + OLD_STATE + A property used to store the state of a concept, primitive or defined, at the time a concept was retired. + OLD_STATE + + + + + + OLD_STATE + PT + NCI + + + + + A property used to store the state of a concept, primitive or defined, at the time a concept was retired. + NCI + + + + + + + + P207 + Conceptual Entity + UMLS CUI + UMLS_CUI + UMLS_CUI + A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. + UMLS_CUI + + + + + + UMLS_CUI + PT + NCI + + + + + A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept. + NCI + + + + + + + + P208 + Conceptual Entity + NCI Metathesaurus CUI + NCI_META_CUI + NCI_META_CUI + A property representing the concept unique identifier (CUI) for those concepts that appear in NCI Metathesaurus but not in the National Library of Medicine Unified Medical Language System (NLM UMLS). + NCI_META_CUI + + + + + + NCI_META_CUI + PT + NCI + + + + + A property representing the concept unique identifier (CUI) for those concepts that appear in NCI Metathesaurus but not in the National Library of Medicine Unified Medical Language System (NLM UMLS). + NCI + + + + + + + + P210 + Conceptual Entity + CAS Registry Number + CAS_Registry + CAS_Registry + A property representing the Chemical Abstracts Service number for a Chemical or Drug. + CAS_Registry + + + + + + CAS_Registry + PT + NCI + + + + + A property representing the Chemical Abstracts Service number for a Chemical or Drug. + NCI + + + + + + + + P211 + Conceptual Entity + GO Annotation + GO_Annotation + GO_Annotation + A property that contains information that can be used for cross-referencing to relevant entries in the Gene Ontology (GO) database including term name, code, and evidence code. + GO_Annotation + + + + + + GO_Annotation + PT + NCI + + + + + A property that contains information that can be used for cross-referencing to relevant entries in the Gene Ontology (GO) database including term name, code, and evidence code. + NCI + + + + + + + + P215 + Conceptual Entity + KEGG ID + KEGG_ID + KEGG_ID + A property representing the KEGG ID code for a pathway. It can be used to link a KEGG pathway reference to the primary pathway information. + KEGG_ID + + + + + + KEGG_ID + PT + NCI + + + + + A property representing the KEGG ID code for a pathway. It can be used to link a KEGG pathway reference to the primary pathway information. + NCI + + + + + + + + P216 + Conceptual Entity + BioCarta ID + BioCarta_ID + BioCarta_ID + A property representing the BioCarta ID code for a pathway. It can be used to link a BioCarta pathway reference to the primary pathway information. + BioCarta_ID + + + + + + BioCarta_ID + PT + NCI + + + + + A property representing the BioCarta ID code for a pathway. It can be used to link a BioCarta pathway reference to the primary pathway information. + NCI + + + + + + + + P302 + Conceptual Entity + Accepted Therapeutic Use For + Accepted_Therapeutic_Use_For + Accepted_Therapeutic_Use_For + A property representing a disease or condition for which this drug is an accepted treatment. Used in the Drug, Food, Chemical or Biomedical Material branch. + Accepted_Therapeutic_Use_For + + + + + + Accepted_Therapeutic_Use_For + PT + NCI + + + + + A property representing a disease or condition for which this drug is an accepted treatment. Used in the Drug, Food, Chemical or Biomedical Material branch. + NCI + + + + + + + + P310 + Conceptual Entity + Concept Status + Concept_Status + Concept_Status + A property used to indicate the standing of a concept in relation to currently accepted classifications and concepts. In NCI Thesaurus concept status subtype indicates concepts with unusual and problematic characteristics that should be evaluated by people and/or programs before those concept are used. + Concept_Status + + + + + + Concept_Status + PT + NCI + + + + + A property used to indicate the standing of a concept in relation to currently accepted classifications and concepts. In NCI Thesaurus concept status subtype indicates concepts with unusual and problematic characteristics that should be evaluated by people and/or programs before those concept are used. + NCI + + + + + + + + P315 + Conceptual Entity + SNP ID + SNP_ID + SNP_ID + A property representing the dbSNP id number for the genetic polymorphism due to base substitutions. + SNP_ID + + + + + + SNP_ID + PT + NCI + + + + + A property representing the dbSNP id number for the genetic polymorphism due to base substitutions. + NCI + + + + + + + + P316 + Conceptual Entity + Relative Enzyme Activity + Relative_Enzyme_Activity + Relative_Enzyme_Activity + A property representing drug efficacy of the allelic product. + Relative_Enzyme_Activity + + + + + + Relative_Enzyme_Activity + PT + NCI + + + + + A property representing drug efficacy of the allelic product. + NCI + + + + + + + + P317 + Conceptual Entity + FDA Table + FDA_Table + FDA_Table + A property used to flag terms that are part of an FDA data standard manual, including Route of Administration, Dosage Form, Package Type and Potency. + FDA_Table + + + + + + FDA_Table + PT + NCI + + + + + A property used to flag terms that are part of an FDA data standard manual, including Route of Administration, Dosage Form, Package Type and Potency. + NCI + + + + + + + + P319 + Conceptual Entity + FDA UNII Code + FDA_UNII_Code + FDA_UNII_Code + A property representing the FDA Unique Ingredient Identifier, a key component of the federal drug information model. + FDA_UNII_Code + + + + + + FDA_UNII_Code + PT + NCI + + + + + A property representing the FDA Unique Ingredient Identifier, a key component of the federal drug information model. + NCI + + + + + + + + P320 + Conceptual Entity + OID + OID + OID + A property representing a globally unique identifier standardized by the International Organization for Standardization (ISO) for naming computational objects consistently and unambiguously. Object identifiers (OID) are assigned by a regulatory association. The NCI Thesaurus OID was asssigned by and is registered with the HL7 OID Registry and is the following string: 2.16.840.1.113883.3.26.1.1. + OID + + + + + + OID + PT + NCI + + + + + A property representing a globally unique identifier standardized by the International Organization for Standardization (ISO) for naming computational objects consistently and unambiguously. Object identifiers (OID) are assigned by a regulatory association. The NCI Thesaurus OID was asssigned by and is registered with the HL7 OID Registry and is the following string: 2.16.840.1.113883.3.26.1.1. + NCI + + + + + + + + P321 + Conceptual Entity + EntrezGene ID + EntrezGene_ID + EntrezGene_ID + GeneID + Locus_ID + A property representing the accession number for a Gene within the Entrez Gene database. + This property has replaced Locus_ID. + EntrezGene_ID + + + + + + EntrezGene_ID + PT + NCI + + + + + GeneID + SY + NCI + + + + + Locus_ID + SY + NCI + + + + + A property representing the accession number for a Gene within the Entrez Gene database. + NCI + + + + + + + + P322 + Conceptual Entity + Contributing Source + Contributing_Source + Contributing_Source + A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. + Contributing_Source + + + + + + Contributing_Source + PT + NCI + + + + + A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake. + NCI + + + + + + + + P325 + Conceptual Entity + [source] Definition + ALT_DEFINITION + ALT_DEFINITION + A property representing the English language definition of a concept from a source other than NCI. + ALT_DEFINITION + + + + + + ALT_DEFINITION + PT + NCI + + + + + A property representing the English language definition of a concept from a source other than NCI. + NCI + + + + + + + + P329 + Conceptual Entity + PDQ Open Trial Search ID + PDQ_Open_Trial_Search_ID + PDQ_Open_Trial_Search_ID + A property representing the identifier used by NCI's Cancer.gov Web site to retrieve PDQ Clinical Trials data for open trials involving specific clinical trials agents. While the identifier is the same for both open and closed trials two properties are used to support requirements of the current browser interface, as well as the possibility of providing values where only open trials will be retrieved. + PDQ_Open_Trial_Search_ID + + + + + + PDQ_Open_Trial_Search_ID + PT + NCI + + + + + A property representing the identifier used by NCI's Cancer.gov Web site to retrieve PDQ Clinical Trials data for open trials involving specific clinical trials agents. While the identifier is the same for both open and closed trials two properties are used to support requirements of the current browser interface, as well as the possibility of providing values where only open trials will be retrieved. + NCI + + + + + + + + P330 + Conceptual Entity + PDQ Closed Trial Search ID + PDQ_Closed_Trial_Search_ID + PDQ_Closed_Trial_Search_ID + A property representing the identifier used by NCI's Cancer.gov web site to retrieve PDQ Clinical Trials data for closed trials that involved specific clinical trials agents. While the identifier is the same for both open and closed trials two properties are used to support requirements of the current browser interface, as well as the possibility of providing values where only closed trials will be retrieved. + PDQ_Closed_Trial_Search_ID + + + + + + PDQ_Closed_Trial_Search_ID + PT + NCI + + + + + A property representing the identifier used by NCI's Cancer.gov web site to retrieve PDQ Clinical Trials data for closed trials that involved specific clinical trials agents. While the identifier is the same for both open and closed trials two properties are used to support requirements of the current browser interface, as well as the possibility of providing values where only closed trials will be retrieved. + NCI + + + + + + + + P331 + Conceptual Entity + NCBI Taxon ID + NCBI_Taxon_ID + NCBI_Taxon_ID + A property that is used to establish correspondence between the NCI Thesaurus concept representing a taxon (species) and the NCBI/NLM Species Taxonomy ID assigned by the NCBI to that taxon. + NCBI_Taxon_ID + + + + + + NCBI_Taxon_ID + PT + NCI + + + + + A property that is used to establish correspondence between the NCI Thesaurus concept representing a taxon (species) and the NCBI/NLM Species Taxonomy ID assigned by the NCBI to that taxon. + NCI + + + + + + + + P332 + Conceptual Entity + MGI Accession ID + MGI_Accession_ID + MGI_Accession_ID + A property representing the identifier used by Jackson Laboratories Mouse Genome Informatics group to label inbred mouse strains maintained by Jackson Laboratory and other things such as mouse genes and alleles. + MGI_Accession_ID + + + + + + MGI_Accession_ID + PT + NCI + + + + + A property representing the identifier used by Jackson Laboratories Mouse Genome Informatics group to label inbred mouse strains maintained by Jackson Laboratory and other things such as mouse genes and alleles. + NCI + + + + + + + + P333 + Conceptual Entity + Use For + Use_For + Use_For + A property representing a term that had been used in a coding system and then subsumed by the given NCIt concept. + Use_For + + + + + + Use_For + PT + NCI + + + + + A property representing a term that had been used in a coding system and then subsumed by the given NCIt concept. + NCI + + + + + + + + P334 + Conceptual Entity + ICD-O-3 Code + ICD-O-3_Code + ICD-O-3_Code + A property representing the matching ICD-O-3 code for the NCI Thesaurus concept. + ICD-O-3_Code + + + + + + ICD-O-3_Code + PT + NCI + + + + + A property representing the matching ICD-O-3 code for the NCI Thesaurus concept. + NCI + + + + + + + + P350 + Conceptual Entity + Chemical Formula + Chemical_Formula + CRCH + Chemical Formula + Chemical_Formula + A property representing a concise expression about the atoms that constitute a particular chemical compound. + Chemical_Formula + + + + + + Chemical Formula + PT + CRCH + + + + + Chemical_Formula + PT + NCI + + + + + A property representing a concise expression about the atoms that constitute a particular chemical compound. + NCI + + + + + + + + P351 + Conceptual Entity + US FNB Recommends Intake + US_Recommended_Intake + CRCH + A property indicating that the Food and Nutrition Board of the National Academy of Science has established an average daily intake for this nutrient that is sufficient to meet the nutritional requirements of most individuals in the general U.S. population. + Recommended Intake + Required_Intake + US_Recommended_Intake + US_Recommended_Intake + + + + + + A property indicating that the Food and Nutrition Board of the National Academy of Science has established an average daily intake for this nutrient that is sufficient to meet the nutritional requirements of most individuals in the general U.S. population. + CRCH + + + + + Recommended Intake + PT + CRCH + + + + + Required_Intake + SY + NCI + + + + + US_Recommended_Intake + PT + NCI + + + + + + + + P352 + Conceptual Entity + Tolerable Level + Tolerable_Level + CRCH + A property indicating that the Food and Nutrition Board of the National Academy of Science has established a highest level of daily intake for this food component that is likely to pose no risk of adverse health effects for almost all individuals in the general U.S. population. + Tolerable Level + Tolerable_Level + Tolerable_Level + + + + + + A property indicating that the Food and Nutrition Board of the National Academy of Science has established a highest level of daily intake for this food component that is likely to pose no risk of adverse health effects for almost all individuals in the general U.S. population. + CRCH + + + + + Tolerable Level + PT + CRCH + + + + + Tolerable_Level + PT + NCI + + + + + + + + P353 + Conceptual Entity + INFOODS Tag Name + INFOODS + CRCH + INFOODS + A property representing uppercase abbreviations assigned by the International Network of Food Data Systems. + INFOODS + + + + + + INFOODS + PT + CRCH + + + + + INFOODS + PT + NCI + + + + + A property representing uppercase abbreviations assigned by the International Network of Food Data Systems. + NCI + + + + + + + + P354 + Conceptual Entity + USDA ID + USDA_ID + CRCH + USDA ID + USDA_ID + A property representing a numeric ID assignment by United States Department of Agriculture. + USDA_ID + + + + + + USDA ID + PT + CRCH + + + + + USDA_ID + PT + NCI + + + + + A property representing a numeric ID assignment by United States Department of Agriculture. + NCI + + + + + + + + P355 + Conceptual Entity + Unit Used + Unit + CRCH + Unit + A property representing the unit of measure in which a nutrient or food component is typically expressed, ex., gram (g), minigram (mg), microgram (mcg), joule, or kilojoule. + Unit + + + + + + Unit + PT + CRCH + + + + + Unit + PT + NCI + + + + + A property representing the unit of measure in which a nutrient or food component is typically expressed, ex., gram (g), minigram (mg), microgram (mcg), joule, or kilojoule. + NCI + + + + + + + + P356 + Conceptual Entity + Is An Essential Amino Acid + Essential_Amino_Acid + Essential_Amino_Acid + A property used to indicate that an amino acid is essential and must be included in the diet. + Essential_Amino_Acid + + + + + + Essential_Amino_Acid + PT + NCI + + + + + A property used to indicate that an amino acid is essential and must be included in the diet. + NCI + + + + + + + + P357 + Conceptual Entity + Is An Essential Fatty Acid + Essential_Fatty_Acid + CRCH + Essential Fatty Acid + Essential_Fatty_Acid + A property used to indicate a fatty acid that is not efficiently synthesized by humans and must be included in the diet. + Essential_Fatty_Acid + + + + + + Essential Fatty Acid + PT + CRCH + + + + + Essential_Fatty_Acid + PT + NCI + + + + + A property used to indicate a fatty acid that is not efficiently synthesized by humans and must be included in the diet. + NCI + + + + + + + + P358 + Conceptual Entity + Is A Nutrient + Nutrient + CRCH + A property indicating that a food component must be taken into the body preformed and in sufficient quantity to meet the body's needs for growth, reproduction and/or maintenance of health. + Nutrient + Nutrient + + + + + + A property indicating that a food component must be taken into the body preformed and in sufficient quantity to meet the body's needs for growth, reproduction and/or maintenance of health. + CRCH + + + + + Nutrient + PT + CRCH + + + + + Nutrient + PT + NCI + + + + + + + + P359 + Conceptual Entity + Is A Micronutrient + Micronutrient + CRCH + A property indicating a class of food components required for proper health and that are typically consumed in microgram or milligram amounts. + mg + Micronutrient + Micronutrient + + + + + + A property indicating a class of food components required for proper health and that are typically consumed in microgram or milligram amounts. + CRCH + + + + + Micronutrient + PT + CRCH + + + + + Micronutrient + PT + NCI + + + + + + + + P360 + Conceptual Entity + Macronutrient + Macronutrient + CRCH + A property indicating a class of food components that contribute energy to the diet and that are typically consumed in multi-gram amounts. + g + Macronutrient + Macronutrient + + + + + + A property indicating a class of food components that contribute energy to the diet and that are typically consumed in multi-gram amounts. + CRCH + + + + + Macronutrient + PT + CRCH + + + + + Macronutrient + PT + NCI + + + + + + + + P361 + Conceptual Entity + Extensible_List + Extensible_List + List Extensible + A property representing the ability to extend the set of values in a particular list. + Extensible_List + + + + + + Extensible_List + PT + NCI + + + + + List Extensible + SY + NCI + + + + + A property representing the ability to extend the set of values in a particular list. + NCI + + + + + + + + P362 + Conceptual Entity + miRBase_ID + miRBase_ID + A property representing the accession number for an miRNA within the Sanger miRBase database. + miRBase_ID + + + + + + miRBase_ID + PT + NCI + + + + + A property representing the accession number for an miRNA within the Sanger miRBase database. + NCI + + + + + + + + P363 + Conceptual Entity + Neoplastic Status + Neoplastic_Status + FDA + Neoplastic_Status + A property representing the morphologic, clinical, and genetic profile of a neoplastic growth that defines it as benign, malignant, or of uncertain cancerous potential. + Neoplastic_Status + + + + + + Neoplastic_Status + PT + NCI + + + + + A property representing the morphologic, clinical, and genetic profile of a neoplastic growth that defines it as benign, malignant, or of uncertain cancerous potential. + NCI + + + + + + + + P364 + Conceptual Entity + OLD_ASSOCIATION + OLD_ASSOCIATION + A property used to store the name and value of associations present at the time a concept was retired. + OLD_ASSOCIATION + + + + + + OLD_ASSOCIATION + PT + NCI + + + + + A property used to store the name and value of associations present at the time a concept was retired. + NCI + + + + + + + + P365 + OLD_SOURCE_ASSOCIATION + OLD_SOURCE_ASSOCIATION + A property used to temporarily store the name and value of associations present at the time a concept is premerged or preretired, where the target of the association is the concept being retired. Values stored in this property are restored as associations on the source concept if the merge or retire is rejected. + OLD_SOURCE_ASSOCIATION + + + + + + OLD_SOURCE_ASSOCIATION + PT + NCI + + + + + A property used to temporarily store the name and value of associations present at the time a concept is premerged or preretired, where the target of the association is the concept being retired. Values stored in this property are restored as associations on the source concept if the merge or retire is rejected. + NCI + + + + + + + + P366 + Conceptual Entity + Legacy Concept Name + Legacy Concept Name + Legacy_Concept_Name + A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. + true + Legacy Concept Name + + + + + + Legacy Concept Name + PT + NCI + + + + + Legacy_Concept_Name + SY + NCI + + + + + A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding. + NCI + + + + + + + + P367 + Conceptual Entity + PID_ID + PID_ID + A property representing the NCI/Nature Pathway Interaction Database (PID) code for a pathway. It can be used by the NCIt Browser to link a pathway concept to the source pathway information. + PID_ID + + + + + + PID_ID + PT + NCI + + + + + A property representing the NCI/Nature Pathway Interaction Database (PID) code for a pathway. It can be used by the NCIt Browser to link a pathway concept to the source pathway information. + NCI + + + + + + + + P368 + Conceptual Entity + CHEBI_ID + CHEBI_ID + A property representing that a concept in the 'Drug, Food, Chemical or Biomedical Material' branch of the NCI thesaurus maps to a specific concept in the EBI Chemical Entities of Biological Interest (CHEBI) database. + CHEBI_ID + + + + + + CHEBI_ID + PT + NCI + + + + + A property representing that a concept in the 'Drug, Food, Chemical or Biomedical Material' branch of the NCI thesaurus maps to a specific concept in the EBI Chemical Entities of Biological Interest (CHEBI) database. + NCI + + + + + + + + P369 + Conceptual Entity + HGNC_ID + HGNC_ID + HUGO_ID + A property representing that a concept in the 'Gene' branch of the NCI thesaurus maps to a HUGO Gene Nomenclature Committee (HGNC) certified gene. + HGNC_ID + + + + + + HGNC_ID + PT + NCI + + + + + HUGO_ID + SY + NCI + + + + + A property representing that a concept in the 'Gene' branch of the NCI thesaurus maps to a HUGO Gene Nomenclature Committee (HGNC) certified gene. + NCI + + + + + + + + P371 + Conceptual Entity + NICHD_Hierarchy_Term + NICHD + NICHD_Hierarchy_Term + A property representing a term chosen by NICHD to be used in the representation of the NICHD hierarchy. + NICHD_Hierarchy_Term + + + + + + NICHD_Hierarchy_Term + PT + NCI + + + + + A property representing a term chosen by NICHD to be used in the representation of the NICHD hierarchy. + NCI + + + + + + + + P372 + Conceptual Entity + Publish_Value_Set + Publish_Value_Set + A property representing whether a value set is ready for publication in the browser. + Publish_Value_Set + + + + + + Publish_Value_Set + PT + NCI + + + + + A property representing whether a value set is ready for publication in the browser. + NCI + + + + + + + + P375 + Conceptual Entity + Maps_To + Maps_To + A property representing that a term in another terminology has been mapped to a term in NCIt and describes the relationship between the mapped terms. + Maps_To + + + + + + Maps_To + PT + NCI + + + + + A property representing that a term in another terminology has been mapped to a term in NCIt and describes the relationship between the mapped terms. + NCI + + + + + + + + P376 + Conceptual Entity + Term_Browser_Value_Set_Description + Term_Browser_Value_Set_Description + A property used to house the text on the introductory page on the NCI Term Browser for the Value Set named by a concept when that text differs from the DEFINITION for that concept. + Term_Browser_Value_Set_Description + + + + + + Term_Browser_Value_Set_Description + PT + NCI + + + + + A property used to house the text on the introductory page on the NCI Term Browser for the Value Set named by a concept when that text differs from the DEFINITION for that concept. + NCI + + + + + + + + P377 + def-definition + def-definition + + + + + + + + P378 + Conceptual Entity + Definition Source + Definition Source + A property representing the organization that is the supplier or owner of each DEFINITION or ALT_DEFINITION associated with a concept. + true + Definition Source + + + + + + Definition Source + PT + NCI + + + + + A property representing the organization that is the supplier or owner of each DEFINITION or ALT_DEFINITION associated with a concept. + NCI + + + + + + + + P379 + Definition_Reviewer_Name + true + Definition_Reviewer_Name + + + + + + + + + P380 + Definition_Review_Date + true + Definition_Review_Date + + + + + + + + + P381 + Conceptual Entity + attribution + attribution + A property indicating that some of the information in a DEFINITION or ALT_DEFINITION was derived from a source other than the def-source. + attribution + + + + + + attribution + PT + NCI + + + + + A property indicating that some of the information in a DEFINITION or ALT_DEFINITION was derived from a source other than the def-source. + NCI + + + + + + + + P382 + term-name + term-name + + + + + + + + P383 + Conceptual Entity + term-group + A property representing a two or three character abbreviation that indicates the nature of each FULL_SYN term associated with a concept. (e.g., PT=Preferred Term; SY=Synonym) + true + Term Type + + + + + + + + + P384 + Conceptual Entity + term-source + NCI + A property representing the organization that is the supplier or owner of each FULL_SYN term. + true + Term Source + + + + + + + + + P385 + Conceptual Entity + Source Code + Source Code + source-code + A property representing an identifier associated with a FULL_SYN term that is supplied by the term-source. + Source Code + + + + + + Source Code + PT + NCI + + + + + source-code + SY + NCI + + + + + A property representing an identifier associated with a FULL_SYN term that is supplied by the term-source. + NCI + + + + + + + + P386 + Conceptual Entity + Subsource Name + Subsource Name + subsource-name + A property indicating that a subgroup within the term-source is the supplier or owner of a FULL_SYN term. + Subsource Name + + + + + + Subsource Name + PT + NCI + + + + + subsource-name + SY + NCI + + + + + A property indicating that a subgroup within the term-source is the supplier or owner of a FULL_SYN term. + NCI + + + + + + + + P387 + go-id + A property representing a unique zero-padded seven digit identifier supplied by the Gene Ontology (GO) that has no inherent meaning or relation to the position of the term in GO and is prefixed by "GO:". + true + go-id + + + + + + A property representing a unique zero-padded seven digit identifier supplied by the Gene Ontology (GO) that has no inherent meaning or relation to the position of the term in GO and is prefixed by "GO:". + NCI + http://www.geneontology.org/page/ontology-structure + + + + + + + + P388 + go-term + go-term + + + + + + + + P389 + go-evi + A property representing a three letter code that indicates the type of supporting evidence for each GO_Annotation associated with a concept. + true + go-evi + + + + + + A property representing a three letter code that indicates the type of supporting evidence for each GO_Annotation associated with a concept. + NCI + http://www.geneontology.org/page/guide-go-evidence-codes + + + + + + + + P390 + go-source + A property representing the organization that is the supplier or owner of each GO_Annotation associated with a concept. + true + go-source + + + + + + A property representing the organization that is the supplier or owner of each GO_Annotation associated with a concept. + NCI + + + + + + + + P391 + source-date + A property representing the date each GO_Annotation was added to a concept. + true + source-date + + + + + + A property representing the date each GO_Annotation was added to a concept. + NCI + + + + + + + + P392 + Target_Term + A property representing the term in an outside source that has been mapped to a term within the NCI Thesaurus. + Target_Term + + + + + + A property representing the term in an outside source that has been mapped to a term within the NCI Thesaurus. + NCI + + + + + + + + P393 + Conceptual Entity + Relationship_to_Target + Relationship_to_Target + A property representing the relationship of the NCI Thesaurus (NCIt) concept to the term from the outside source. There are four possibilities: 1) Has Synonym: the two terms are synonymous; 2) Broader Than: the NCIt concept is broader than the mapped (target) term; 3) Narrower Than: the NCIt concept is narrower than the mapped (target) term; 4) Related To: the NCIt concept is somehow related to the mapped (target) term. + true + Relationship_to_Target + + + + + + Relationship_to_Target + PT + NCI + + + + + A property representing the relationship of the NCI Thesaurus (NCIt) concept to the term from the outside source. There are four possibilities: 1) Has Synonym: the two terms are synonymous; 2) Broader Than: the NCIt concept is broader than the mapped (target) term; 3) Narrower Than: the NCIt concept is narrower than the mapped (target) term; 4) Related To: the NCIt concept is somehow related to the mapped (target) term. + NCI + + + + + + + + P394 + Conceptual Entity + Target_Term_Type + Target_Term_Type + A property representing the term type designation in the mapped (target) database. + true + Target_Term_Type + + + + + + Target_Term_Type + PT + NCI + + + + + A property representing the term type designation in the mapped (target) database. + NCI + + + + + + + + P395 + Conceptual Entity + Target_Code + NCI + Target_Code + A property representing the code assigned to the target term in the mapped (target) database. Some databases may not have codes. + true + Target_Code + + + + + + Target_Code + PT + NCI + + + + + A property representing the code assigned to the target term in the mapped (target) database. Some databases may not have codes. + NCI + + + + + + + + P396 + Conceptual Entity + Target_Terminology + Target_Terminology + A property representing the name of the terminology to which the NCI Thesaurus term is being mapped. + true + Target_Terminology + + + + + + Target_Terminology + PT + NCI + + + + + A property representing the name of the terminology to which the NCI Thesaurus term is being mapped. + NCI + + + + + + + + P397 + Conceptual Entity + Target_Terminology_Version + Target_Terminology_Version + A property representing the version of the terminology to which the NCI Thesaurus term is being mapped. + Target_Terminology_Version + + + + + + Target_Terminology_Version + PT + NCI + + + + + A property representing the version of the terminology to which the NCI Thesaurus term is being mapped. + NCI + + + + + + + + P398 + Conceptual Entity + Value_Set_Pair + CDISC + Value_Set_Pair + A property that indicates whether or not a value set is part of a paired set of codelists for publication processing purposes. + Value_Set_Pair + + + + + + Value_Set_Pair + PT + NCI + + + + + A property that indicates whether or not a value set is part of a paired set of codelists for publication processing purposes. + NCI + + + + + + + + P399 + Conceptual Entity + NCI_Drug_Dictionary_ID + NCI_Drug_Dictionary_ID + A property representing the numerical CDR ID, which is the NCI Drug Dictionary identifier for a chemical or pharmaceutical agent. + NCI_Drug_Dictionary_ID + + + + + + NCI_Drug_Dictionary_ID + PT + NCI + + + + + A property representing the numerical CDR ID, which is the NCI Drug Dictionary identifier for a chemical or pharmaceutical agent. + NCI + + + + + + + + P400 + Conceptual Entity + ClinVar_Variation_ID + ClinVar_Variation_ID + A property representing the numerical Variation ID assigned to a molecular abnormality entry by ClinVar. + ClinVar_Variation_ID + + + + + + ClinVar_Variation_ID + PT + NCI + + + + + A property representing the numerical Variation ID assigned to a molecular abnormality entry by ClinVar. + NCI + + + + + + + + P90 + Conceptual Entity + Term & Source Data + FULL_SYN + FULL_SYN + Synonym with Source Data + A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. + FULL_SYN + + + + + + FULL_SYN + PT + NCI + + + + + Synonym with Source Data + SY + NCI + + + + + A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. + NCI + + + + + + + + P92 + Conceptual Entity + Subsource + Subsource + Subsource + A property used by MMHCC to identify the source of various mouse disease concepts. + Subsource + + + + + + Subsource + PT + NCI + + + + + A property used by MMHCC to identify the source of various mouse disease concepts. + NCI + + + + + + + + P93 + Conceptual Entity + Swiss Prot + Swiss_Prot + Swiss_Prot + A property representing the accession number for a protein within the Swiss-Prot database. + Swiss_Prot + + + + + + Swiss_Prot + PT + NCI + + + + + A property representing the accession number for a protein within the Swiss-Prot database. + NCI + + + + + + + + P96 + Conceptual Entity + Gene Encodes Product + Gene_Encodes_Product + Gene_Encodes_Product + A property representing the protein or RNA product expressed by a gene. + This represents the reciprocal relationship of the role Gene_Product_Encoded_by_Gene + Gene_Encodes_Product + + + + + + Gene_Encodes_Product + PT + NCI + + + + + A property representing the protein or RNA product expressed by a gene. + NCI + + + + + + + + P97 + Conceptual Entity + Definition + DEFINITION + DEFINITION + A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. + DEFINITION + + + + + + DEFINITION + PT + NCI + + + + + A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. + NCI + + + + + + + + P98 + Conceptual Entity + DesignNote + DesignNote + DesignNote + A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. + DesignNote + + + + + + DesignNote + PT + NCI + + + + + A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept. + NCI + + + + + + + + + + + + + + + + + + + + + + + + Conceptual Entity + xRef Source + A property representing the name of the organization to which an NCI Thesaurus concept is being linked to by cross reference. + xRef Source + + + + + + A property representing the name of the organization to which an NCI Thesaurus concept is being linked to by cross reference. + NCI + + + + + + + + + + + + + + + + + + + + + + + + + + + + Conceptual Entity + xRef + A property representing a reference to an identical or very similar object in another database. + xRef + + + + + A property representing a reference to an identical or very similar object in another database. + NCI + http://www.geneontology.org/page/ontology-structure + + + + + + + + + + + + + + + + label + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Concept_Pending_Approval + + + + Deprecated_Concept + + + + Header_Concept + + + + Obsolete_Concept + + + + Provisional_Concept + + + + Retired_Concept + + + + + + + + + + + + + + + + + + + + + + + + + + + + ACC + + + + ACC/AHA + + + + BRIDG + + + + CBDD + + + + CCPS + + + + CDISC + + + + CDISC-GLOSS + + + + COH + + + + CPTAC + + + + CRCH + + + + CTCAE + + + + CTDC + + + + CTEP + + + + CTRP + + + + CareLex + + + + Cellosaurus + + + + DIPG/DMG + + + + EDQM-HC + + + + FDA + + + + GAIA + + + + GDC + + + + HL7 + + + + HemOnc + + + + ICD-10 + + + + ICDC + + + + ICH + + + + INC + + + + MedDRA + + + + NAACCR + + + + NCCN + + + + NCPDP + + + + NDC + + + + NICHD + + + + OORO + + + + ORCHESTRA + + + + PCDC + + + + PI-RADS + + + + SEER + + + + SeroNet + + + + UBERON + + + + UCUM + + + + WHO + + + + mCode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NCI Drug Dictionary + + + + + + + + + + + + + + + + + + NA + + + + No + + + + Yes + + + + + + + + + + + + + + + + + + + + + + Device Problem Code (Appendix B) + + + + Dosage Form (C-DRG-00201) + + + + Marketing Category (C-DRG-0935) + + + + Package Type (C-DRG-00907) + + + + Patient Code (Appendix B) + + + + Plant Part (C-DRG-00924) + + + + Potency (C-DRG-00501) + + + + Route of Administration (C-DRG-00301) + + + + SPL Color (C-DRG-00927) + + + + SPL DEA Schedule (C-DRG-0933) + + + + SPL Flavor (C-DRG-0934) + + + + SPL Shape (C-DRG-00929) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Benign + + + + Malignant + + + + Precancerous + + + + Uncertain Malignant Potential + + + + Undetermined + + + + + + + + + + + + + + + + + + + + + + + + + + Alliance + + + + CCDI + + + + COG + + + + CTRP Biomarker Abstraction + + + + DCP + + + + DSS + + + + Data Commons Framework + + + + Duke Sarcoma Project + + + + GDC + + + + NCCN + + + + NCI CCR + + + + PDC + + + + PopSci SIG + + + + Rave + + + + SEER + + + + SEER CAN + + + + TCGA + + + + caDSR General + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + No + + + + Yes + + + + + + + + + + + + + + + + + + + + Broader Than + + + + Has Synonym + + + + Narrower Than + + + + Related To + + + + + + + + + + + + + + + + + + + + + + + + Acquired Abnormality + + + + Activity + + + + Age Group + + + + Amino Acid Sequence + + + + Amino Acid, Peptide, or Protein + + + + Amphibian + + + + Anatomical Abnormality + + + + Anatomical Structure + + + + Animal + + + + Antibiotic + + + + Archaeon + + + + Bacterium + + + + Behavior + + + + Biologic Function + + + + Biologically Active Substance + + + + Biomedical Occupation or Discipline + + + + Biomedical or Dental Material + + + + Bird + + + + Body Location or Region + + + + Body Part, Organ, or Organ Component + + + + Body Space or Junction + + + + Body Substance + + + + Body System + + + + Carbohydrate Sequence + + + + Cell + + + + Cell Component + + + + Cell Function + + + + Cell or Molecular Dysfunction + + + + Chemical + + + + Chemical Viewed Functionally + + + + Chemical Viewed Structurally + + + + Classification + + + + Clinical Attribute + + + + Clinical Drug + + + + Conceptual Entity + + + + Congenital Abnormality + + + + Daily or Recreational Activity + + + + Diagnostic Procedure + + + + Disease or Syndrome + + + + Drug Delivery Device + + + + Educational Activity + + + + Element, Ion, or Isotope + + + + Embryonic Structure + + + + Entity + + + + Environmental Effect of Humans + + + + Enzyme + + + + Eukaryote + + + + Event + + + + Experimental Model of Disease + + + + Family Group + + + + Finding + + + + Fish + + + + Food + + + + Fully Formed Anatomical Structure + + + + Functional Concept + + + + Fungus + + + + Gene or Genome + + + + Genetic Function + + + + Geographic Area + + + + Governmental or Regulatory Activity + + + + Group + + + + Group Attribute + + + + Hazardous or Poisonous Substance + + + + Health Care Activity + + + + Health Care Related Organization + + + + Hormone + + + + Human + + + + Human-caused Phenomenon or Process + + + + Idea or Concept + + + + Immunologic Factor + + + + Indicator, Reagent, or Diagnostic Aid + + + + Individual Behavior + + + + Injury or Poisoning + + + + Inorganic Chemical + + + + Intellectual Product + + + + Laboratory Procedure + + + + Laboratory or Test Result + + + + Language + + + + Machine Activity + + + + Mammal + + + + Manufactured Object + + + + Medical Device + + + + Mental Process + + + + Mental or Behavioral Dysfunction + + + + Molecular Biology Research Technique + + + + Molecular Function + + + + Molecular Sequence + + + + Natural Phenomenon or Process + + + + Neoplastic Process + + + + Nucleic Acid, Nucleoside, or Nucleotide + + + + Nucleotide Sequence + + + + Occupation or Discipline + + + + Occupational Activity + + + + Organ or Tissue Function + + + + Organic Chemical + + + + Organism + + + + Organism Attribute + + + + Organism Function + + + + Organization + + + + Pathologic Function + + + + Patient or Disabled Group + + + + Pharmacologic Substance + + + + Phenomenon or Process + + + + Physical Object + + + + Physiologic Function + + + + Plant + + + + Population Group + + + + Professional Society + + + + Professional or Occupational Group + + + + Qualitative Concept + + + + Quantitative Concept + + + + Receptor + + + + Regulation or Law + + + + Reptile + + + + Research Activity + + + + Research Device + + + + Self-help or Relief Organization + + + + Sign or Symptom + + + + Social Behavior + + + + Spatial Concept + + + + Substance + + + + Temporal Concept + + + + Therapeutic or Preventive Procedure + + + + Tissue + + + + Vertebrate + + + + Virus + + + + Vitamin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + TVS_ADaM_Component + + + + TVS_CDASH_Component + + + + TVS_CDISC_ADaM + + + + TVS_CDISC_CDASH + + + + TVS_CDISC_Clinical_Classification + + + + TVS_CDISC_Component + + + + TVS_CDISC_Functional_Test + + + + TVS_CDISC_Glossary + + + + TVS_CDISC_Protocol + + + + TVS_CDISC_Questionnaire + + + + TVS_CDISC_SDTM + + + + TVS_CDISC_SEND + + + + TVS_CDRH_GUID_Component + + + + TVS_CareLex + + + + TVS_Clinical_Classification_Component + + + + TVS_DICOM_Component + + + + TVS_EDQM-HC + + + + TVS_EDQM-HC_Component + + + + TVS_FDA_Device + + + + TVS_FDA_Device_Component + + + + TVS_FDA_PQCMC + + + + TVS_FDA_PQCMC_Component + + + + TVS_FDA_PQCMC_Test_Category + + + + TVS_FDA_PQCMC_Test_Category_Component + + + + TVS_FDA_QM + + + + TVS_FDA_QM_Component + + + + TVS_FDA_SPL + + + + TVS_FDA_SPL_Biz_Ops + + + + TVS_FDA_SPL_Biz_Ops_Component + + + + TVS_FDA_SPL_Blood + + + + TVS_FDA_SPL_Blood_Component + + + + TVS_FDA_SPL_Blood_Tissue + + + + TVS_FDA_SPL_Blood_Tissue_Component + + + + TVS_FDA_SPL_Component + + + + TVS_FDA_SPL_REMS + + + + TVS_FDA_SPL_REMS_Component + + + + TVS_FDA_SPL_Tissue + + + + TVS_FDA_SPL_Tissue_Component + + + + TVS_FDA_UNII + + + + TVS_FDA_eManufacturing_Component + + + + TVS_Functional_Test_Component + + + + TVS_GAIA + + + + TVS_GAIA_Component + + + + TVS_ICSR + + + + TVS_ICSR_Component + + + + TVS_IDMP_Component + + + + TVS_NCI_CTS-API_Disease_Category + + + + TVS_NCI_CTS-API_Disease_Category_Component + + + + TVS_NCI_Component + + + + TVS_NCI_Drug_Component + + + + TVS_NCI_Neoplasm_Component + + + + TVS_NCPDP + + + + TVS_NCPDP_Component + + + + TVS_NICHD + + + + TVS_NICHD_Component + + + + TVS_PIRADS_Component + + + + TVS_Protocol_Component + + + + TVS_Questionnaire_Component + + + + TVS_SDTM_Component + + + + TVS_SEND_Component + + + + TVS_UCUM_Component + + + + TVS_eCTD_Component + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + LLT + + + + PT + + + + SY + + + + + + + + + + + + + + + + + + + + + + EDQM-HC + + + + GAIA + + + + GDC + + + + ICD10 2016 + + + + ICD10CM 2017 + + + + ICD9CM 2014 + + + + ICDO3 + + + + MedDRA + + + + MedDRA 18.1 + + + + MedDRA 20.1 + + + + MedDRA 22.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + No + + + + Yes + + + + + + + + + + + + + + + + + + + + + + + + + + ACC + + + + ACC/AHA + + + + BIOCARTA + + + + BRIDG + + + + BRIDG 3.0.3 + + + + BRIDG 5.3 + + + + CBDD + + + + CCPS + + + + CDISC + + + + CDISC-GLOSS + + + + CRCH + + + + CSP2000 + + + + CSP2003 + + + + CTCAE + + + + CTCAE 3.0 + + + + CTCAE 5.0 + + + + CTDC + + + + CTEP + + + + CareLex + + + + DICOM + + + + DIPG/DMG + + + + EDQM-HC + + + + FDA + + + + GAIA + + + + ICD03 + + + + INC + + + + KEGG + + + + MMHCC + + + + MSH2001 + + + + MSH2002_06_01 + + + + MSH2003_2003_05_12 + + + + NAACCR + + + + NCI + + + + NCI-DEFCURATOR + + + + NCI-GLOSS + + + + NICHD + + + + OORO + + + + PCDC + + + + PQCMC + + + + SPL + + + + UBERON + + + + WHO + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CGAP + + + + NCBI + + + + NCI + + + + + + + + + + + + + + + + + + + + + + AB + + + + AD + + + + AQ + + + + AQS + + + + BR + + + + CA2 + + + + CA3 + + + + CN + + + + CNU + + + + CS + + + + DN + + + + FB + + + + HD + + + + LLT + + + + PT + + + + SN + + + + SY + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ACC + + + + ACC/AHA + + + + ANSI + + + + BIOCARTA + + + + BRIDG + + + + BRIDG 3.0.3 + + + + BRIDG 5.3 + + + + CBDD + + + + CCPS + + + + CDC + + + + CDISC + + + + CDISC-GLOSS + + + + CPTAC + + + + CRCH + + + + CTCAE + + + + CTCAE 3.0 + + + + CTCAE 5.0 + + + + CTDC + + + + CTEP + + + + CTRP + + + + CareLex + + + + Cellosaurus + + + + DCP + + + + DICOM + + + + DIPG/DMG + + + + DTP + + + + EDQM-HC + + + + FDA + + + + GAIA + + + + GDC + + + + GENC + + + + HGNC + + + + HL7 + + + + HemOnc + + + + ICD-10 + + + + ICDC + + + + ICH + + + + INC + + + + JAX + + + + KEGG + + + + MTH + + + + MedDRA + + + + NAACCR + + + + NCI + + + + NCI-GLOSS + + + + NCPDP + + + + NDC + + + + NICHD + + + + OORO + + + + ORCHESTRA + + + + PCDC + + + + PI-RADS + + + + PID + + + + SEER + + + + SeroNet + + + + UBERON + + + + UCUM + + + + WHO + + + + caDSR + + + + mCode + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + IMDRF + + + + UBERON + + + + + + + + + + + + + + + + + + + + R100 + Conceptual Entity + Has Associated Anatomic Site + Disease_Has_Associated_Anatomic_Site + Disease_Has_Associated_Anatomic_Site + A role used to relate a disease to the general site, structure or system where the specific pathological process is located. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + The role, Disease_Has_Associated_Anatomic_Site, is more general than the role, Disease_Has_Primary_Anatomic_Site. Furthermore, when viewed with the role, Disease_Has_Metastatic_Anatomic_Site, there emerges a role hierarchy, where one role specializes the meaning of another, more general role. Roles relating disease to anatomy start with a general assertion of association, often at very high level (e.g. Skin Disorder and Skin), and then add more specific primary/metastatic associations where appropriate for more specific concepts. + Disease_Has_Associated_Anatomic_Site + + + + + Disease_Has_Associated_Anatomic_Site + PT + NCI + + + + + A role used to relate a disease to the general site, structure or system where the specific pathological process is located. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R101 + Conceptual Entity + Has Primary Anatomic Site + Disease_Has_Primary_Anatomic_Site + Disease_Has_Primary_Anatomic_Site + A role used to relate a disease to the anatomical site where the originating pathological process is located. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + This role can be viewed as a specialization of Disease_Has_Associated_Anatomic_Site. + Disease_Has_Primary_Anatomic_Site + + + + + Disease_Has_Primary_Anatomic_Site + PT + NCI + + + + + A role used to relate a disease to the anatomical site where the originating pathological process is located. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R102 + Conceptual Entity + Has Metastatic Anatomic Site + Disease_Has_Metastatic_Anatomic_Site + Disease_Has_Metastatic_Anatomic_Site + A role used to relate a disease to the site of a metastatic lesion associated with the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + The role can be viewed as a specialization of Disease_Has_Associated_Anatomic_Site. + Disease_Has_Metastatic_Anatomic_Site + + + + + Disease_Has_Metastatic_Anatomic_Site + PT + NCI + + + + + A role used to relate a disease to the site of a metastatic lesion associated with the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R103 + Conceptual Entity + Has Normal Tissue Origin + Disease_Has_Normal_Tissue_Origin + Disease_Has_Normal_Tissue_Origin + A role used to relate a disease to the type of normal tissue in which the disease process began. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + This non-defining role represents non-essential characteristics which are true in some, but not all, cases, yet have an association frequent enough to be of interest. + Disease_Has_Normal_Tissue_Origin + + + + + Disease_Has_Normal_Tissue_Origin + PT + NCI + + + + + A role used to relate a disease to the type of normal tissue in which the disease process began. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R104 + Conceptual Entity + Has Normal Cell Origin + Disease_Has_Normal_Cell_Origin + Disease_Has_Normal_Cell_Origin + A role used to relate a disease to the type of normal cell in which the disease process begins. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + Disease_Has_Normal_Cell_Origin + + + + + Disease_Has_Normal_Cell_Origin + PT + NCI + + + + + A role used to relate a disease to the type of normal cell in which the disease process begins. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R105 + Conceptual Entity + Has Abnormal Cell + Disease_Has_Abnormal_Cell + Disease_Has_Abnormal_Cell + A role used to relate a disease to the type of neoplastic cell present in and characteristic of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Abnormal Cell', respectively. + Disease_Has_Abnormal_Cell + + + + + Disease_Has_Abnormal_Cell + PT + NCI + + + + + A role used to relate a disease to the type of neoplastic cell present in and characteristic of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Abnormal Cell', respectively. + NCI + + + + + + + + R106 + Conceptual Entity + Has Molecular Abnormality + Disease_Has_Molecular_Abnormality + Disease_Has_Molecular_Abnormality + A role used to relate a disease to a molecular abnormality that is present in the specified disease state. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + Disease_Has_Molecular_Abnormality + + + + + Disease_Has_Molecular_Abnormality + PT + NCI + + + + + A role used to relate a disease to a molecular abnormality that is present in the specified disease state. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + R107 + Conceptual Entity + Has Cytogenetic Abnormality + Disease_Has_Cytogenetic_Abnormality + Disease_Has_Cytogenetic_Abnormality + A role used to relate a disease to the type of chromosomal abnormality present in the specified disease state. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + Disease_Has_Cytogenetic_Abnormality + + + + + Disease_Has_Cytogenetic_Abnormality + PT + NCI + + + + + A role used to relate a disease to the type of chromosomal abnormality present in the specified disease state. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + R108 + Conceptual Entity + Has Finding + Disease_Has_Finding + Disease_Has_Finding + A role used to relate a disease to a clinical observation, sign or symptom present in and characteristic of the disease. Both the domain and range for this role are 'Disease, Disorder or Finding'. + Disease_Has_Finding + + + + + Disease_Has_Finding + PT + NCI + + + + + A role used to relate a disease to a clinical observation, sign or symptom present in and characteristic of the disease. Both the domain and range for this role are 'Disease, Disorder or Finding'. + NCI + + + + + + + + R110 + Conceptual Entity + Is Grade + Disease_Is_Grade + Disease_Is_Grade + A role used to relate a disease to a grading system which classifies the cancer cells in terms of how abnormal they appear when examined under a microscope. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Property or_Attribute', respectively. + Disease_Is_Grade + + + + + Disease_Is_Grade + PT + NCI + + + + + A role used to relate a disease to a grading system which classifies the cancer cells in terms of how abnormal they appear when examined under a microscope. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Property or_Attribute', respectively. + NCI + + + + + + + + R111 + Conceptual Entity + May Have Normal Tissue Origin + Disease_May_Have_Normal_Tissue_Origin + Disease_May_Have_Normal_Tissue_Origin + A role used to represent that a normal tissue type will only be the type of origin in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + Disease_May_Have_Normal_Tissue_Origin + + + + + Disease_May_Have_Normal_Tissue_Origin + PT + NCI + + + + + A role used to represent that a normal tissue type will only be the type of origin in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R112 + Conceptual Entity + May Have Normal Cell Origin + Disease_May_Have_Normal_Cell_Origin + Disease_May_Have_Normal_Cell_Origin + A role used to represent that a normal cell type will only be the type of origin in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + Disease_May_Have_Normal_Cell_Origin + + + + + Disease_May_Have_Normal_Cell_Origin + PT + NCI + + + + + A role used to represent that a normal cell type will only be the type of origin in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R113 + Conceptual Entity + May Have Abnormal Cell + Disease_May_Have_Abnormal_Cell + Disease_May_Have_Abnormal_Cell + A role used to represent that particular neoplastic cell types will only be present in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Abnormal Cell', respectively. + Disease_May_Have_Abnormal_Cell + + + + + Disease_May_Have_Abnormal_Cell + PT + NCI + + + + + A role used to represent that particular neoplastic cell types will only be present in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Abnormal Cell', respectively. + NCI + + + + + + + + R114 + Conceptual Entity + May Have Cytogenetic Abnormality + Disease_May_Have_Cytogenetic_Abnormality + Disease_May_Have_Cytogenetic_Abnormality + A role used to represent that a particular cytogenetic abnormality will only be present in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + Disease_May_Have_Cytogenetic_Abnormality + + + + + Disease_May_Have_Cytogenetic_Abnormality + PT + NCI + + + + + A role used to represent that a particular cytogenetic abnormality will only be present in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + R115 + Conceptual Entity + May Have Finding + Disease_May_Have_Finding + Disease_May_Have_Finding + A role used to represent that a clinical observation, sign or symptom will only be observed in some cases of the disease. Both the domain and range for this role are 'Disease, Disorder or Finding'. + Disease_May_Have_Finding + + + + + Disease_May_Have_Finding + PT + NCI + + + + + A role used to represent that a clinical observation, sign or symptom will only be observed in some cases of the disease. Both the domain and range for this role are 'Disease, Disorder or Finding'. + NCI + + + + + + + + R116 + Conceptual Entity + May Have Associated Disease + Disease_May_Have_Associated_Disease + Disease_May_Have_Associated_Disease + A role used to represent that another disease or disorder will only be observed in some cases of the specified disease. Both the domain and the range for this role are 'Disease, Disorder or Finding'. + Disease_May_Have_Associated_Disease + + + + + Disease_May_Have_Associated_Disease + PT + NCI + + + + + A role used to represent that another disease or disorder will only be observed in some cases of the specified disease. Both the domain and the range for this role are 'Disease, Disorder or Finding'. + NCI + + + + + + + + R122 + Conceptual Entity + Is Metabolized By Enzyme + Chemical_Or_Drug_Is_Metabolized_By_Enzyme + Chemical_Or_Drug_Is_Metabolized_By_Enzyme + A role used to specify that an enzyme is directly responsible for metabolizing a chemical or drug into an active form, inactive form, or both. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Gene Product', respectively. + Chemical_Or_Drug_Is_Metabolized_By_Enzyme + + + + + Chemical_Or_Drug_Is_Metabolized_By_Enzyme + PT + NCI + + + + + A role used to specify that an enzyme is directly responsible for metabolizing a chemical or drug into an active form, inactive form, or both. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Gene Product', respectively. + NCI + + + + + + + + R123 + Conceptual Entity + Has Component + Chemotherapy_Regimen_Has_Component + Chemotherapy_Regimen_Has_Component + A role used to specify the component agents which are used in a particular chemotherapy regimen or agent combination. The domain and the range for this role are 'Chemotherapy Regimen or Agent Combination' and 'Drug, Food, Chemical or Biomedical Material', respectively. + Chemotherapy_Regimen_Has_Component + + + + + Chemotherapy_Regimen_Has_Component + PT + NCI + + + + + A role used to specify the component agents which are used in a particular chemotherapy regimen or agent combination. The domain and the range for this role are 'Chemotherapy Regimen or Agent Combination' and 'Drug, Food, Chemical or Biomedical Material', respectively. + NCI + + + + + + + + + R124 + Conceptual Entity + Has Mechanism Of Action + Chemical_Or_Drug_Has_Mechanism_Of_Action + Chemical_Or_Drug_Has_Mechanism_Of_Action + A role used to imply the interaction or binding of an active ingredient of a drug/chemical agent at the molecular level with its target. When possible, the role value should reflect the direct alteration of function of a target molecule or complex. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Biological Process', respectively. + Chemical_Or_Drug_Has_Mechanism_Of_Action + + + + + Chemical_Or_Drug_Has_Mechanism_Of_Action + PT + NCI + + + + + A role used to imply the interaction or binding of an active ingredient of a drug/chemical agent at the molecular level with its target. When possible, the role value should reflect the direct alteration of function of a target molecule or complex. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Biological Process', respectively. + NCI + + + + + + + + + R125 + Conceptual Entity + Has Physiologic Effect + Chemical_Or_Drug_Has_Physiologic_Effect + Chemical_Or_Drug_Has_Physiologic_Effect + A role used to describe the primary detectable alterations of subcellular, cellular, tissue, or organ functions that directly result from alteration of function of a target biological molecule or complex caused by interaction of a therapeutic agent with a target molecule or complex. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Biological Process', respectively. + Chemical_Or_Drug_Has_Physiologic_Effect + + + + + Chemical_Or_Drug_Has_Physiologic_Effect + PT + NCI + + + + + A role used to describe the primary detectable alterations of subcellular, cellular, tissue, or organ functions that directly result from alteration of function of a target biological molecule or complex caused by interaction of a therapeutic agent with a target molecule or complex. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Biological Process', respectively. + NCI + + + + + + + + R126 + Conceptual Entity + Has Associated Disease + Disease_Has_Associated_Disease + Disease_Has_Associated_Disease + A role used to relate a disease to another disease or disorder, but without specification or limitation of the relationship (causality or timing for example). Both the domain and the range for this role are 'Disease, Disorder or Finding'. + Disease_Has_Associated_Disease + + + + + Disease_Has_Associated_Disease + PT + NCI + + + + + A role used to relate a disease to another disease or disorder, but without specification or limitation of the relationship (causality or timing for example). Both the domain and the range for this role are 'Disease, Disorder or Finding'. + NCI + + + + + + + + R130 + Conceptual Entity + Is Element In Pathway + Gene_Is_Element_In_Pathway + Gene_Is_Element_In_Pathway + A role used to assert a relationship between a gene and a biochemical pathway in which its encoded gene product(s) participate. This relationship is used only when gene has been implicated in a pathway by the curated source (Biocarta, KEGG or PID). The domain and range for this role are 'Gene' and 'Biochemical Pathway', respectively. + In NCI Thesaurus, pathways are derived from BioCarta and KEGG and are associated with genes and proteins that comprise these pathways. + Gene_Is_Element_In_Pathway + + + + + Gene_Is_Element_In_Pathway + PT + NCI + + + + + A role used to assert a relationship between a gene and a biochemical pathway in which its encoded gene product(s) participate. This relationship is used only when gene has been implicated in a pathway by the curated source (Biocarta, KEGG or PID). The domain and range for this role are 'Gene' and 'Biochemical Pathway', respectively. + NCI + + + + + + + + R131 + Conceptual Entity + Is Element In Pathway + Gene_Product_Is_Element_In_Pathway + Gene_Product_Is_Element_In_Pathway + A role used to assert a relationship between a gene product and a biochemical pathway in which it participates. This relationship is used only when a gene product has been implicated in a pathway by the curated source (Biocarta, KEGG or PID). The domain and range for this role are 'Gene Product' and 'Biochemical Pathway', respectively. + In NCI Thesaurus, pathways are derived from BioCarta and KEGG and are associated with genes and proteins that comprise these pathways. + Gene_Product_Is_Element_In_Pathway + + + + + Gene_Product_Is_Element_In_Pathway + PT + NCI + + + + + A role used to assert a relationship between a gene product and a biochemical pathway in which it participates. This relationship is used only when a gene product has been implicated in a pathway by the curated source (Biocarta, KEGG or PID). The domain and range for this role are 'Gene Product' and 'Biochemical Pathway', respectively. + NCI + + + + + + + + R132 + Conceptual Entity + Has Abnormality + Gene_Has_Abnormality + Gene_Has_Abnormality + A role used to establish a link between a gene and the genetic or molecular abnormalities that have been observed in human cells and tissues associated with cancers (e.g., over- or under-expressed, amplified, translocated). The domain and range for this role are 'Gene' and 'Molecular Abnormality', respectively. + Gene_Has_Abnormality + + + + + Gene_Has_Abnormality + PT + NCI + + + + + A role used to establish a link between a gene and the genetic or molecular abnormalities that have been observed in human cells and tissues associated with cancers (e.g., over- or under-expressed, amplified, translocated). The domain and range for this role are 'Gene' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + R133 + Conceptual Entity + Has Abnormality + Gene_Product_Has_Abnormality + Gene_Product_Has_Abnormality + A role used to establish a link between a gene product and the molecular abnormalities that are observed in human cells and tissues in association with diseases such as cancers (e.g., over or under-expression of gene product). The domain and range for this role are 'Gene Product' and 'Molecular Abnormality', respectively. + Gene_Product_Has_Abnormality + + + + + Gene_Product_Has_Abnormality + PT + NCI + + + + + A role used to establish a link between a gene product and the molecular abnormalities that are observed in human cells and tissues in association with diseases such as cancers (e.g., over or under-expression of gene product). The domain and range for this role are 'Gene Product' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + R135 + Conceptual Entity + Excludes Primary Anatomic Site + Disease_Excludes_Primary_Anatomic_Site + Disease_Excludes_Primary_Anatomic_Site + A specializing role which may be used to override Disease_Has_Associated_Anatomic_Site. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + Disease_Excludes_Primary_Anatomic_Site + + + + + Disease_Excludes_Primary_Anatomic_Site + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_Associated_Anatomic_Site. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R136 + Conceptual Entity + Excludes Metastatic Anatomic Site + Disease_Excludes_Metastatic_Anatomic_Site + Disease_Excludes_Metastatic_Anatomic_Site + A specializing role which may be used to override Disease_Has_ Metastatic_Anatomic_Site. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + Disease_Excludes_Metastatic_Anatomic_Site + + + + + Disease_Excludes_Metastatic_Anatomic_Site + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_ Metastatic_Anatomic_Site. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R137 + Conceptual Entity + Excludes Normal Tissue Origin + Disease_Excludes_Normal_Tissue_Origin + Disease_Excludes_Normal_Tissue_Origin + A specializing role which may be used to override Disease_Has_Normal_Tissue_Origin. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + Disease_Excludes_Normal_Tissue_Origin + + + + + Disease_Excludes_Normal_Tissue_Origin + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_Normal_Tissue_Origin. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R138 + Conceptual Entity + Excludes Normal Cell Origin + Disease_Excludes_Normal_Cell_Origin + Disease_Excludes_Normal_Cell_Origin + A specializing role which may be used to override Disease_Has_Normal_Cell_Origin. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + Disease_Excludes_Normal_Cell_Origin + + + + + Disease_Excludes_Normal_Cell_Origin + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_Normal_Cell_Origin. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R139 + Conceptual Entity + Excludes Abnormal Cell + Disease_Excludes_Abnormal_Cell + Disease_Excludes_Abnormal_Cell + A specializing role which may be used to override Disease_Has_Abnormal_Cell. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Abnormal Cell', respectively. + Disease_Excludes_Abnormal_Cell + + + + + Disease_Excludes_Abnormal_Cell + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_Abnormal_Cell. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Abnormal Cell', respectively. + NCI + + + + + + + + R140 + Conceptual Entity + Excludes Molecular Abnormality + Disease_Excludes_Molecular_Abnormality + Disease_Excludes_Molecular_Abnormality + A specializing role which may be used to override Disease_Has_ Molecular_Abnormality. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + Disease_Excludes_Molecular_Abnormality + + + + + Disease_Excludes_Molecular_Abnormality + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_ Molecular_Abnormality. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + R141 + Conceptual Entity + Excludes Cytogenetic Abnormality + Disease_Excludes_Cytogenetic_Abnormality + Disease_Excludes_Cytogenetic_Abnormality + A specializing role which may be used to override Disease_Has_Cytogenetic_Abnormality. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + Disease_Excludes_Cytogenetic_Abnormality + + + + + Disease_Excludes_Cytogenetic_Abnormality + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_Cytogenetic_Abnormality. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + R142 + Conceptual Entity + Excludes Finding + Disease_Excludes_Finding + Disease_Excludes_Finding + A specializing role which may be used to override Disease_Has_Finding. Both the domain and range for this role are 'Disease, Disorder or Finding'. + Disease_Excludes_Finding + + + + + Disease_Excludes_Finding + PT + NCI + + + + + A specializing role which may be used to override Disease_Has_Finding. Both the domain and range for this role are 'Disease, Disorder or Finding'. + NCI + + + + + + + + R145 + Conceptual Entity + Has Physical Location + Gene_Has_Physical_Location + Gene_Has_Physical_Location + A role used to link a gene with its physical extent on a chromosome, denoted by the chromosome number and start and end base positions (with numbering beginning at the telomere of the short p arm). The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + The standard for the numbering system is that assigned by the Human Genome Consortium and found at Entrez Gene. The role is considered as supplementary to the role Gene_In Chromosomal_Location + Gene_Has_Physical_Location + + + + + Gene_Has_Physical_Location + PT + NCI + + + + + A role used to link a gene with its physical extent on a chromosome, denoted by the chromosome number and start and end base positions (with numbering beginning at the telomere of the short p arm). The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R146 + Conceptual Entity + Affects Gene Product + Chemical_Or_Drug_Affects_Gene_Product + Chemical_Or_Drug_Affects_Gene_Product + A role used to assert that a gene product is the target of a therapeutic agent. The role implies a direct interaction between the product and the therapeutic agent but it does not specify the type of association (e.g., involvement, interference, inhibition or cleavage). The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Gene Product', respectively. + Chemical_Or_Drug_Affects_Gene_Product + + + + + Chemical_Or_Drug_Affects_Gene_Product + PT + NCI + + + + + A role used to assert that a gene product is the target of a therapeutic agent. The role implies a direct interaction between the product and the therapeutic agent but it does not specify the type of association (e.g., involvement, interference, inhibition or cleavage). The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Gene Product', respectively. + NCI + + + + + + + + + R150 + Conceptual Entity + Affects Abnormal Cell + Chemical_Or_Drug_Affects_Abnormal_Cell + Chemical_Or_Drug_Affects_Abnormal_Cell + A role used to establish the relationship between a therapeutic agent and an abnormal cell type associated with a disease condition. By pointing to abnormal cells, the therapeutic target of a drug can be more clearly conveyed. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Abnormal Cell', respectively. + Chemical_Or_Drug_Affects_Abnormal_Cell + + + + + Chemical_Or_Drug_Affects_Abnormal_Cell + PT + NCI + + + + + A role used to establish the relationship between a therapeutic agent and an abnormal cell type associated with a disease condition. By pointing to abnormal cells, the therapeutic target of a drug can be more clearly conveyed. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Abnormal Cell', respectively. + NCI + + + + + + + + + R153 + Conceptual Entity + Has Abnormality + Allele_Has_Abnormality + Allele_Has_Abnormality + A specializing role which may be used to override Gene_Has_Abnormality that has been asserted for the gene class. This role is used to establish a link between a specific allele and genetic or molecular abnormalities that have been observed in human cells and tissues associated with cancer or another disease of interest. The domain and range for this role are 'Gene' and 'Molecular Abnormality', respectively. + Allele_Has_Abnormality + + + + + Allele_Has_Abnormality + PT + NCI + + + + + A specializing role which may be used to override Gene_Has_Abnormality that has been asserted for the gene class. This role is used to establish a link between a specific allele and genetic or molecular abnormalities that have been observed in human cells and tissues associated with cancer or another disease of interest. The domain and range for this role are 'Gene' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + + R155 + Conceptual Entity + In Chromosomal Location + Allele_In_Chromosomal_Location + Allele_In_Chromosomal_Location + A role used for an allele whose location has changed from the wild-type gene chromosomal location. This role is used to assert a new location that differs from the wild-type gene chromosomal location. The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + Allele_In_Chromosomal_Location + + + + + Allele_In_Chromosomal_Location + PT + NCI + + + + + A role used for an allele whose location has changed from the wild-type gene chromosomal location. This role is used to assert a new location that differs from the wild-type gene chromosomal location. The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R156 + Conceptual Entity + Absent From Wild-type Chromosomal Location + Allele_Absent_From_Wild-type_Chromosomal_Location + Allele_Absent_From_Wild-type_Chromosomal_Location + A role used for an allele whose location has changed from the wild-type gene chromosomal location. This role is used to negate an inherited role relationship that is asserted between the parent gene class and a chromosomal location when an allele has moved (e.g., translocation, inversion, etc.). The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + Allele_Absent_From_Wild-type_Chromosomal_Location + + + + + Allele_Absent_From_Wild-type_Chromosomal_Location + PT + NCI + + + + + A role used for an allele whose location has changed from the wild-type gene chromosomal location. This role is used to negate an inherited role relationship that is asserted between the parent gene class and a chromosomal location when an allele has moved (e.g., translocation, inversion, etc.). The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R158 + Conceptual Entity + Plays Altered Role In Process + Allele_Plays_Altered_Role_In_Process + Allele_Plays_Altered_Role_In_Process + A specializing role which may be used for an allele whose encoded product functions differently (qualitatively or quantitatively) from the function asserted on its parent. It specializes the function of the wild type gene/gene product. The domain and range for this role are 'Gene' and 'Biological Process', respectively. + Allele_Plays_Altered_Role_In_Process + + + + + Allele_Plays_Altered_Role_In_Process + PT + NCI + + + + + A specializing role which may be used for an allele whose encoded product functions differently (qualitatively or quantitatively) from the function asserted on its parent. It specializes the function of the wild type gene/gene product. The domain and range for this role are 'Gene' and 'Biological Process', respectively. + NCI + + + + + + + + R159 + Conceptual Entity + Has Activity + Allele_Has_Activity + Allele_Has_Activity + A role used to assert the observed level of activity associated with an allele in a given biological process, compared to the wild-type gene. The domain and range for this role are 'Gene' and 'Property or Attribute', respectively. + Allele_Has_Activity + + + + + Allele_Has_Activity + PT + NCI + + + + + A role used to assert the observed level of activity associated with an allele in a given biological process, compared to the wild-type gene. The domain and range for this role are 'Gene' and 'Property or Attribute', respectively. + NCI + + + + + + + + R160 + Conceptual Entity + Plays Role In Metabolism Of Chemical Or Drug + Allele_Plays_Role_In_Metabolism_Of_Chemical_Or_Drug + Allele_Plays_Role_In_Metabolism_Of_Chemical_Or_Drug + A role used to assert a relationship between a specific allele (product; enzyme) and drug-metabolizing efficacy. The domain and range for this role are 'Gene' and 'Drug, Food, Chemical or Biomedical Material', respectively. + Allele_Plays_Role_In_Metabolism_Of_Chemical_Or_Drug + + + + + Allele_Plays_Role_In_Metabolism_Of_Chemical_Or_Drug + PT + NCI + + + + + A role used to assert a relationship between a specific allele (product; enzyme) and drug-metabolizing efficacy. The domain and range for this role are 'Gene' and 'Drug, Food, Chemical or Biomedical Material', respectively. + NCI + + + + + + + + R163 + Conceptual Entity + Has Target Anatomy + Procedure_Has_Target_Anatomy + Procedure_Has_Target_Anatomy + A role used to assert a relationship between a procedure and its target anatomy, specifically that a particular procedure always has an association with the target anatomy. This role should be used when a more specific role cannot be asserted, including procedures targeting blood and other fluids. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_Has_Target_Anatomy + + + + + Procedure_Has_Target_Anatomy + PT + NCI + + + + + A role used to assert a relationship between a procedure and its target anatomy, specifically that a particular procedure always has an association with the target anatomy. This role should be used when a more specific role cannot be asserted, including procedures targeting blood and other fluids. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R165 + Conceptual Entity + Has Imaged Anatomy + Procedure_Has_Imaged_Anatomy + Procedure_Has_Imaged_Anatomy + A role used to assert a relationship between an imaging procedure and its target anatomy, specifically that a particular procedure always involves imaging the specified anatomy. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_Has_Imaged_Anatomy + + + + + Procedure_Has_Imaged_Anatomy + PT + NCI + + + + + A role used to assert a relationship between an imaging procedure and its target anatomy, specifically that a particular procedure always involves imaging the specified anatomy. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R166 + Conceptual Entity + May Have Excised Anatomy + Procedure_May_Have_Excised_Anatomy + Procedure_May_Have_Excised_Anatomy + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure sometimes results in excision of some or all of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs. It should be used when a more specific role cannot be asserted. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_May_Have_Excised_Anatomy + + + + + Procedure_May_Have_Excised_Anatomy + PT + NCI + + + + + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure sometimes results in excision of some or all of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs. It should be used when a more specific role cannot be asserted. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R167 + Conceptual Entity + Has Excised Anatomy + Procedure_Has_Excised_Anatomy + Procedure_Has_Excised_Anatomy + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure always involves excision of some or all of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs. It should be used when a more specific role cannot be asserted. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_Has_Excised_Anatomy + + + + + Procedure_Has_Excised_Anatomy + PT + NCI + + + + + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure always involves excision of some or all of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs. It should be used when a more specific role cannot be asserted. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R168 + Conceptual Entity + May Have Partially Excised Anatomy + Procedure_May_Have_Partially_Excised_Anatomy + Procedure_May_Have_Partially_Excised_Anatomy + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure sometimes results in partial excision of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where partial excision is explicit or can be inferred (e.g. biopsy). The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_May_Have_Partially_Excised_Anatomy + + + + + Procedure_May_Have_Partially_Excised_Anatomy + PT + NCI + + + + + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure sometimes results in partial excision of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where partial excision is explicit or can be inferred (e.g. biopsy). The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R169 + Conceptual Entity + Has Partially Excised Anatomy + Procedure_Has_Partially_Excised_Anatomy + Procedure_Has_Partially_Excised_Anatomy + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure always involves partial excision of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where partial excision is explicit or can be inferred (e.g. biopsy). The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_Has_Partially_Excised_Anatomy + + + + + Procedure_Has_Partially_Excised_Anatomy + PT + NCI + + + + + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure always involves partial excision of the specified anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where partial excision is explicit or can be inferred (e.g. biopsy). The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R170 + Conceptual Entity + May Have Completely Excised Anatomy + Procedure_May_Have_Completely_Excised_Anatomy + Procedure_May_Have_Completely_Excised_Anatomy + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure sometimes results in complete excision of the target anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where complete excision is explicit or can be inferred. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_May_Have_Completely_Excised_Anatomy + + + + + Procedure_May_Have_Completely_Excised_Anatomy + PT + NCI + + + + + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure sometimes results in complete excision of the target anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where complete excision is explicit or can be inferred. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R171 + Conceptual Entity + Has Completely Excised Anatomy + Procedure_Has_Completely_Excised_Anatomy + Procedure_Has_Completely_Excised_Anatomy + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure always is intended for the complete excision of the target anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where complete excision is explicit or can be inferred. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + Procedure_Has_Completely_Excised_Anatomy + + + + + Procedure_Has_Completely_Excised_Anatomy + PT + NCI + + + + + A role used to assert a relationship between a surgical procedure and its target anatomy, specifically that a particular procedure always is intended for the complete excision of the target anatomy. This role is applicable to procedures or techniques that involve excision of solid tissues or organs, and where complete excision is explicit or can be inferred. The domain and range for this role are 'Clinical or Research Activity' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R172 + Conceptual Entity + Has Accepted Use For Disease + Regimen_Has_Accepted_Use_For_Disease + Regimen_Has_Accepted_Use_For_Disease + A role used to link established therapeutic regimens to their corresponding cancers or other diseases. Only established regimens published in NCI's Physician Data Query (PDQ), National Comprehensive Cancer Network (NCCN) Guidelines (http://www.nccn.org), or a limited number of other authoritative sources such as the Physician's Cancer Chemotherapy Manual are included. The domain and range for this role are 'Chemotherapy Regimen or Agent Combination' and 'Disease, Disorder or Finding', respectively. + Regimen_Has_Accepted_Use_For_Disease + + + + + Regimen_Has_Accepted_Use_For_Disease + PT + NCI + + + + + A role used to link established therapeutic regimens to their corresponding cancers or other diseases. Only established regimens published in NCI's Physician Data Query (PDQ), National Comprehensive Cancer Network (NCCN) Guidelines (http://www.nccn.org), or a limited number of other authoritative sources such as the Physician's Cancer Chemotherapy Manual are included. The domain and range for this role are 'Chemotherapy Regimen or Agent Combination' and 'Disease, Disorder or Finding', respectively. + NCI + + + + + + + + R173 + Conceptual Entity + Cytogenetic_Abnormality_Involves_Chromosome + Cytogenetic_Abnormality_Involves_Chromosome + A role used to assert a direct relationship between a cytogenetic abnormality and a chromosome. The domain and range for this role are 'Cytogenetic Abnormality' and 'Chromosome', respectively. The range for this role excludes chromosomal bands and physical locations. + Cytogenetic_Abnormality_Involves_Chromosome + + + + + Cytogenetic_Abnormality_Involves_Chromosome + PT + NCI + + + + + A role used to assert a direct relationship between a cytogenetic abnormality and a chromosome. The domain and range for this role are 'Cytogenetic Abnormality' and 'Chromosome', respectively. The range for this role excludes chromosomal bands and physical locations. + NCI + + + + + + + + R174 + Conceptual Entity + Disease_Mapped_To_Chromosome + Disease_Mapped_To_Chromosome + A role used to assert a relationship between a disease, disorder or finding and a chromosome. This restriction should be used when a disease or disorder maps to a chromosome. It is not meant to be used when a specific cytogenetic abnormality is known (e.g. translocation, inversion). The domain and range for this role are 'Disease, Disorder or Finding' and 'Chromosome', respectively. The range for this role excludes chromosomal bands and physical locations. + Disease_Mapped_To_Chromosome + + + + + Disease_Mapped_To_Chromosome + PT + NCI + + + + + A role used to assert a relationship between a disease, disorder or finding and a chromosome. This restriction should be used when a disease or disorder maps to a chromosome. It is not meant to be used when a specific cytogenetic abnormality is known (e.g. translocation, inversion). The domain and range for this role are 'Disease, Disorder or Finding' and 'Chromosome', respectively. The range for this role excludes chromosomal bands and physical locations. + NCI + + + + + + + + R175 + Conceptual Entity + Gene_Involved_In_Pathogenesis_Of_Disease + Gene_Involved_In_Pathogenesis_Of_Disease + A role used to assert a direct relationship between a gene and a disease. This restriction should only be used when an abnormality in a gene a causative event for a disease. The domain and range for this role are 'Gene' and 'Disease or Disorder', respectively. + Gene_Involved_In_Pathogenesis_Of_Disease + + + + + Gene_Involved_In_Pathogenesis_Of_Disease + PT + NCI + + + + + A role used to assert a direct relationship between a gene and a disease. This restriction should only be used when an abnormality in a gene a causative event for a disease. The domain and range for this role are 'Gene' and 'Disease or Disorder', respectively. + NCI + + + + + + + + R176 + Conceptual Entity + Disease_Mapped_To_Gene + Disease_Mapped_To_Gene + A role used to assert a direct relationship between a disease, disorder or finding and a gene. This restriction can be used when a polymorphism or an abnormality in a gene is either a clinical marker for, a causative event for, or predisposes a subject to a disease. The domain and range for this role are 'Disease, Disorder or Finding' and 'Gene', respectively. + Disease_Mapped_To_Gene + + + + + Disease_Mapped_To_Gene + PT + NCI + + + + + A role used to assert a direct relationship between a disease, disorder or finding and a gene. This restriction can be used when a polymorphism or an abnormality in a gene is either a clinical marker for, a causative event for, or predisposes a subject to a disease. The domain and range for this role are 'Disease, Disorder or Finding' and 'Gene', respectively. + NCI + + + + + + + + R177 + Conceptual Entity + Molecular_Abnormality_Involves_Gene + Molecular_Abnormality_Involves_Gene + A role used to assert a direct relationship between a molecular abnormality and a gene. The domain and range for this role are 'Molecular Abnormality' and 'Gene', respectively. + Molecular_Abnormality_Involves_Gene + + + + + Molecular_Abnormality_Involves_Gene + PT + NCI + + + + + A role used to assert a direct relationship between a molecular abnormality and a gene. The domain and range for this role are 'Molecular Abnormality' and 'Gene', respectively. + NCI + + + + + + + + R178 + Conceptual Entity + Gene_Mutant_Encodes_Gene_Product_Sequence_Variation + Gene_Mutant_Encodes_Gene_Product_Sequence_Variation + A role used to indicate that a specific molecular variation or mutation in a gene encodes a gene product sequence variant. The domain and range for this role are 'Gene Mutant' and 'Gene Product Sequence Variation', respectively. + Gene_Mutant_Encodes_Gene_Product_Sequence_Variation + + + + + Gene_Mutant_Encodes_Gene_Product_Sequence_Variation + PT + NCI + + + + + A role used to indicate that a specific molecular variation or mutation in a gene encodes a gene product sequence variant. The domain and range for this role are 'Gene Mutant' and 'Gene Product Sequence Variation', respectively. + NCI + + + + + + + + R179 + Conceptual Entity + Gene_Product_Sequence_Variation_Encoded_By_Gene_Mutant + Gene_Product_Sequence_Variation_Encoded_By_Gene_Mutant + A role used to indicate that a gene product sequence variation is encoded by a specific gene mutant. The domain and range for this role are 'Gene Product Sequence Variation' and 'Gene Mutant', respectively. + Gene_Product_Sequence_Variation_Encoded_By_Gene_Mutant + + + + + Gene_Product_Sequence_Variation_Encoded_By_Gene_Mutant + PT + NCI + + + + + A role used to indicate that a gene product sequence variation is encoded by a specific gene mutant. The domain and range for this role are 'Gene Product Sequence Variation' and 'Gene Mutant', respectively. + NCI + + + + + + + + R180 + Conceptual Entity + Procedure_Has_Target_Disease + Procedure_Has_Target_Disease + A role used to assert that a procedure or technical method detects, diagnoses, or treats a specified disease state. The domain and range for this role are 'Activity' and 'Disease, Disorder or Finding', respectively. + Procedure_Has_Target_Disease + + + + + Procedure_Has_Target_Disease + PT + NCI + + + + + A role used to assert that a procedure or technical method detects, diagnoses, or treats a specified disease state. The domain and range for this role are 'Activity' and 'Disease, Disorder or Finding', respectively. + NCI + + + + + + + + R181 + Conceptual Entity + Procedure_Uses_Manufactured_Object + Procedure_Uses_Manufactured_Object + A role used to assert that a procedure or technical method requires use of specific artifacts or pieces of equipment. The domain and range for this role are 'Activity' and 'Manufactured Object', respectively. + Procedure_Uses_Manufactured_Object + + + + + Procedure_Uses_Manufactured_Object + PT + NCI + + + + + A role used to assert that a procedure or technical method requires use of specific artifacts or pieces of equipment. The domain and range for this role are 'Activity' and 'Manufactured Object', respectively. + NCI + + + + + + + + R182 + Conceptual Entity + Gene_Product_Variant_Of_Gene_Product + Gene_Product_Variant_Of_Gene_Product + A role used to indicate that a gene product sequence variation is related to a wild-type gene product. The domain and range for this role are 'Gene Product Sequence Variation' and 'Gene Product', respectively. + Gene_Product_Variant_Of_Gene_Product + + + + + Gene_Product_Variant_Of_Gene_Product + PT + NCI + + + + + A role used to indicate that a gene product sequence variation is related to a wild-type gene product. The domain and range for this role are 'Gene Product Sequence Variation' and 'Gene Product', respectively. + NCI + + + + + + + + R23 + Conceptual Entity + Has Associated Cell Type + EO_Disease_Has_Associated_Cell_Type + EO_Disease_Has_Associated_Cell_Type + A role used to specify the associated cell type of a disease in an experimental organism. The domain and range for this role are 'Experimental Organism Diagnosis' and 'Experimental Organism Anatomical Concept', respectively. + EO_Disease_Has_Associated_Cell_Type + + + + + EO_Disease_Has_Associated_Cell_Type + PT + NCI + + + + + A role used to specify the associated cell type of a disease in an experimental organism. The domain and range for this role are 'Experimental Organism Diagnosis' and 'Experimental Organism Anatomical Concept', respectively. + NCI + + + + + + + + R24 + Conceptual Entity + Maps To Human Disease + EO_Disease_Maps_To_Human_Disease + EO_Disease_Maps_To_Human_Disease + A role is used to establish a relationship between a disease in an experimental organism and a corresponding human disease. The domain and the range for this role are 'Experimental Organism Diagnosis' and 'Disease, Disorder or Finding', respectively. + EO_Disease_Maps_To_Human_Disease + + + + + EO_Disease_Maps_To_Human_Disease + PT + NCI + + + + + A role is used to establish a relationship between a disease in an experimental organism and a corresponding human disease. The domain and the range for this role are 'Experimental Organism Diagnosis' and 'Disease, Disorder or Finding', respectively. + NCI + + + + + + + + R25 + Conceptual Entity + Has Associated EO Anatomy + EO_Disease_Has_Associated_EO_Anatomy + EO_Disease_Has_Associated_EO_Anatomy + A role used to specify the general site, structure or system where a pathological process is located in an experimental organism. The domain and range for this role are 'Experimental Organism Diagnosis' and 'Experimental Organism Anatomical Concept', respectively. + EO_Disease_Has_Associated_EO_Anatomy + + + + + EO_Disease_Has_Associated_EO_Anatomy + PT + NCI + + + + + A role used to specify the general site, structure or system where a pathological process is located in an experimental organism. The domain and range for this role are 'Experimental Organism Diagnosis' and 'Experimental Organism Anatomical Concept', respectively. + NCI + + + + + + + + R26 + Conceptual Entity + Has Property Or Attribute + EO_Disease_Has_Property_Or_Attribute + EO_Disease_Has_Property_Or_Attribute + A role used to specify the clinical behavior, or other characteristic, of a disease in an experimental organism. The domain and range for this role are 'Experimental Organism Diagnosis' and 'Property or Attribute', respectively. + EO_Disease_Has_Property_Or_Attribute + + + + + EO_Disease_Has_Property_Or_Attribute + PT + NCI + + + + + A role used to specify the clinical behavior, or other characteristic, of a disease in an experimental organism. The domain and range for this role are 'Experimental Organism Diagnosis' and 'Property or Attribute', respectively. + NCI + + + + + + + + R27 + Conceptual Entity + Part Of + Conceptual_Part_Of + Conceptual_Part_Of + A role used to indicate that a conceptual entity is a sub-entity of another conceptual entity. Both the domain and the range for this role are 'Conceptual Entity'. + Conceptual_Part_Of + + + + + Conceptual_Part_Of + PT + NCI + + + + + A role used to indicate that a conceptual entity is a sub-entity of another conceptual entity. Both the domain and the range for this role are 'Conceptual Entity'. + NCI + + + + + + + + + + R28 + Conceptual Entity + Has Initiator Process + Biological_Process_Has_Initiator_Process + Biological_Process_Has_Initiator_Process + A role used to assert that the initiation of the stated biological process is dependent on the progression or completion of another process. The role implies a direct physical and functional interaction of an element from the preceding biological process with a target molecule or complex involved in the initial stages of the stated process. Both the domain and the range for this role are 'Biological Process'. + Biological_Process_Has_Initiator_Process + + + + + Biological_Process_Has_Initiator_Process + PT + NCI + + + + + A role used to assert that the initiation of the stated biological process is dependent on the progression or completion of another process. The role implies a direct physical and functional interaction of an element from the preceding biological process with a target molecule or complex involved in the initial stages of the stated process. Both the domain and the range for this role are 'Biological Process'. + NCI + + + + + + + + + R29 + Conceptual Entity + Has Result Chemical Or Drug + Biological_Process_Has_Result_Chemical_Or_Drug + Biological_Process_Has_Result_Chemical_Or_Drug + A role used to assert that the endpoint of a biological process is the creation of a drug, chemical or biomedical material. The domain and range for this role are 'Biological Process' and 'Drug, Food, Chemical or Biomedical Material', respectively. + Biological_Process_Has_Result_Chemical_Or_Drug + + + + + Biological_Process_Has_Result_Chemical_Or_Drug + PT + NCI + + + + + A role used to assert that the endpoint of a biological process is the creation of a drug, chemical or biomedical material. The domain and range for this role are 'Biological Process' and 'Drug, Food, Chemical or Biomedical Material', respectively. + NCI + + + + + + + + + R30 + Conceptual Entity + Has Associated Location + Biological_Process_Has_Associated_Location + Biological_Process_Has_Associated_Location + A role used to indicate the organ, organ system, cellular or subcellular location where a process occurs in a living system. The domain and range for this role are 'Biological Process' and 'Anatomic Structure, System, or Substance', respectively. + Biological_Process_Has_Associated_Location + + + + + Biological_Process_Has_Associated_Location + PT + NCI + + + + + A role used to indicate the organ, organ system, cellular or subcellular location where a process occurs in a living system. The domain and range for this role are 'Biological Process' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R31 + Conceptual Entity + Has Result Anatomy + Biological_Process_Has_Result_Anatomy + Biological_Process_Has_Result_Anatomy + A role used to assert that some biological event results in the formation of a subcellular complex, structure, cell, tissue or organ. This role is used to establish this relationship between the biological process and the anatomical factor formed. The domain and range for this role are 'Biological Process' and 'Anatomic Structure, System, or Substance', respectively. + Biological_Process_Has_Result_Anatomy + + + + + Biological_Process_Has_Result_Anatomy + PT + NCI + + + + + A role used to assert that some biological event results in the formation of a subcellular complex, structure, cell, tissue or organ. This role is used to establish this relationship between the biological process and the anatomical factor formed. The domain and range for this role are 'Biological Process' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R32 + Conceptual Entity + Has Initiator Chemical Or Drug + Biological_Process_Has_Initiator_Chemical_Or_Drug + Biological_Process_Has_Initiator_Chemical_Or_Drug + A role used to assert the relationship between a biological process and a drug or chemical that stimulates the process. The role implies the direct physical interaction of a chemical or drug with a target molecule or complex that results in the initiation of the process. The domain and range for this role are 'Biological Process' and 'Drug, Food, Chemical or Biomedical Material', respectively. + Biological_Process_Has_Initiator_Chemical_Or_Drug + + + + + Biological_Process_Has_Initiator_Chemical_Or_Drug + PT + NCI + + + + + A role used to assert the relationship between a biological process and a drug or chemical that stimulates the process. The role implies the direct physical interaction of a chemical or drug with a target molecule or complex that results in the initiation of the process. The domain and range for this role are 'Biological Process' and 'Drug, Food, Chemical or Biomedical Material', respectively. + NCI + + + + + + + + + + R34 + Conceptual Entity + Has Result Biological Process + Biological_Process_Has_Result_Biological_Process + Biological_Process_Has_Result_Biological_Process + A role used to assert that the end result of a biological process initiates a subsequent biological process. Both the domain and the range for this role is 'Biological Process'. + Biological_Process_Has_Result_Biological_Process + + + + + Biological_Process_Has_Result_Biological_Process + PT + NCI + + + + + A role used to assert that the end result of a biological process initiates a subsequent biological process. Both the domain and the range for this role is 'Biological Process'. + NCI + + + + + + + + + + R35 + Conceptual Entity + Is Part Of Process + Biological_Process_Is_Part_Of_Process + Biological_Process_Is_Part_Of_Process + A role used to assert that a biological process operates as a component of another biological process. Both the domain and the range for this role is 'Biological Process'. + Biological_Process_Is_Part_Of_Process + + + + + Biological_Process_Is_Part_Of_Process + PT + NCI + + + + + A role used to assert that a biological process operates as a component of another biological process. Both the domain and the range for this role is 'Biological Process'. + NCI + + + + + + + + R36 + Conceptual Entity + Is Biomarker Type + Gene_Is_Biomarker_Type + Gene_Is_Biomarker_Type + A role used to designate the type of biomarker a gene is; it points to a small tree of biomarker types (e.g., Disease Marker, Metabolic Marker, Prognostic Marker). The domain and range for this role are 'Gene' and 'Diagnostic or Prognostic Factor', respectively. + Gene_Is_Biomarker_Type + + + + + Gene_Is_Biomarker_Type + PT + NCI + + + + + A role used to designate the type of biomarker a gene is; it points to a small tree of biomarker types (e.g., Disease Marker, Metabolic Marker, Prognostic Marker). The domain and range for this role are 'Gene' and 'Diagnostic or Prognostic Factor', respectively. + NCI + + + + + + + + + R37 + Conceptual Entity + Plays Role In Process + Gene_Plays_Role_In_Process + Gene_Plays_Role_In_Process + A role used to assert a relationship between a gene and a biological process in which its encoded gene product(s) participate. The domain and range for this role are 'Gene' and 'Biological Process', respectively. + Gene_Plays_Role_In_Process + + + + + Gene_Plays_Role_In_Process + PT + NCI + + + + + A role used to assert a relationship between a gene and a biological process in which its encoded gene product(s) participate. The domain and range for this role are 'Gene' and 'Biological Process', respectively. + NCI + + + + + + + + R38 + Conceptual Entity + Associated With Disease + Gene_Associated_With_Disease + Gene_Associated_With_Disease + A role used to indicate that molecular abnormalities in a gene may be associated with the manifestation of a disease. The role is used to assert a link between a gene and a disease when the association is considered to have clinical relevance. The domain and range for this role are 'Gene' and 'Disease, Disorder or Finding', respectively. + Gene_Associated_With_Disease + + + + + Gene_Associated_With_Disease + PT + NCI + + + + + A role used to indicate that molecular abnormalities in a gene may be associated with the manifestation of a disease. The role is used to assert a link between a gene and a disease when the association is considered to have clinical relevance. The domain and range for this role are 'Gene' and 'Disease, Disorder or Finding', respectively. + NCI + + + + + + + + R39 + Conceptual Entity + Gene_Is_Biomarker_Of + Gene_Is_Biomarker_Of + A role used to assert that expression or alteration of a gene is correlated with a particular disease or disease state or is predictive of the disease or disease state. The domain and range for this role are 'Gene' and Findings_and_Disorder_Kind, respectively. + Gene_Is_Biomarker_Of + + + + + Gene_Is_Biomarker_Of + NCI + PT + + + + + A role used to assert that expression or alteration of a gene is correlated with a particular disease or disease state or is predictive of the disease or disease state. The domain and range for this role are 'Gene' and Findings_and_Disorder_Kind, respectively. + NCI + + + + + + + + R40 + Conceptual Entity + In Chromosomal Location + Gene_In_Chromosomal_Location + Gene_In_Chromosomal_Location + A role used to assert a relationship between a gene and its general location, specified by chromosomal band position (infrequently by chromosome number or chromosome arm). The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + Gene_In_Chromosomal_Location + + + + + Gene_In_Chromosomal_Location + PT + NCI + + + + + A role used to assert a relationship between a gene and its general location, specified by chromosomal band position (infrequently by chromosome number or chromosome arm). The domain and range for this role are 'Gene' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R41 + Conceptual Entity + Found In Organism + Gene_Found_In_Organism + Gene_Found_In_Organism + A role used to specify the organism of origin for a gene. It may be used to differentiate genes with the same name and functions that originate from different organisms. The domain and range for this role are 'Gene' and 'Organism', respectively. + Currently, we only model human genes, but this role has obvious utility in future, if other organisms are modeled as well. + Gene_Found_In_Organism + + + + + Gene_Found_In_Organism + PT + NCI + + + + + A role used to specify the organism of origin for a gene. It may be used to differentiate genes with the same name and functions that originate from different organisms. The domain and range for this role are 'Gene' and 'Organism', respectively. + NCI + + + + + + + + R42 + Conceptual Entity + Is Biomarker Type + Gene_Product_Is_Biomarker_Type + Gene_Product_Is_Biomarker_Type + A role used to designate the type of biomarker a gene product is; it points to a small tree of biomarker types (e.g., Disease Marker, Metabolic Marker, Prognostic Marker). The domain and range for this role are 'Gene Product' and 'Diagnostic or Prognostic Factor', respectively. + Gene_Product_Is_Biomarker_Type + + + + + Gene_Product_Is_Biomarker_Type + PT + NCI + + + + + A role used to designate the type of biomarker a gene product is; it points to a small tree of biomarker types (e.g., Disease Marker, Metabolic Marker, Prognostic Marker). The domain and range for this role are 'Gene Product' and 'Diagnostic or Prognostic Factor', respectively. + NCI + + + + + + + + R44 + Conceptual Entity + Has Chemical Classification + Gene_Product_Has_Chemical_Classification + Gene_Product_Has_Chemical_Classification + A role used to specify the physical structure type of a protein molecule (e.g. metalloprotein, transmembrane protein). Both the domain and range for this role are 'Gene Product'. + The role was originally intended for protein structure tagging (e.g., Phosphoprotein, Lipoprotein). Was extended to also tag for Membrane Protein, Protein Complex Subunit, etc. + Gene_Product_Has_Chemical_Classification + + + + + Gene_Product_Has_Chemical_Classification + PT + NCI + + + + + A role used to specify the physical structure type of a protein molecule (e.g. metalloprotein, transmembrane protein). Both the domain and range for this role are 'Gene Product'. + NCI + + + + + + + + R45 + Conceptual Entity + Has Organism Source + Gene_Product_Has_Organism_Source + Gene_Product_Has_Organism_Source + A role used to differentiate homologous proteins from different organisms. The domain and range for this role are 'Gene Product' and 'Organism', respectively. + Gene_Product_Has_Organism_Source + + + + + Gene_Product_Has_Organism_Source + PT + NCI + + + + + A role used to differentiate homologous proteins from different organisms. The domain and range for this role are 'Gene Product' and 'Organism', respectively. + NCI + + + + + + + + R46 + Conceptual Entity + Has Associated Anatomy + Gene_Product_Has_Associated_Anatomy + Gene_Product_Has_Associated_Anatomy + A role used to specify physical structures or typical subcellular locations of a gene product. The domain and range for this role are 'Gene Product' and 'Anatomic Structure, System, or Substance', respectively. + Gene_Product_Has_Associated_Anatomy + + + + + Gene_Product_Has_Associated_Anatomy + PT + NCI + + + + + A role used to specify physical structures or typical subcellular locations of a gene product. The domain and range for this role are 'Gene Product' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R47 + Conceptual Entity + Is Biomarker Of + Gene_Product_Is_Biomarker_Of + Gene_Product_Is_Biomarker_Of + A role used to indicate that presence of a gene product may contribute to clinical diagnosis, treatment selection, or prediction of clinical outcome. The domain and range for this role are 'Gene Product' and 'Disease, Disorder or Finding', respectively. + This role does not imply a cause and effect. + Gene_Product_Is_Biomarker_Of + + + + + Gene_Product_Is_Biomarker_Of + PT + NCI + + + + + A role used to indicate that presence of a gene product may contribute to clinical diagnosis, treatment selection, or prediction of clinical outcome. The domain and range for this role are 'Gene Product' and 'Disease, Disorder or Finding', respectively. + NCI + + + + + + + + R48 + Conceptual Entity + Malfunction Associated With Disease + Gene_Product_Malfunction_Associated_With_Disease + Gene_Product_Malfunction_Associated_With_Disease + A role used to indicate that molecular abnormalities in a gene product may be associated with the manifestation of a disease. The role is used to assert a link between a gene product and a disease when the association is considered to have clinical relevance. The domain and range for this role are 'Gene Product' and 'Disease, Disorder or Finding', respectively. + Gene_Product_Malfunction_Associated_With_Disease + + + + + Gene_Product_Malfunction_Associated_With_Disease + PT + NCI + + + + + A role used to indicate that molecular abnormalities in a gene product may be associated with the manifestation of a disease. The role is used to assert a link between a gene product and a disease when the association is considered to have clinical relevance. The domain and range for this role are 'Gene Product' and 'Disease, Disorder or Finding', respectively. + NCI + + + + + + + + R49 + Conceptual Entity + Expressed In Tissue + Gene_Product_Expressed_In_Tissue + Gene_Product_Expressed_In_Tissue + A role used to specify that a normal tissue is the normal location for the expression of a gene product. The domain and range for this role are 'Gene Product' and 'Anatomic Structure, System, or Substance', respectively. + This information is often useful to researchers. However, we no longer curate this information and now favor linking out to externally curated databases. Source database for the link has yet to be decided. + Gene_Product_Expressed_In_Tissue + + + + + Gene_Product_Expressed_In_Tissue + PT + NCI + + + + + A role used to specify that a normal tissue is the normal location for the expression of a gene product. The domain and range for this role are 'Gene Product' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R50 + Conceptual Entity + Has Structural Domain Or Motif + Gene_Product_Has_Structural_Domain_Or_Motif + Gene_Product_Has_Structural_Domain_Or_Motif + A role used specify information about protein domains or motifs present in a protein that can give insight into protein function. The domain and range for this role are 'Gene Product' and 'Anatomic Structure, System, or Substance', respectively. + We no longer curate this information and now favor linking out to externally curated databases. The source database for the link has yet to be decided. + Gene_Product_Has_Structural_Domain_Or_Motif + + + + + Gene_Product_Has_Structural_Domain_Or_Motif + PT + NCI + + + + + A role used specify information about protein domains or motifs present in a protein that can give insight into protein function. The domain and range for this role are 'Gene Product' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + R51 + Conceptual Entity + Is Physical Part Of + Gene_Product_Is_Physical_Part_Of + Gene_Product_Is_Physical_Part_Of + A role used to indicate that a gene product normally functions as a component of a "functional complex". Both the domain and range for this role are 'Gene Product'. + Gene_Product_Is_Physical_Part_Of + + + + + Gene_Product_Is_Physical_Part_Of + PT + NCI + + + + + A role used to indicate that a gene product normally functions as a component of a "functional complex". Both the domain and range for this role are 'Gene Product'. + NCI + + + + + + + + R52 + Conceptual Entity + Has Biochemical Function + Gene_Product_Has_Biochemical_Function + Gene_Product_Has_Biochemical_Function + A role used to denote the biochemical activity of a gene product. Both the domain and range for this role are 'Gene Product'. + Gene_Product_Has_Biochemical_Function + + + + + Gene_Product_Has_Biochemical_Function + PT + NCI + + + + + A role used to denote the biochemical activity of a gene product. Both the domain and range for this role are 'Gene Product'. + NCI + + + + + + + + + R53 + Conceptual Entity + Plays Role In Biological Process + Gene_Product_Plays_Role_In_Biological_Process + Gene_Product_Plays_Role_In_Biological_Process + A role used to assert that a gene product participates in a specific biological process. The domain and range for this role are 'Gene Product' and 'Biological Process', respectively. + Considered by most researchers to be essential, definitional information about a gene product. + Gene_Product_Plays_Role_In_Biological_Process + + + + + Gene_Product_Plays_Role_In_Biological_Process + PT + NCI + + + + + A role used to assert that a gene product participates in a specific biological process. The domain and range for this role are 'Gene Product' and 'Biological Process', respectively. + NCI + + + + + + + + R54 + Conceptual Entity + Encoded By Gene + Gene_Product_Encoded_By_Gene + Gene_Product_Encoded_By_Gene + A role used to assert a relationship between a gene product and the gene that encodes it. The domain and range for this role are 'Gene Product' and 'Gene', respectively. + The reciprocal relationship is represented in the property Gene_Encodes_Product + Gene_Product_Encoded_By_Gene + + + + + Gene_Product_Encoded_By_Gene + PT + NCI + + + + + A role used to assert a relationship between a gene product and the gene that encodes it. The domain and range for this role are 'Gene Product' and 'Gene', respectively. + NCI + + + + + + + + + R66 + Conceptual Entity + Plays Role In Biological Process + Chemical_Or_Drug_Plays_Role_In_Biological_Process + Chemical_Or_Drug_Plays_Role_In_Biological_Process + A role used to assert that an active ingredient of a drug or chemical agent influences a biological process. The role implies a direct association with a target biological molecule or complex involved in the process. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Biological Process', respectively. + to be deleted + Chemical_Or_Drug_Plays_Role_In_Biological_Process + + + + + Chemical_Or_Drug_Plays_Role_In_Biological_Process + PT + NCI + + + + + A role used to assert that an active ingredient of a drug or chemical agent influences a biological process. The role implies a direct association with a target biological molecule or complex involved in the process. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Biological Process', respectively. + NCI + + + + + + + + R72 + Conceptual Entity + Affects Cell Type Or Tissue + Chemical_Or_Drug_Affects_Cell_Type_Or_Tissue + Chemical_Or_Drug_Affects_Cell_Type_Or_Tissue + A role used to represent the intended target cells for a chemical or drug. This does not include unintended target cells or tissues that are associated with side effects or toxicity of the chemical or drug. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Anatomic Structure, System, or Substance', respectively. + Chemical_Or_Drug_Affects_Cell_Type_Or_Tissue + + + + + Chemical_Or_Drug_Affects_Cell_Type_Or_Tissue + PT + NCI + + + + + A role used to represent the intended target cells for a chemical or drug. This does not include unintended target cells or tissues that are associated with side effects or toxicity of the chemical or drug. The domain and range for this role are 'Drug, Food, Chemical or Biomedical Material' and 'Anatomic Structure, System, or Substance', respectively. + NCI + + + + + + + + + R81 + Conceptual Entity + Has Location + Anatomic_Structure_Has_Location + Anatomic_Structure_Has_Location + A role used to indicate the physical location of an anatomic structure in the body. Both the domain and range for this role are 'Anatomic Structure, System, or Substance'. + Anatomic_Structure_Has_Location + + + + + Anatomic_Structure_Has_Location + PT + NCI + + + + + A role used to indicate the physical location of an anatomic structure in the body. Both the domain and range for this role are 'Anatomic Structure, System, or Substance'. + NCI + + + + + + + + + R82 + Conceptual Entity + Is Physical Part Of + Anatomic_Structure_Is_Physical_Part_Of + Anatomic_Structure_Is_Physical_Part_Of + A role used to indicate that an anatomic structure has a physical association with a broader system or organ. Both the domain and range for this role are 'Anatomic Structure, System, or Substance'. + Anatomic_Structure_Is_Physical_Part_Of + + + + + Anatomic_Structure_Is_Physical_Part_Of + PT + NCI + + + + + A role used to indicate that an anatomic structure has a physical association with a broader system or organ. Both the domain and range for this role are 'Anatomic Structure, System, or Substance'. + NCI + + + + + + + + R88 + Conceptual Entity + Is Stage + Disease_Is_Stage + Disease_Is_Stage + A role used to specify the disease stage of a disease, the extent to which a cancer has spread from the original site to other parts of the body. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Property or_Attribute', respectively. + Disease_Is_Stage + + + + + Disease_Is_Stage + PT + NCI + + + + + A role used to specify the disease stage of a disease, the extent to which a cancer has spread from the original site to other parts of the body. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Property or_Attribute', respectively. + NCI + + + + + + + + R89 + Conceptual Entity + May Have Molecular Abnormality + Disease_May_Have_Molecular_Abnormality + Disease_May_Have_Molecular_Abnormality + A role used to represent that a molecular abnormality will only be present in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + Disease_May_Have_Molecular_Abnormality + + + + + Disease_May_Have_Molecular_Abnormality + PT + NCI + + + + + A role used to represent that a molecular abnormality will only be present in some cases of the disease. The domain and the range for this role are 'Disease, Disorder or Finding' and 'Molecular Abnormality', respectively. + NCI + + + + + + + + + + + + + + C104080 + Mental Process + Enjoyment of Life + C0424131 + Enjoyment of Life + The level of happiness or contentment that an individual professes, or is observed to display with regards to their life situation. + Enjoyment of Life + + + + + Enjoyment of Life + PT + NCI + + + + + Enjoyment of Life + SY + caDSR + + + + + The level of happiness or contentment that an individual professes, or is observed to display with regards to their life situation. + NCI + + + + + + + + + C113416 + Mental Process + Consideration + C0518609 + Consideration + Careful thought or deliberation. + Consideration + + + + + Consideration + PT + NCI + + + + + Consideration + SY + caDSR + + + + + Careful thought or deliberation. + NCI + + + + + + + + + C113697 + Mental Process + Delight + C3830544 + Delight + Delighted + A feeling of extreme pleasure or satisfaction. + Delight + + + + + Delight + PT + NCI + + + + + Delighted + SY + NCI + + + + + A feeling of extreme pleasure or satisfaction. + NCI + + + + + + + + + C114729 + Phenomenon or Process + Pyroptosis + C2610960 + Pyroptosis + An inflammatory form of programmed cell death characterized by caspase-dependent formation of plasma-membrane pores, which leads to pathological changes in osmotic potential that ultimately result in cellular lysis and release of pro-inflammatory cytokines. It occurs most frequently following infection with intracellular pathogens, but also has a role in tumor suppression and the initiation of anti-tumor immune responses, as well as in autoimmune and cardiovascular diseases. + Pyroptosis is dependent on caspase-1 activation. + Pyroptosis + + + + + Pyroptosis + PT + NCI + + + + + An inflammatory form of programmed cell death characterized by caspase-dependent formation of plasma-membrane pores, which leads to pathological changes in osmotic potential that ultimately result in cellular lysis and release of pro-inflammatory cytokines. It occurs most frequently following infection with intracellular pathogens, but also has a role in tumor suppression and the initiation of anti-tumor immune responses, as well as in autoimmune and cardiovascular diseases. + NCI + + + + + + + + + C114847 + Molecular Function + Human Leukocyte Antigen Sensitization + C2242570 + MedDRA + NICHD + Presence of preformed antibodies to donor human leukocyte antigen (HLA). + Human leukocyte antigen test positive + HLA Sensitization + Human Leukocyte Antigen Sensitization + Presence of preformed antibodies to donor human leukocyte antigen (HLA). + Human Leukocyte Antigen Sensitization + + + + + Presence of preformed antibodies to donor human leukocyte antigen (HLA). + NICHD + + + + + Human leukocyte antigen test positive + Has Synonym + LLT + 10073015 + MedDRA + 18.1 + + + + + HLA Sensitization + SY + NCI + + + + + Human Leukocyte Antigen Sensitization + PT + NCI + + + + + Human Leukocyte Antigen Sensitization + PT + NICHD + + + + + Presence of preformed antibodies to donor human leukocyte antigen (HLA). + NCI + + + + + + + + + C122669 + Mental Process + Recollect + C0034770 + Recall + Recollect + Recollection + Remember + The act of recalling information by mental effort. + Recollect + + + + + Recall + SY + caDSR + + + + + Recollect + PT + NCI + + + + + Recollect + SY + caDSR + + + + + Recollection + SY + caDSR + + + + + Remember + SY + caDSR + + + + + The act of recalling information by mental effort. + NCI + + + + + + + + + C12560 + Cell + Foam Cell + Foam Cell + C0016390 + Foam_Cell + Foam Cell + Foam Cells + Foamy Macrophage + A type of macrophage that ingests low-density lipoproteins found in fatty deposits on blood vessel walls, resulting in a foamy appearance. + Foam Cell + + + + + Foam Cell + PT + NCI + + + + + Foam Cells + SY + NCI + + + + + Foamy Macrophage + SY + NCI + + + + + A type of macrophage that ingests low-density lipoproteins found in fatty deposits on blood vessel walls, resulting in a foamy appearance. + NCI + + + + + + + + + C126426 + Organ or Tissue Function + Hepatopetal Portal Venous Flow + CL504963 + Hepatopetal Portal Venous Flow + The normal pattern of blood flow towards the liver through the portal vein. + Hepatopetal Portal Venous Flow + + + + + Hepatopetal Portal Venous Flow + PT + NCI + + + + + Hepatopetal Portal Venous Flow + SY + caDSR + + + + + The normal pattern of blood flow towards the liver through the portal vein. + NCI + + + + + + + + + C12913 + Cell + Abnormal Cell + C0333717 + Abnormal_Cell + Abnormal Cell + An abnormal human cell type which can occur in either disease states or disease models. + Abnormal Cell + + + + + Abnormal Cell + PT + NCI + + + + + An abnormal human cell type which can occur in either disease states or disease models. + NCI + + + + + + + + + C129398 + Phenomenon or Process + Mitotic Catastrophe + Mitotic Catastrophe + C2610961 + CTRP + Mitotic Catastrophe + Programmed cell death that occurs during mitosis caused by various types of cellular damage that lead to the failure of cell cycle checkpoint(s). Micronucleation and multinuceation can occur in cells undergoing this process. + Mitotic Catastrophe + + + + + Mitotic Catastrophe + DN + CTRP + + + + + Mitotic Catastrophe + PT + NCI + + + + + Programmed cell death that occurs during mitosis caused by various types of cellular damage that lead to the failure of cell cycle checkpoint(s). Micronucleation and multinuceation can occur in cells undergoing this process. + NCI + + + + + + + + + C129692 + Phenomenon or Process + White Blood Cell Lysis + CL512934 + Lysed WBC + White Blood Cell Lysis + Disruption and destruction of the white blood cell membrane. + White Blood Cell Lysis + + + + + Lysed WBC + SY + caDSR + + + + + White Blood Cell Lysis + PT + NCI + + + + + White Blood Cell Lysis + SY + caDSR + + + + + Disruption and destruction of the white blood cell membrane. + NCI + + + + + + + + + C131082 + Mental Process + Impression + C0596764 + CDISC + A diagnostic statement that is an interpretation or abstraction of an observation(s). + IMPRESSION + Imp + Impression + Mental Impression + An effect produced upon the mind or senses as a consequence of experience. + Impression + + + + + A diagnostic statement that is an interpretation or abstraction of an observation(s). + CDISC + + + + + IMPRESSION + PT + CDISC + + + + + Imp + SY + CDISC + + + + + Impression + PT + NCI + + + + + Impression + SY + caDSR + + + + + Mental Impression + SY + NCI + + + + + An effect produced upon the mind or senses as a consequence of experience. + NCI + + + + + + + + + C141517 + Cell + Atypical Glandular Cell-Favor Neoplasia + CL539562 + Atypical Glandular Cell-Favor Neoplasia + An abnormal endocervical or endometrial cell found in a cervical smear with cytologic features suggestive of a neoplastic process. + Atypical Glandular Cell-Favor Neoplasia + + + + + Atypical Glandular Cell-Favor Neoplasia + PT + NCI + + + + + An abnormal endocervical or endometrial cell found in a cervical smear with cytologic features suggestive of a neoplastic process. + NCI + + + + + + + + + C141518 + Cell + Atypical Endocervical Cell + C1455886 + Atypical Endocervical Cell + An abnormal endocervical cell found in a cervical smear. It may be related to an inflammatory or neoplastic process. + Atypical Endocervical Cell + + + + + Atypical Endocervical Cell + PT + NCI + + + + + An abnormal endocervical cell found in a cervical smear. It may be related to an inflammatory or neoplastic process. + NCI + + + + + + + + + C141519 + Cell + Atypical Squamous Cell-Favor High-Grade Squamous Intraepithelial Lesion + CL539561 + ASC-Favor HSIL + Atypical Squamous Cell-Favor HSIL + Atypical Squamous Cell-Favor High-Grade Squamous Intraepithelial Lesion + An abnormal squamous cell found in a cervical smear with cytologic features suggestive of high-grade squamous intraepithelial lesion. + Atypical Squamous Cell-Favor High-Grade Squamous Intraepithelial Lesion + + + + + ASC-Favor HSIL + SY + NCI + + + + + Atypical Squamous Cell-Favor HSIL + SY + NCI + + + + + Atypical Squamous Cell-Favor High-Grade Squamous Intraepithelial Lesion + PT + NCI + + + + + An abnormal squamous cell found in a cervical smear with cytologic features suggestive of high-grade squamous intraepithelial lesion. + NCI + + + + + + + + + C142557 + Mental Process + Feels + CL540493 + CDISC-GLOSS + A patient's physical sensation (e.g., symptoms) or perceived mental state. A patient may feel pain, feel feverish, or perceive a severely low mood (as with depression). [FDA Clinical Outcome Assessment (COA) Glossary] + Feels + feels + Feels + + + + + A patient's physical sensation (e.g., symptoms) or perceived mental state. A patient may feel pain, feel feverish, or perceive a severely low mood (as with depression). [FDA Clinical Outcome Assessment (COA) Glossary] + CDISC-GLOSS + + + + + Feels + PT + NCI + + + + + feels + PT + CDISC-GLOSS + + + + + + + + + C151402 + Organ or Tissue Function + Septation + CL568584 + Septation + The formation of a division between cavities or parts of an organism. + Septation + + + + + Septation + PT + NCI + + + + + Septation + SY + caDSR + + + + + The formation of a division between cavities or parts of an organism. + NCI + + + + + + + + + C156451 + Organ or Tissue Function + Tolerance Induction in Solid Organ Transplantation + CL563166 + Tolerance Induction in Solid Organ Transplantation + Tolerance induction associated with solid organ transplant + Transplantation Tolerance Induction + An immunological environment, mediated by T-regulatory cells, favoring regulation, supporting graft survival, without interfering with crucial immune surveillance mechanisms and, concurrently, abolishing immunosuppressant-related toxicity. + Tolerance Induction in Solid Organ Transplantation + + + + + Tolerance Induction in Solid Organ Transplantation + PT + NCI + + + + + Tolerance induction associated with solid organ transplant + SY + caDSR + + + + + Transplantation Tolerance Induction + SY + NCI + + + + + An immunological environment, mediated by T-regulatory cells, favoring regulation, supporting graft survival, without interfering with crucial immune surveillance mechanisms and, concurrently, abolishing immunosuppressant-related toxicity. + NCI + + + + + + + + + C162251 + Mental Process + Semantic Clustering + CL970714 + Semantic Clustering + The tendency to group items according to their semantic category. + Semantic Clustering + + + + + Semantic Clustering + PT + NCI + + + + + Semantic Clustering + SY + caDSR + + + + + The tendency to group items according to their semantic category. + NCI + + + + + + + + + C16298 + Cell Function + Antibody-Dependent Cellular Cytotoxicity + C0003272 + A type of immune reaction in which a target cell or microbe is coated with antibodies and killed by certain types of white blood cells. The white blood cells bind to the antibodies and release substances that kill the target cells or microbes. + Antibody-Dependent_Cellular_Cytotoxicity + ADCC + Antibody-Dependent Cellular Cytotoxicity + Antibody-Mediated Lympholysis + antibody-dependent cell-mediated cytotoxicity + antibody-dependent cellular cytotoxicity + The target killing of a cell depending on antibody recognition. An antibody is directed to the target by antigen-binding arms and anchors to the killer cell by an Fc receptor. The identity of the target cell varies, but it must possess surface IgG whose Fc portion is intact. The effector "killer" cell possesses Fc receptors. It may be a lymphocyte lacking conventional B- or T-cell markers, or a monocyte, macrophage, or polynuclear leukocyte, depending on the identity of the target cell. The reaction is complement-independent. + Antibody-Dependent Cellular Cytotoxicity + + + + + A type of immune reaction in which a target cell or microbe is coated with antibodies and killed by certain types of white blood cells. The white blood cells bind to the antibodies and release substances that kill the target cells or microbes. + NCI-GLOSS + + + + + ADCC + AB + NCI + + + + + ADCC + PT + NCI-GLOSS + CDR0000653101 + + + + + Antibody-Dependent Cellular Cytotoxicity + PT + NCI + + + + + Antibody-Mediated Lympholysis + SY + NCI + + + + + antibody-dependent cell-mediated cytotoxicity + PT + NCI-GLOSS + CDR0000653102 + + + + + antibody-dependent cellular cytotoxicity + PT + NCI-GLOSS + CDR0000653103 + + + + + The target killing of a cell depending on antibody recognition. An antibody is directed to the target by antigen-binding arms and anchors to the killer cell by an Fc receptor. The identity of the target cell varies, but it must possess surface IgG whose Fc portion is intact. The effector "killer" cell possesses Fc receptors. It may be a lymphocyte lacking conventional B- or T-cell markers, or a monocyte, macrophage, or polynuclear leukocyte, depending on the identity of the target cell. The reaction is complement-independent. + NCI + + + + + + + + + C16299 + Molecular Function + Negative Regulation of Coagulation + C2917212 + Anticoagulation + Anticoagulation + Negative Regulation of Coagulation + Events or activities that prevent or inhibit coagulation. + Negative Regulation of Coagulation + + + + + Anticoagulation + SY + NCI + + + + + Negative Regulation of Coagulation + PT + NCI + + + + + Events or activities that prevent or inhibit coagulation. + NCI + + + + + + + + + C16353 + Organ or Tissue Function + Blood Circulation + C0005775 + In the body, the flow of blood through the heart and blood vessels, and the flow of lymph through the lymph vessels. + Blood_Circulation + Blood Circulation + Blood Flow + Bloodstream + Circulation + Circulatory + circulation + The movement of blood to and from the heart and to the rest of the body's organs, tissues, and cells through the network of arteries, veins, and capillaries. (NCI) + Blood Circulation + + + + + In the body, the flow of blood through the heart and blood vessels, and the flow of lymph through the lymph vessels. + NCI-GLOSS + + + + + Blood Circulation + PT + NCI + + + + + Blood Flow + SY + NCI + + + + + Bloodstream + SY + NCI + + + + + Circulation + SY + NCI + + + + + Circulatory + AD + NCI + + + + + circulation + PT + NCI-GLOSS + CDR0000476484 + + + + + The movement of blood to and from the heart and to the rest of the body's organs, tissues, and cells through the network of arteries, veins, and capillaries. (NCI) + NCI + + + + + + + + + C16394 + Cell Function + Cell Aging + C0007581 + Cell_Aging + Aging, Cellular + Cell Aging + Cell Senescence + Cellular Aging + Cellular Senescence + Progression of the cell from its inception to the end of its lifespan. + Cell Aging + + + + + Aging, Cellular + SY + NCI + + + + + Cell Aging + PT + NCI + + + + + Cell Senescence + SY + NCI + + + + + Cellular Aging + SY + NCI + + + + + Cellular Senescence + SY + NCI + + + + + Progression of the cell from its inception to the end of its lifespan. + NCI + + + + + + + + + C164387 + Mental Process + General Statistical Consideration + CL977606 + BRIDG + Information needed for conducting multiple analyses. EXAMPLE(S): Centers within a region with fewer than 3 subjects will be grouped into a pooled center for the region. OTHER NAME(S): NOTE(S): + General Statistical Consideration + GeneralStatisticalConsideration + Careful thought or deliberation related to the planned conduct of statistical analyses. + General Statistical Consideration + + + + + Information needed for conducting multiple analyses. EXAMPLE(S): Centers within a region with fewer than 3 subjects will be grouped into a pooled center for the region. OTHER NAME(S): NOTE(S): + BRIDG 5.3 + + + + + General Statistical Consideration + PT + NCI + + + + + GeneralStatisticalConsideration + PT + BRIDG 5.3 + + + + + Careful thought or deliberation related to the planned conduct of statistical analyses. + NCI + + + + + + + + + C164424 + Mental Process + Sample Size Consideration + CL977538 + BRIDG + Information needed for computing the sample size, including any detail not provided in the study protocol. EXAMPLE(S): "Approximately 100 patients will be randomized to each of the 3 treatment groups. Previous experience with the oral formulation of xanomeline suggests that this sample size has 90% power to detect a 3.0 mean treatment difference in ADAS-Cog (p<.05, two-sided), based on a standard deviation of 6.5. Furthermore, this sample size has 80% power to detect a 0.36 mean treatment difference in CIBIC+ (p<.05, two-sided), based on a standard deviation of 0.9." OTHER NAME(S): NOTE(S): InterventionalStudyProtocolVersion.interventionGroupQuantity, Arm.targetAccrualNumberRange, and StudyProtocolVersion.targetAccrualNumberRange are all related to parts of the SampleSizeConsideration that are not yet fully modeled here. + Sample Size Consideration + SampleSizeConsideration + Careful thought or deliberation related to the calculation of the sample size. + Sample Size Consideration + + + + + Information needed for computing the sample size, including any detail not provided in the study protocol. EXAMPLE(S): "Approximately 100 patients will be randomized to each of the 3 treatment groups. Previous experience with the oral formulation of xanomeline suggests that this sample size has 90% power to detect a 3.0 mean treatment difference in ADAS-Cog (p<.05, two-sided), based on a standard deviation of 6.5. Furthermore, this sample size has 80% power to detect a 0.36 mean treatment difference in CIBIC+ (p<.05, two-sided), based on a standard deviation of 0.9." OTHER NAME(S): NOTE(S): InterventionalStudyProtocolVersion.interventionGroupQuantity, Arm.targetAccrualNumberRange, and StudyProtocolVersion.targetAccrualNumberRange are all related to parts of the SampleSizeConsideration that are not yet fully modeled here. + BRIDG 5.3 + + + + + Sample Size Consideration + PT + NCI + + + + + SampleSizeConsideration + PT + BRIDG 5.3 + + + + + Careful thought or deliberation related to the calculation of the sample size. + NCI + + + + + + + + + + + + + + + C16446 + Mental Process + Cognition + C0009240 + The mental process of thinking, learning, remembering, being aware of surroundings, and using judgment. + Cognition + Cognition + cognition + The mental process of knowing, thinking, learning and judging; the psychological result of perception and learning and reasoning. + Cognition + + + + + The mental process of thinking, learning, remembering, being aware of surroundings, and using judgment. + NCI-GLOSS + + + + + Cognition + PT + NCI + + + + + cognition + PT + NCI-GLOSS + CDR0000476290 + + + + + The mental process of knowing, thinking, learning and judging; the psychological result of perception and learning and reasoning. + NCI + + + + + + + + + + + + + + + C16559 + Cell Function + Erythropoiesis + C0014819 + Erythropoiesis + Erythropoiesis + A hematopoietic process that refers to the production of erythrocytes. + Erythropoiesis + + + + + Erythropoiesis + PT + NCI + + + + + A hematopoietic process that refers to the production of erythrocytes. + NCI + + + + + + + + + C16648 + Organ or Tissue Function + Tissue Growth + C1621966 + Tissue_Growth + Growth + Tissue Growth + An increase is the size or mass of a tissue due to an increase in cell number. + Tissue Growth + + + + + Growth + SY + NCI + + + + + Tissue Growth + PT + NCI + + + + + An increase is the size or mass of a tissue due to an increase in cell number. + NCI + + + + + + + + + C16670 + Organism Function + Hearing + C0018767 + Hearing + Hearing + The auditory faculty, the perception of sound by the ear. + Hearing + + + + + Hearing + PT + NCI + + + + + The auditory faculty, the perception of sound by the ear. + NCI + + + + + + + + + C16674 + Cell Function + Hematopoietic Process + C0018951 + The formation of new blood cells. + Hematopoiesis + Hematopoiesis + Hematopoietic Process + Hemopoiesis + hematopoiesis + A process of blood formation and more specifically formation of blood cells that are all derived from hematopoietic stem cells. + Hematopoietic Process + + + + + The formation of new blood cells. + NCI-GLOSS + + + + + Hematopoiesis + SY + NCI + + + + + Hematopoietic Process + PT + NCI + + + + + Hemopoiesis + SY + NCI + + + + + hematopoiesis + PT + NCI-GLOSS + CDR0000044035 + + + + + A process of blood formation and more specifically formation of blood cells that are all derived from hematopoietic stem cells. + NCI + + + + + + + + + + + + + + + C16710 + Organ or Tissue Function + Immunity + C0020964 + The condition of being protected against an infectious disease. Immunity can be caused by a vaccine, previous infection with the same agent, or by transfer of immune substances from another person or animal. + Immunity + Immunity + immunity + The protection against infectious disease conferred by the immune response. It encompasses the capacity to distinguish foreign material from self, and to neutralize, eliminate, or metabolize that which is foreign. + Immunity + + + + + The condition of being protected against an infectious disease. Immunity can be caused by a vaccine, previous infection with the same agent, or by transfer of immune substances from another person or animal. + NCI-GLOSS + + + + + Immunity + PT + NCI + + + + + immunity + SY + NCI-GLOSS + CDR0000468803 + + + + + The protection against infectious disease conferred by the immune response. It encompasses the capacity to distinguish foreign material from self, and to neutralize, eliminate, or metabolize that which is foreign. + NCI + + + + + + + + + C16711 + Cell Function + Cell-Mediated Immunity + C0020966 + Cell-Mediated_Immunity + Cell Mediated Immunity + Cell Mediated Immunology + Cell-Mediated Immunity + Cellular Immunity + Those manifestations of the immune response which are mediated by antigen-sensitized T-lymphocytes via lymphokines or direct cytotoxicity. This takes place in the absence of circulating antibody or where antibody plays a subordinate role. + Cell-Mediated Immunity + + + + + Cell Mediated Immunity + SY + NCI + + + + + Cell Mediated Immunology + SY + NCI + + + + + Cell-Mediated Immunity + PT + NCI + + + + + Cellular Immunity + SY + NCI + + + + + Those manifestations of the immune response which are mediated by antigen-sensitized T-lymphocytes via lymphokines or direct cytotoxicity. This takes place in the absence of circulating antibody or where antibody plays a subordinate role. + NCI + + + + + + + + + C16712 + Cell Function + Humoral Immunity + C0020967 + Humoral_Immunity + Humoral Immune Response + Humoral Immunity + Immune processes mediated by antibodies + Humoral Immunity + + + + + Humoral Immune Response + SY + NCI + + + + + Humoral Immunity + PT + NCI + + + + + Immune processes mediated by antibodies + NCI + + + + + + + + + C16840 + Mental Process + Mental Process + C0025361 + Mental_Process + Mental Process + Any cognitive activity. + Mental Process + + + + + Mental Process + PT + NCI + + + + + Mental Process + SY + caDSR + + + + + Any cognitive activity. + NCI + + + + + + + + + C168534 + Cell + Cancer-Associated Fibroblast + Cancer-Associated Fibroblast + C4277548 + CTRP + CAF + CAFs + Cancer Associated Fibroblast + Cancer-Associated Fibroblast + TAF + Tumor Associated Fibroblast + Tumor-Associated Fibroblast + A fibroblast found proximal to or within cancerous tissue. + Cancer-Associated Fibroblast + + + + + CAF + AB + NCI + + + + + CAFs + SY + NCI + + + + + Cancer Associated Fibroblast + SY + NCI + + + + + Cancer-Associated Fibroblast + DN + CTRP + + + + + Cancer-Associated Fibroblast + PT + NCI + + + + + TAF + AB + NCI + + + + + Tumor Associated Fibroblast + SY + NCI + + + + + Tumor-Associated Fibroblast + SY + NCI + + + + + A fibroblast found proximal to or within cancerous tissue. + NCI + + + + + + + + + C168535 + Cell + Circulating Cancer-Associated Fibroblast + Circulating Cancer-Associated Fibroblast + CL972863 + CTRP + Circulating Cancer Associated Fibroblast + Circulating Cancer-Associated Fibroblast + cCAF + cCAFs + A fibroblast found in the peripheral blood that is associated with a neoplastic disease and may colocalize with circulating tumor cells. + Circulating Cancer-Associated Fibroblast + + + + + Circulating Cancer Associated Fibroblast + SY + NCI + + + + + Circulating Cancer-Associated Fibroblast + DN + CTRP + + + + + Circulating Cancer-Associated Fibroblast + PT + NCI + + + + + cCAF + AB + NCI + + + + + cCAFs + SY + NCI + + + + + A fibroblast found in the peripheral blood that is associated with a neoplastic disease and may colocalize with circulating tumor cells. + NCI + + + + + + + + + + + + + + + C16879 + Organ or Tissue Function + Morphogenesis + C0026559 + Morphogenesis + Morphogenesis + The process of shape formation: the processes that are responsible for producing the complex shapes of adults from the simple ball of cells that derives from division of the fertilized egg. + Morphogenesis + + + + + Morphogenesis + PT + NCI + + + + + The process of shape formation: the processes that are responsible for producing the complex shapes of adults from the simple ball of cells that derives from division of the fertilized egg. + NCI + On-line Medical Dictionary + + + + + + + + + + + + + + + + + + + + + C16967 + Mental Process + Perception + C0030971 + Perception + Perceived + Perception + The process of producing an internal, conscious image through stimulating a sensory system; it involves the recognition that stimulation has occurred, and the ability to discriminate various aspects of the stimulus. + Perception + + + + + Perceived + SY + NCI + + + + + Perception + PT + NCI + + + + + The process of producing an internal, conscious image through stimulating a sensory system; it involves the recognition that stimulation has occurred, and the ability to discriminate various aspects of the stimulus. + NCI + + + + + + + + + C16999 + Phenomenon or Process + Platelet Aggregation Process + Platelet Aggregation Process + C0032176 + CTRP + Platelet_Aggregation + Platelet Aggregation + Platelet Aggregation Process + Any cell adhesion process that involves the association of platelets via adhesion molecules. + Platelet dysfunction can result in blood clotting and bleeding disorders. + Platelet Aggregation Process + + + + + Platelet Aggregation + SY + NCI + + + + + Platelet Aggregation Process + DN + CTRP + + + + + Platelet Aggregation Process + PT + NCI + + + + + Any cell adhesion process that involves the association of platelets via adhesion molecules. + NCI + + + + + + + + + + + + + + + C17086 + Mental Process + Repression + C0035143 + Repression + Repression + A psychological mechanism utilized by humans to shield themselves from painful memories or traumatic events. This protection entails the exclusion of memories or thoughts from consciousness. + Repression + + + + + Repression + PT + NCI + + + + + Repression + SY + NCI + + + + + A psychological mechanism utilized by humans to shield themselves from painful memories or traumatic events. This protection entails the exclusion of memories or thoughts from consciousness. + NCI + + + + + + + + + C17139 + Organism Function + Olfaction + C0037361 + The sense of smell. + Olfaction + Olfaction + Olfactory + Smell + olfaction + olfactory + The faculty of smell. + Olfaction + + + + + The sense of smell. + NCI-GLOSS + + + + + Olfaction + PT + NCI + + + + + Olfactory + AD + NCI + + + + + Smell + SY + NCI + + + + + olfaction + PT + NCI-GLOSS + CDR0000462691 + + + + + olfactory + PT + NCI-GLOSS + CDR0000462692 + + + + + The faculty of smell. + NCI + + + + + + + + + + + + + + + C17257 + Mental Process + Visual Perception + C0042830 + Visual_Perception + Visual Perception + An individual's interpretation of the visual stimuli in their environment. + Visual Perception + + + + + Visual Perception + PT + NCI + + + + + An individual's interpretation of the visual stimuli in their environment. + NCI + + + + + + + + + C173774 + Organ or Tissue Function + Antibody-Dependent Enhancement of Infection + C0282632 + Antibody-Dependent Enhancement + Antibody-Dependent Enhancement of Infection + A phenomenon that occurs when antibodies present in the body from a primary infection bind to an infecting viral particle during a subsequent infection with a different serotype. The antibodies from the primary infection cannot neutralize the virus. Instead, the Ab-virus complexes attach to Fc receptors on circulating monocytes. The antibodies then facilitate more efficient viral infection of monocytes. The outcome is an increase in the overall replication of the virus and a higher risk of disease that is more severe than the initial infection. + Antibody-Dependent Enhancement of Infection + + + + + Antibody-Dependent Enhancement + SY + NCI + + + + + Antibody-Dependent Enhancement of Infection + PT + NCI + + + + + A phenomenon that occurs when antibodies present in the body from a primary infection bind to an infecting viral particle during a subsequent infection with a different serotype. The antibodies from the primary infection cannot neutralize the virus. Instead, the Ab-virus complexes attach to Fc receptors on circulating monocytes. The antibodies then facilitate more efficient viral infection of monocytes. The outcome is an increase in the overall replication of the virus and a higher risk of disease that is more severe than the initial infection. + NCI + + + + + + + + + C173782 + Organ or Tissue Function + Herd Immunity + C1135927 + Herd Immunity + Immunity (via exposure to a pathogen or via vaccination) for a majority of the individuals in a community that serves to protect a naïve segment of that same population who cannot receive vaccination (contraindicated) and is therefore especially vulnerable to disease. The effect is described by the epidemiological principle that if immunity (via successful vaccination) was delivered at random and if members of a population mixed at random, such that on average each individual contacted R0 individuals in a manner sufficient to transmit the infection, then incidence of the infection would decline if the proportion immune exceeded (R0 - 1)/R0, or 1 -1/R0, where R0 is the basic reproductive number. + Herd Immunity + + + + + Herd Immunity + PT + NCI + + + + + Immunity (via exposure to a pathogen or via vaccination) for a majority of the individuals in a community that serves to protect a naïve segment of that same population who cannot receive vaccination (contraindicated) and is therefore especially vulnerable to disease. The effect is described by the epidemiological principle that if immunity (via successful vaccination) was delivered at random and if members of a population mixed at random, such that on average each individual contacted R0 individuals in a manner sufficient to transmit the infection, then incidence of the infection would decline if the proportion immune exceeded (R0 - 1)/R0, or 1 -1/R0, where R0 is the basic reproductive number. + NCI + + + + + + + + + C17557 + Phenomenon or Process + Apoptosis + C0162638 + CDISC + A form of programmed cell death triggered by internal or external signals that results in a series of characteristic morphological changes. + A type of cell death in which a series of molecular steps in a cell leads to its death. This is the body's normal way of getting rid of unneeded or abnormal cells. The process of programmed cell death may be blocked in cancer cells. + Apoptosis + APOPTOSIS + Apoptosis + Apoptotic Process + PCD + Programmed Cell Death + apoptosis + programmed cell death + A form of programmed cell death that begins when a cell receives internal or external signals, then proceeds through a series of characteristic stages typically including rounding-up of the cell, retraction of pseudopods, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), and plasma membrane blebbing, and ends with the death of the cell. + Important in ontogenesis, tumorigenesis, tissue turnover, lymphocyte selection and function and hormone-induced atrophy. + Apoptosis + + + + + A form of programmed cell death triggered by internal or external signals that results in a series of characteristic morphological changes. + CDISC + + + + + A type of cell death in which a series of molecular steps in a cell leads to its death. This is the body's normal way of getting rid of unneeded or abnormal cells. The process of programmed cell death may be blocked in cancer cells. + NCI-GLOSS + + + + + APOPTOSIS + PT + CDISC + + + + + Apoptosis + PT + NCI + + + + + Apoptotic Process + SY + NCI + + + + + PCD + AB + NCI + + + + + Programmed Cell Death + SY + NCI + + + + + apoptosis + PT + NCI-GLOSS + CDR0000046524 + + + + + programmed cell death + PT + NCI-GLOSS + CDR0000407582 + + + + + A form of programmed cell death that begins when a cell receives internal or external signals, then proceeds through a series of characteristic stages typically including rounding-up of the cell, retraction of pseudopods, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), and plasma membrane blebbing, and ends with the death of the cell. + NCI + + + + + + + + + C176396 + Cell Function + Neuronal Autophagy + CL1642470 + CDISC + A degradative change in neurons that is typically spontaneous, and is characterized by distinct membrane bound pale eosinophilic cytoplasm, dark eosinophilic globular material, and usually occurs with no discernable reaction of surrounding cells and a lack of infiltrating inflammatory cells. + NEURONAL AUTOPHAGY + Neuronal Autophagy + A degradative process in neurons that is typically spontaneous and is characterized by distinct membrane bound pale eosinophilic cytoplasm, dark eosinophilic globular material. It usually occurs with no discernable reaction of surrounding cells and a lack of inflammatory cells. + Neuronal Autophagy + + + + + A degradative change in neurons that is typically spontaneous, and is characterized by distinct membrane bound pale eosinophilic cytoplasm, dark eosinophilic globular material, and usually occurs with no discernable reaction of surrounding cells and a lack of infiltrating inflammatory cells. + CDISC + + + + + NEURONAL AUTOPHAGY + PT + CDISC + + + + + Neuronal Autophagy + PT + NCI + + + + + A degradative process in neurons that is typically spontaneous and is characterized by distinct membrane bound pale eosinophilic cytoplasm, dark eosinophilic globular material. It usually occurs with no discernable reaction of surrounding cells and a lack of inflammatory cells. + NCI + + + + + + + + + + + + + + + C17656 + Cell Function + Clonal Regression + C1516677 + Clonal_Regression + Clonal Regression + A biological process that selectively removes autoantigenic lymphocytes by targeting them for programmed cell death. + Clonal Regression + + + + + Clonal Regression + PT + NCI + + + + + A biological process that selectively removes autoantigenic lymphocytes by targeting them for programmed cell death. + NCI + + + + + + + + + + + + + + + C17662 + Molecular Function + Antigen Processing + C0206430 + Antigen_Processing + Antigen Processing + The process by which foreign molecules are taken up by antigen presenting cells, proteolytically cleaved, and displayed on the cell surface in complex with MHC molecules. + Antigen Processing + + + + + Antigen Processing + PT + NCI + + + + + The process by which foreign molecules are taken up by antigen presenting cells, proteolytically cleaved, and displayed on the cell surface in complex with MHC molecules. + NCI + + + + + + + + + + + + + + + C17663 + Molecular Function + Antigen Presentation + C0206431 + Antigen_Presentation + Antigen Presentation + The event of providing fragments of foreign proteins, including viruses and bacteria, to the helper T cells. The presentation occurs through the display of the fragments of foreign proteins on the surface of the antigen-presenting cells (APC). + Antigen Presentation + + + + + Antigen Presentation + PT + NCI + + + + + The event of providing fragments of foreign proteins, including viruses and bacteria, to the helper T cells. The presentation occurs through the display of the fragments of foreign proteins on the surface of the antigen-presenting cells (APC). + NCI + HIV Glossary; http://aidsinfo.nih.gov + + + + + + + + + + + + + + + C17706 + Cell Function + Anergy + C0206120 + NICHD + Diminished cellular immune responsiveness to one or more antigens. + Anergy + Anergy + Clonal Anergy + Diminished immune responsiveness to specific antigens. Induced or programmed clonal lymphocyte anergy is believed to be the second major mechanism (after clonal deletion) of the development of self tolerance by the immune system. + Anergy + + + + + Diminished cellular immune responsiveness to one or more antigens. + NICHD + + + + + Anergy + PT + NCI + + + + + Anergy + PT + NICHD + + + + + Clonal Anergy + SY + NCI + + + + + Diminished immune responsiveness to specific antigens. Induced or programmed clonal lymphocyte anergy is believed to be the second major mechanism (after clonal deletion) of the development of self tolerance by the immune system. + NCI + + + + + + + + + + + + + + + C17707 + Cell Function + Thrombopoiesis + C0221145 + Thrombopoiesis + Thrombocytopoiesis + Thrombopoiesis + A hematopoietic process that refers to the production of thrombocytes. + Thrombopoiesis + + + + + Thrombocytopoiesis + SY + NCI + + + + + Thrombopoiesis + PT + NCI + + + + + A hematopoietic process that refers to the production of thrombocytes. + NCI + + + + + + + + + + + + + + + C17709 + Cell Function + Cell-Mediated Cytotoxicity + C0301896 + Cell-Mediated_Cytolysis + Cell-Mediated Cytolysis + Cell-Mediated Cytotoxicity + Cell-Mediated Lympholysis + Cellular Cytotoxicity + Cytotoxicity, Immunologic + Lymphocyte Cytotoxicity + Lymphocytotoxicity + Any of the processes involved in cytolysis of a target cell by effector lymphocytes, such as cytotoxic T lymphocytes or NK cells; it may be antibody-dependent or independent. + Cell-Mediated Cytotoxicity + + + + + Cell-Mediated Cytolysis + SY + NCI + + + + + Cell-Mediated Cytotoxicity + PT + NCI + + + + + Cell-Mediated Lympholysis + SY + NCI + + + + + Cellular Cytotoxicity + SY + NCI + + + + + Cytotoxicity, Immunologic + SY + NCI + + + + + Lymphocyte Cytotoxicity + SY + NCI + + + + + Lymphocytotoxicity + SY + NCI + + + + + Any of the processes involved in cytolysis of a target cell by effector lymphocytes, such as cytotoxic T lymphocytes or NK cells; it may be antibody-dependent or independent. + NCI + + + + + + + + + C17712 + Cell or Molecular Dysfunction + Immunologic Tolerance + C0020963 + The failure of the immune system to respond to an antigen that previously caused an immune response. + Immunologic_Tolerance + Immune Tolerance + Immunologic Tolerance + Immunological Tolerance + Self Tolerance + Tolerance + immune system tolerance + An innate tolerance that prevents the body from attacking native proteins and tissue. + Immunologic Tolerance + + + + + The failure of the immune system to respond to an antigen that previously caused an immune response. + NCI-GLOSS + + + + + Immune Tolerance + SY + NCI + + + + + Immunologic Tolerance + PT + NCI + + + + + Immunological Tolerance + SY + NCI + + + + + Self Tolerance + SY + NCI + + + + + Tolerance + SY + NCI + + + + + immune system tolerance + SY + NCI-GLOSS + CDR0000044598 + + + + + An innate tolerance that prevents the body from attacking native proteins and tissue. + NCI + + + + + + + + + C17729 + Phenomenon or Process + Organogenesis + C0242290 + Organogenesis + Organogenesis + Formation of organs during development. + Organogenesis + + + + + Organogenesis + PT + NCI + + + + + Formation of organs during development. + NCI + + + + + + + + + C178241 + Cell + Circulating Endothelial Cell + CL1647988 + CEC + Circulating Endothelial Cell + Circulating Endothelial Cells + An endothelial cell found in the peripheral blood. + Circulating Endothelial Cell + + + + + CEC + SY + NCI + + + + + CEC + SY + caDSR + + + + + Circulating Endothelial Cell + PT + NCI + + + + + Circulating Endothelial Cells + SY + caDSR + + + + + An endothelial cell found in the peripheral blood. + NCI + + + + + + + + C17828 + Biologic Function + Biological Process + C0031845 + Biological_Process + Biological Function + Biological Process + An activity occurring within an organism, between organisms or among organisms and the mechanisms underlying such events. + Biological Process + + + + + Biological Function + SY + NCI + + + + + Biological Process + PT + NCI + + + + + An activity occurring within an organism, between organisms or among organisms and the mechanisms underlying such events. + NCI + + + + + + + + + C17889 + Organ or Tissue Function + Mucosal Immunity + C0282558 + Mucosal_Immunity + Mucosal Immunity + Immunoglobulin A secretion by mucosal epithelia in the gastrointestinal, respiratory, and genitourinary tracts. Mucosal immunity promotes resistance toward bacteria, viruses, and parasites in these ports of entry into the body. + Mucosal Immunity + + + + + Mucosal Immunity + PT + NCI + + + + + Immunoglobulin A secretion by mucosal epithelia in the gastrointestinal, respiratory, and genitourinary tracts. Mucosal immunity promotes resistance toward bacteria, viruses, and parasites in these ports of entry into the body. + NCI + + + + + + + + + + + + + + + C17930 + Organ or Tissue Function + Immune Response Process + C0301872 + The activity of the immune system against foreign substances (antigens). + Immune_Response + Immune Response + Immune Response Process + immune response + Any immune system response of an organisms to an internal or invasive threat. + Immune Response Process + + + + + The activity of the immune system against foreign substances (antigens). + NCI-GLOSS + + + + + Immune Response + SY + NCI + + + + + Immune Response Process + PT + NCI + + + + + immune response + SY + NCI-GLOSS + CDR0000045722 + + + + + Any immune system response of an organisms to an internal or invasive threat. + NCI + + + + + + + + + + + + + + + C17932 + Organism Function + Angiogenic Process + C0302600 + Angiogenesis + Angiogenesis + Angiogenic + Angiogenic Process + A process that results in the development of new blood vessels. + Angiogenic Process + + + + + Angiogenesis + SY + NCI + + + + + Angiogenic + AD + NCI + + + + + Angiogenic Process + PT + NCI + + + + + A process that results in the development of new blood vessels. + NCI + + + + + + + + + C17937 + Cell Function + Immune System Process + C1817756 + Production and action of cells that fight disease or infection. + Immune_Function + Immune Function + Immune Function, Multicellular + Immune System Process + Multicellular Immune Function + immune function + Any multicellular process of immune cells effecting or involved with the immune response or immune maintenance. (NCI) + Immune System Process + + + + + Production and action of cells that fight disease or infection. + NCI-GLOSS + + + + + Immune Function + SY + NCI + + + + + Immune Function, Multicellular + SY + NCI + + + + + Immune System Process + PT + NCI + + + + + Multicellular Immune Function + SY + NCI + + + + + immune function + PT + NCI-GLOSS + CDR0000045721 + + + + + Any multicellular process of immune cells effecting or involved with the immune response or immune maintenance. (NCI) + NCI + + + + + + + + + + + + + + + + + + + + + C18013 + Cell Function + Megakaryocyte Differentiation + C0522310 + Megakaryopoiesis + Megakaryocyte Differentiation + A biological process that refers to the maturation of megakaryocytes and the release of platelets. + Megakaryocyte Differentiation + + + + + Megakaryocyte Differentiation + PT + NCI + + + + + A biological process that refers to the maturation of megakaryocytes and the release of platelets. + NCI + + + + + + + + + + + + + + + C18019 + Cell Function + Leukopoiesis + C0525007 + Leukopoiesis + Leukopoiesis + White Blood Cells/Stem Cells/Leukopoiesis + The hematopoietic process that refers to production of leukocytes in the bone marrow. + Leukopoiesis + + + + + Leukopoiesis + PT + NCI + + + + + White Blood Cells/Stem Cells/Leukopoiesis + SY + NCI + + + + + The hematopoietic process that refers to production of leukocytes in the bone marrow. + NCI + + + + + + + + + + + + + + + C18095 + Organ or Tissue Function + Immunoregulation + C0678889 + Change in the body's immune system, caused by agents that activate or suppress its function. + Immunoregulation + Immunomodulation + Immunoregulation + immunomodulation + Physiologic control of immune function. Includes all levels of regulation from gene expression mechanisms, through cell-cell interactions, to organism-wide responses. + Immunoregulation + + + + + Change in the body's immune system, caused by agents that activate or suppress its function. + NCI-GLOSS + + + + + Immunomodulation + SY + NCI + + + + + Immunoregulation + PT + NCI + + + + + immunomodulation + PT + NCI-GLOSS + CDR0000367426 + + + + + Physiologic control of immune function. Includes all levels of regulation from gene expression mechanisms, through cell-cell interactions, to organism-wide responses. + NCI + + + + + + + + + + + + + + + C18100 + Organ or Tissue Function + Myogenesis + C0596997 + Myogenesis + Myogenesis + Skeletal Muscle Tissue Development + Embryonic formation of muscle cells or fibers. + Myogenesis + + + + + Myogenesis + PT + NCI + + + + + Skeletal Muscle Tissue Development + SY + NCI + + + + + Embryonic formation of muscle cells or fibers. + NCI + + + + + + + + + C18156 + Organ or Tissue Function + Graft-vs-Leukemia Effect + C0600554 + Graft-vs-Leukemia_Effect + GVL + Graft-Versus-Leukemia Effect + Graft-vs-Leukemia Effect + an advantageous side-effect of a graft-vs-host reaction in which a leukemia patient is first irradiated to kill residual leukemic cells and is then given a bone marrow graft to replenish the immune system. If cytotoxic T cells are not depleted from the bone marrow graft, these alloreactive T cells can attack the host's cells (graft-vs-host reaction) but can also attack the host's residual leukemic cells, thereby assisting in preventing recurrence of disease. + Graft-vs-Leukemia Effect + + + + + GVL + SY + NCI + + + + + Graft-Versus-Leukemia Effect + SY + NCI + + + + + Graft-vs-Leukemia Effect + PT + NCI + + + + + an advantageous side-effect of a graft-vs-host reaction in which a leukemia patient is first irradiated to kill residual leukemic cells and is then given a bone marrow graft to replenish the immune system. If cytotoxic T cells are not depleted from the bone marrow graft, these alloreactive T cells can attack the host's cells (graft-vs-host reaction) but can also attack the host's residual leukemic cells, thereby assisting in preventing recurrence of disease. + NCI + + + + + + + + + C18209 + Organ or Tissue Function + Lymph Node Drainage + C1518045 + The flow of lymph from an area of tissue into a particular lymph node. + Lymph_Node_Drainage + Lymph Node Drainage + lymph node drainage + The flow of fluids and lymphocytes in the lymphatic vessels, which are concentrated from tissue fluids, into a particular lymph node. Once the fluid has transited the lymph node, it is returned to the blood via the lymphatic system. + Lymph Node Drainage + + + + + The flow of lymph from an area of tissue into a particular lymph node. + NCI-GLOSS + + + + + Lymph Node Drainage + PT + NCI + + + + + lymph node drainage + SY + NCI-GLOSS + CDR0000045760 + + + + + The flow of fluids and lymphocytes in the lymphatic vessels, which are concentrated from tissue fluids, into a particular lymph node. Once the fluid has transited the lymph node, it is returned to the blood via the lymphatic system. + NCI + + + + + + + + + C18732 + Organism Function + Development + CL448270 + Development-Other + Development + Development, Other + Processes that involve and promote formation of more mature organs, organ systems, or organisms; general development. (NCI) + Development + + + + + Development + PT + NCI + + + + + Development, Other + SY + NCI + + + + + Processes that involve and promote formation of more mature organs, organ systems, or organisms; general development. (NCI) + NCI + + + + + + + + + C187401 + Cell + Antigen-Presenting Cancer-Associated Fibroblast + CL1792115 + Antigen-Presenting Cancer-Associated Fibroblast + MHC II-Positive CAF + apCAF + apCAFs + A cancer-associated fibroblast characterized by novel expression of major histocompatibility complex class II molecules, which are capable of antigen presentation. These cells may mediate immune evasion. + Antigen-Presenting Cancer-Associated Fibroblast + + + + + Antigen-Presenting Cancer-Associated Fibroblast + PT + NCI + + + + + MHC II-Positive CAF + SY + NCI + + + + + apCAF + AB + NCI + + + + + apCAFs + SY + NCI + + + + + A cancer-associated fibroblast characterized by novel expression of major histocompatibility complex class II molecules, which are capable of antigen presentation. These cells may mediate immune evasion. + NCI + + + + + + + + + C18776 + Organ or Tissue Function + Epithelial-Stromal Communication + C1516929 + Epithelial-Stromal_Communication + Epithelial-Stromal Communication + Epithelial-Stromal Interaction + Any process in which stromal cells secrete signaling molecules that are received by epithelial cells. This process is involved in promoting cell growth and differentiation of epithelium. + Epithelial-Stromal Communication + + + + + Epithelial-Stromal Communication + PT + NCI + + + + + Epithelial-Stromal Interaction + SY + NCI + + + + + Any process in which stromal cells secrete signaling molecules that are received by epithelial cells. This process is involved in promoting cell growth and differentiation of epithelium. + NCI + + + + + + + + + C18839 + Organism Function + Host Defense Mechanism + C0520990 + Host_Defense_Mechanism + Host Defense + Host Defense Mechanism + Host Defenses against pathology include physical barriers to pathogens, immediate nonspecific and constitutive (innate) defenses, specific inducible immune responses, metabolic and physiologic homeostatic mechanisms, detoxification, repair processes, and healing mechanisms. + Host Defense Mechanism + + + + + Host Defense + SY + NCI + + + + + Host Defense Mechanism + PT + NCI + + + + + Host Defenses against pathology include physical barriers to pathogens, immediate nonspecific and constitutive (innate) defenses, specific inducible immune responses, metabolic and physiologic homeostatic mechanisms, detoxification, repair processes, and healing mechanisms. + NCI + + + + + + + + + + + + + + + C189807 + Mental Process + Light Perception + CL1798701 + Light Perception + The process by which an organism perceives and interprets light from the environment. + Light Perception + + + + + Light Perception + PT + NCI + + + + + Light Perception + SY + caDSR + + + + + The process by which an organism perceives and interprets light from the environment. + NCI + + + + + + + + + C18992 + Molecular Function + Receptor Signaling + C1514762 + Receptor_Signaling + Receptor Signaling + An intercellular process that involves a cellular receptor binding to a cognate ligand and results in a specific cellular response. + Receptor Signaling + + + + + Receptor Signaling + PT + NCI + + + + + An intercellular process that involves a cellular receptor binding to a cognate ligand and results in a specific cellular response. + NCI + + + + + + + + + + + + + + + C19053 + Cell Function + T-Cell Activation + T-Cell Activation + C1155065 + CTRP + T-Cell_Activation + T Cell Activation + T Lymphocyte Activation + T-Cell Activation + T-Lymphocyte Activation + T-Cell Activation involves stimulation of T lymphocytes by receptor interaction with mitogens or cell surface-displayed antigens resulting in biosynthesis of lymphokines, cell proliferation, cell differentiation, and maturation to support immune activity. + T-Cell Activation + + + + + T Cell Activation + SY + NCI + + + + + T Lymphocyte Activation + SY + NCI + + + + + T-Cell Activation + DN + CTRP + + + + + T-Cell Activation + PT + NCI + + + + + T-Lymphocyte Activation + SY + NCI + + + + + T-Cell Activation involves stimulation of T lymphocytes by receptor interaction with mitogens or cell surface-displayed antigens resulting in biosynthesis of lymphokines, cell proliferation, cell differentiation, and maturation to support immune activity. + NCI + + + + + + + + + C19099 + Phenomenon or Process + Cellular Tumor Suppression + C1516376 + Cellular_Tumor_Suppression + Cellular Tumor Suppression + Multicellular Tumor Suppression + Cellular Tumor Suppression is thought to involve elimination of cells that have undergone malignant transformation by patrolling cytotoxic T cells, NK cells, and macrophages due to recognition of altered cell surface antigens on the cancer cells. + Cellular Tumor Suppression + + + + + Cellular Tumor Suppression + PT + NCI + + + + + Multicellular Tumor Suppression + SY + NCI + + + + + Cellular Tumor Suppression is thought to involve elimination of cells that have undergone malignant transformation by patrolling cytotoxic T cells, NK cells, and macrophages due to recognition of altered cell surface antigens on the cancer cells. + NCI + + + + + + + + + C19143 + Molecular Function + Environment-to-Cell Communication + C1516882 + Environment-to-Cell_Communication + Environment to Cell Communication and Signaling + Environment-to-Cell Communication + Environment-to-Cell Communication and Signaling + Long-Range Cell Communication + Any process by which signals are passed between two distinct cell types over a distance, typically through the circulatory system. This process is employed in most hormone-receptor communication, and is involved in metabolism, immune response, sexual development, behavior, nervous system function, regulation of mood and circadian rhythms, as well as other processes. + Environment-to-Cell Communication + + + + + Environment to Cell Communication and Signaling + SY + NCI + + + + + Environment-to-Cell Communication + PT + NCI + + + + + Environment-to-Cell Communication and Signaling + SY + NCI + + + + + Long-Range Cell Communication + SY + NCI + + + + + Any process by which signals are passed between two distinct cell types over a distance, typically through the circulatory system. This process is employed in most hormone-receptor communication, and is involved in metabolism, immune response, sexual development, behavior, nervous system function, regulation of mood and circadian rhythms, as well as other processes. + NCI + + + + + + + + + C191636 + Therapeutic or Preventive Procedure + Thrombolysis for Pulmonary Embolism + CL1904911 + ACC/AHA + Treatment to remove a blood clot from a pulmonary artery in a patient with acute ischemic stroke + Thrombolysis for Pulmonary Embolism + Thrombolysis for pulmonary embolism + Medical treatment to break up a blood clot from a pulmonary artery in a patient with acute pulmonary embolism. + Thrombolysis for Pulmonary Embolism + + + + + Treatment to remove a blood clot from a pulmonary artery in a patient with acute ischemic stroke + ACC/AHA + SARS2 + + + + + Thrombolysis for Pulmonary Embolism + PT + NCI + + + + + Thrombolysis for pulmonary embolism + PT + ACC/AHA + VAR + SARS2 + + + + + Medical treatment to break up a blood clot from a pulmonary artery in a patient with acute pulmonary embolism. + NCI + + + + + + + + + C191637 + Therapeutic or Preventive Procedure + Thrombolysis for Stroke + CL1904918 + ACC/AHA + Treatment to remove a blood clot from an artery in a patient with acute ischemic stroke + Thrombolysis for Stroke + Thrombolysis for stroke + Medical treatment to break up a blood clot from an artery in a patient with acute ischemic stroke. + Thrombolysis for Stroke + + + + + Treatment to remove a blood clot from an artery in a patient with acute ischemic stroke + ACC/AHA + SARS2 + + + + + Thrombolysis for Stroke + PT + NCI + + + + + Thrombolysis for stroke + PT + ACC/AHA + VAR + SARS2 + + + + + Medical treatment to break up a blood clot from an artery in a patient with acute ischemic stroke. + NCI + + + + + + + + + + + + + + + C19255 + Cell Function + B-Cell Activation + C1155003 + B-Cell_Activation + B-Cell Activation + A set of events occurring in B lymphocytes following stimulation with cognate antigen. Crosslinking the B cell antigen receptor (surface immunoglobulin) leads to increased expression of MHC class II molecules, exit from the resting state (G0) into the G1 phase of the cell cycle, and in the case of a strong antigenic stimulus, proliferation. + B-Cell Activation + + + + + B-Cell Activation + PT + NCI + + + + + A set of events occurring in B lymphocytes following stimulation with cognate antigen. Crosslinking the B cell antigen receptor (surface immunoglobulin) leads to increased expression of MHC class II molecules, exit from the resting state (G0) into the G1 phase of the cell cycle, and in the case of a strong antigenic stimulus, proliferation. + NCI + + + + + + + + + C19266 + Organ or Tissue Function + Immune Surveillance + C0021059 + Immune_Surveillance + Immune Surveillance + Immunological Surveillance + Immune Surveillance refers to processes by which transformed or virally infected cells are eliminated by a normal immune response. + Immune Surveillance + + + + + Immune Surveillance + PT + NCI + + + + + Immunological Surveillance + SY + NCI + + + + + Immune Surveillance refers to processes by which transformed or virally infected cells are eliminated by a normal immune response. + NCI + + + + + + + + + + + + + + + C19369 + Mental Process + Learning + C0023185 + Learning + Learning + The act, process, or experience of gaining knowledge or skill. + Learning + + + + + Learning + PT + NCI + + + + + The act, process, or experience of gaining knowledge or skill. + NCI + + + + + + + + + + + + + + + C19375 + Cell Function + Neural Development + C0814002 + Neural_Development + Neural Development + Neural Growth + Neurogenesis + Neuronal Growth + Neural Development involves proliferation, differentiation, and/or maturation of neural cells. + Neural Development + + + + + Neural Development + PT + NCI + + + + + Neural Growth + SY + NCI + + + + + Neurogenesis + SY + NCI + + + + + Neuronal Growth + SY + NCI + + + + + Neural Development involves proliferation, differentiation, and/or maturation of neural cells. + NCI + + + + + + + + + C19392 + Molecular Function + Carcinogen Resistance + C1516273 + Carcinogen_Resistance + Carcinogen Resistance + The natural or acquired ability of an organism to maintain its immunity to or to resist the effects of a cancer causing agent. + Carcinogen Resistance + + + + + Carcinogen Resistance + PT + NCI + + + + + The natural or acquired ability of an organism to maintain its immunity to or to resist the effects of a cancer causing agent. + NCI + + + + + + + + + C19413 + Organ or Tissue Function + Eye Development + C1517080 + Eye_Development + Eye Development + Human Eye Development involves bilateral outpouchings of optic vesicles, from the neural tube, that each form optic cups. By cell division, migration, differentiation, and synaptogenesis, the inner surface becomes the multi-layer neuroepithelial retina; the outer monolayer becomes the retinal pigment epithelium. Surface membranes cover the eye and develop into the lens, iris and cornea. + Eye Development + + + + + Eye Development + PT + NCI + + + + + Human Eye Development involves bilateral outpouchings of optic vesicles, from the neural tube, that each form optic cups. By cell division, migration, differentiation, and synaptogenesis, the inner surface becomes the multi-layer neuroepithelial retina; the outer monolayer becomes the retinal pigment epithelium. Surface membranes cover the eye and develop into the lens, iris and cornea. + NCI + + + + + + + + + C19443 + Organ or Tissue Function + Lung Development + C1160389 + Lung_Development + Lung Development + For the lung, the act or process of natural progression in physical and physiological maturation from a previous, lower, or embryonic stage to a later, more complex, or adult stage. + Lung Development + + + + + Lung Development + PT + NCI + + + + + For the lung, the act or process of natural progression in physical and physiological maturation from a previous, lower, or embryonic stage to a later, more complex, or adult stage. + NCI + + + + + + + + + C19663 + Cell Function + Cell-Cell Adhesion Process + C2987363 + Cell-Cell_Adhesion + Cell-Cell Adhesion Process + Any cellular process in which one cell attaches to another via cell adhesion molecules. + Cell-Cell Adhesion Process + + + + + Cell-Cell Adhesion Process + PT + NCI + + + + + Any cellular process in which one cell attaches to another via cell adhesion molecules. + NCI + + + + + + + + + C19932 + Phenomenon or Process + Negative Regulation of Apoptosis + C1512772 + Inhibition_of_Apoptosis + Apoptosis Inhibition + Inhibition of Apoptosis + Negative Regulation of Apoptosis + Any cellular process that decreases the frequency, rate or extent of cell death by apoptosis. + Negative Regulation of Apoptosis + + + + + Apoptosis Inhibition + SY + NCI + + + + + Inhibition of Apoptosis + SY + NCI + + + + + Negative Regulation of Apoptosis + PT + NCI + + + + + Any cellular process that decreases the frequency, rate or extent of cell death by apoptosis. + NCI + + + + + + + + + C19940 + Cell Function + NK Cell Activation + C1155064 + NK-Cell_Activation + NK Cell Activation + Natural Killer Cell Activation + NK Cell Activation involves interaction with virus-infected or transformed cells by diverse adhesion or co-stimulatory molecules and release of cytokines, chemokines, and lethal chemicals from granules. + NK Cell Activation + + + + + NK Cell Activation + PT + NCI + + + + + Natural Killer Cell Activation + SY + NCI + + + + + NK Cell Activation involves interaction with virus-infected or transformed cells by diverse adhesion or co-stimulatory molecules and release of cytokines, chemokines, and lethal chemicals from granules. + NCI + + + + + + + + + C19946 + Organ or Tissue Function + Limb Development + C1517884 + Limb_Development + Limb Development + Interdependent positional signaling by the apical ectodermal ridge, the posterior mesenchyme zone of polarizing activity, and the non ridge ectoderm coordinate limb bud outgrowth and patterning, Limb Development, by migrated lateral plate mesoderm and somite cells. Proximal-distal differentiating mesenchymal cells condense to form the limb skeletal primordia. + Limb Development + + + + + Limb Development + PT + NCI + + + + + Interdependent positional signaling by the apical ectodermal ridge, the posterior mesenchyme zone of polarizing activity, and the non ridge ectoderm coordinate limb bud outgrowth and patterning, Limb Development, by migrated lateral plate mesoderm and somite cells. Proximal-distal differentiating mesenchymal cells condense to form the limb skeletal primordia. + NCI + + + + + + + + + C19953 + Organ or Tissue Function + Spleen Development + C1519473 + Spleen_Development + Spleen Development + Human Spleen Development involves formation of the spleen, initially as a long strip of cells adjacent to the forming stomach, from mesoderm in the dorsal mesogastrium. Initially an important organ for hematopoiesis (but lost with development), migration of lymphoid precursor cells into the spleen primordium leads to a gradual conversion of the spleen to an organ of the immune system. + Spleen Development + + + + + Spleen Development + PT + NCI + + + + + Human Spleen Development involves formation of the spleen, initially as a long strip of cells adjacent to the forming stomach, from mesoderm in the dorsal mesogastrium. Initially an important organ for hematopoiesis (but lost with development), migration of lymphoid precursor cells into the spleen primordium leads to a gradual conversion of the spleen to an organ of the immune system. + NCI + + + + + + + + + C19970 + Organ or Tissue Function + Pattern Formation + C1160421 + Pattern_Formation + Pattern Formation + Pattern Formation is a developmental morphogenetic process that establishes basic configurations of cellular organization necessary for further and accurate development of the spatial arrangements of embryonic tissue. + Pattern Formation + + + + + Pattern Formation + PT + NCI + + + + + Pattern Formation + SY + caDSR + + + + + Pattern Formation is a developmental morphogenetic process that establishes basic configurations of cellular organization necessary for further and accurate development of the spatial arrangements of embryonic tissue. + NCI + + + + + + + + + C19971 + Organ or Tissue Function + Dorsal-Ventral Pattern Formation + C1160449 + Dorsal-Ventral_Pattern_Formation + Dorsal-Ventral Pattern Formation + A developmental morphogenetic process that establishes the basic configuration of cellular organization necessary for further and accurate development of the spatial arrangement of embryonic tissue along the dorsal-ventral axis. + Dorsal-Ventral Pattern Formation + + + + + Dorsal-Ventral Pattern Formation + PT + NCI + + + + + A developmental morphogenetic process that establishes the basic configuration of cellular organization necessary for further and accurate development of the spatial arrangement of embryonic tissue along the dorsal-ventral axis. + NCI + + + + + + + + + C19988 + Organism Function + Organismal Process + CL415389 + NICHD + Organismal_Process + Organism-Level Process + Organismal Process + Physiological Process + A biologic function, activity, or process involving either specialized organ functions, individual organs, organ systems, body parts, or whole organisms. + Organismal Process + + + + + Organism-Level Process + SY + NCI + + + + + Organismal Process + PT + NCI + + + + + Organismal Process + PT + NICHD + + + + + Physiological Process + SY + NCI + + + + + A biologic function, activity, or process involving either specialized organ functions, individual organs, organ systems, body parts, or whole organisms. + NCI + + + + + + + + + C19989 + Organ or Tissue Function + Sensation + C1327511 + Sensory_Process + Sensation + Sensory Process + The perceptible result of stimulation of a sense organ, such as touch, temperature, pressure, and pain. + Sensation + + + + + Sensation + PT + NCI + + + + + Sensation + SY + caDSR + + + + + Sensory Process + SY + NCI + + + + + The perceptible result of stimulation of a sense organ, such as touch, temperature, pressure, and pain. + NCI + + + + + + + + + C20138 + Organ or Tissue Function + Skeletal Development + C1160401 + Skeletal_Development + Skeletal Development + Human Skeletal Development involves growth and differentiation of axial, limb, and cranial elements of the skeletal system. Axial vertebrae and ribs derive from cartilage precursors of the paired segmented paraxial mesodermal somite sclerotomes. Interdependent positional signaling by the apical ectodermal ridge, the posterior mesenchyme zone of polarizing activity, and the non ridge ectoderm coordinate limb bud outgrowth and patterning by migrated lateral plate mesoderm and somite cells. Proximal-distal differentiating mesenchymal cells condense to form the limb skeletal primordia. The skull forms by direct ossification of, or cartilage condensation from neural crest-derived, ectomesenchyme. + Skeletal Development + + + + + Skeletal Development + PT + NCI + + + + + Human Skeletal Development involves growth and differentiation of axial, limb, and cranial elements of the skeletal system. Axial vertebrae and ribs derive from cartilage precursors of the paired segmented paraxial mesodermal somite sclerotomes. Interdependent positional signaling by the apical ectodermal ridge, the posterior mesenchyme zone of polarizing activity, and the non ridge ectoderm coordinate limb bud outgrowth and patterning by migrated lateral plate mesoderm and somite cells. Proximal-distal differentiating mesenchymal cells condense to form the limb skeletal primordia. The skull forms by direct ossification of, or cartilage condensation from neural crest-derived, ectomesenchyme. + NCI + + + + + + + + + + + + + + + C20150 + Phenomenon or Process + Positive Regulation of Apoptosis + C1326205 + Induction_of_Apoptosis + Apoptosis Induction + Induction of Apoptosis + Positive Regulation of Apoptosis + Any cellular process that increases the frequency, rate or extent of cell death by apoptosis. + Positive Regulation of Apoptosis + + + + + Apoptosis Induction + SY + NCI + + + + + Induction of Apoptosis + SY + NCI + + + + + Positive Regulation of Apoptosis + PT + NCI + + + + + Any cellular process that increases the frequency, rate or extent of cell death by apoptosis. + NCI + + + + + + + + + + + + + + + C20151 + Organ or Tissue Function + Inflammatory Response + C1155266 + Inflammatory_Response + Inflammation Process + Inflammation Process, Multicellular + Inflammatory Response + A part of innate immunity, the Inflammatory Response occurs when injured tissues induce release of vasodilatory, opsonizing, and chemotactic mediators that attract macrophages and leukocytes to phagocytize and destroy foreign substances; dilate local blood vessels increasing local blood flow; increase capillary permeability; produce edematous swelling; and induce pain. Plasma- and cell-derived inflammatory mediators include Prostaglandins, Leukotrines, Cytokines, Lymphokines, Monokines, PAF, Histamine, Bradykinin, Complement, and Interferons. + Inflammatory Response + + + + + Inflammation Process + SY + NCI + + + + + Inflammation Process, Multicellular + SY + NCI + + + + + Inflammatory Response + PT + NCI + + + + + A part of innate immunity, the Inflammatory Response occurs when injured tissues induce release of vasodilatory, opsonizing, and chemotactic mediators that attract macrophages and leukocytes to phagocytize and destroy foreign substances; dilate local blood vessels increasing local blood flow; increase capillary permeability; produce edematous swelling; and induce pain. Plasma- and cell-derived inflammatory mediators include Prostaglandins, Leukotrines, Cytokines, Lymphokines, Monokines, PAF, Histamine, Bradykinin, Complement, and Interferons. + NCI + + + + + + + + + C20191 + Phenomenon or Process + Cell-Matrix Adhesion Process + CL449027 + Cell-Matrix_Adhesion + Cell Attachment + Cell-Matrix Adhesion Process + Any cellular process in which a cell attaches to the extracellular matrix via adhesion molecules. + Cell-Matrix Adhesion Process + + + + + Cell Attachment + SY + NCI + + + + + Cell-Matrix Adhesion Process + PT + NCI + + + + + Any cellular process in which a cell attaches to the extracellular matrix via adhesion molecules. + NCI + + + + + + + + + C20480 + Cell Function + Cellular Process + C0007613 + Cellular_Process + Cell Function + Cell Process + Cellular Function + Cellular Process + Any process that takes place on the cellular level, though not necessarily restricted to a single cell. + Cellular Process + + + + + Cell Function + SY + NCI + + + + + Cell Process + SY + NCI + + + + + Cellular Function + SY + NCI + + + + + Cellular Process + PT + NCI + + + + + Any process that takes place on the cellular level, though not necessarily restricted to a single cell. + NCI + + + + + + + + + C20620 + Organism Function + Gustation + C0039336 + Gustation + Gustation + Taste + The faculty of taste, distinguishing substances by means of the taste buds. + Gustation + + + + + Gustation + PT + NCI + + + + + Taste + SY + NCI + + + + + The faculty of taste, distinguishing substances by means of the taste buds. + NCI + + + + + + + + + C20624 + Cell Function + Embryonic Induction + C0013947 + Embryonic_Induction + Embryonic Induction + Induction, Embryonic + A process that stimulates and directs a morphogenetic influence on a population of cells. These populations are often differentiating cells or adjacent neighboring cells that are not fixed on a developmental path. Embryonic induction plays a regulatory role in the development and construction of embryos. + Embryonic Induction + + + + + Embryonic Induction + PT + NCI + + + + + Induction, Embryonic + SY + NCI + + + + + A process that stimulates and directs a morphogenetic influence on a population of cells. These populations are often differentiating cells or adjacent neighboring cells that are not fixed on a developmental path. Embryonic induction plays a regulatory role in the development and construction of embryos. + NCI + + + + + + + + + C20914 + Organ or Tissue Function + Uterine Swelling + C1519873 + Uterine_Swelling + Uterine Swelling + With a high concentration of estrogen receptors, the uterus is one of the most sensitive tissues to the hormone and demonstrates two basic responses to estrogen: it swells by influx of water into the lumen of the uterus, and it increases in weight by the growth of the endometrial layer. + Uterine Swelling + + + + + Uterine Swelling + PT + NCI + + + + + With a high concentration of estrogen receptors, the uterus is one of the most sensitive tissues to the hormone and demonstrates two basic responses to estrogen: it swells by influx of water into the lumen of the uterus, and it increases in weight by the growth of the endometrial layer. + NCI + + + + + + + + + C21045 + Physiologic Function + Coagulation Process + C1328723 + Coagulation_Process + Blood Coagulation + Clotting + Coagulation + Coagulation Process + Coagulation-Related Process + Any of the sequential processes by which coagulation factors interact to form a fibrin clot. + Coagulation Process + + + + + Blood Coagulation + SY + NCI + + + + + Clotting + SY + NCI + + + + + Coagulation + SY + NCI + + + + + Coagulation Process + PT + NCI + + + + + Coagulation-Related Process + SY + NCI + + + + + Any of the sequential processes by which coagulation factors interact to form a fibrin clot. + NCI + + + + + + + + + C21074 + Organ or Tissue Function + Neurologic Process + C1518289 + Neurologic_Process + Neurologic Process + A biological function or activity involving the cells or tissue components of the nervous system. + Neurologic Process + + + + + Neurologic Process + PT + NCI + + + + + A biological function or activity involving the cells or tissue components of the nervous system. + NCI + + + + + + + + + C21075 + Physiologic Function + Nociception + C0234194 + Nociception + Nociception + The stimulus-response process involving the stimulation of peripheral pain-carrying nerve fibers (e.g., C-fibers, A-delta fibers) and the transmission of impulses along peripheral nerves of the central nervous system, where the stimulus is perceived as pain. (Taber's) + Nociception + + + + + Nociception + PT + NCI + + + + + The stimulus-response process involving the stimulation of peripheral pain-carrying nerve fibers (e.g., C-fibers, A-delta fibers) and the transmission of impulses along peripheral nerves of the central nervous system, where the stimulus is perceived as pain. (Taber's) + NCI + + + + + + + + + + + + + + + C21077 + Physiologic Function + Nociceptive Reflex + C0277847 + Nociceptive_Reflex + Nociceptive Reflex + A reflex initiated by a painful stimulus. + Nociceptive Reflex + + + + + Nociceptive Reflex + PT + NCI + + + + + A reflex initiated by a painful stimulus. + NCI + + + + + + + + + + + + + + + C21078 + Molecular Function + Nociceptive Stimulus + C1518343 + Nociceptive_Stimulus + Nociceptive Impulse + Nociceptive Stimulus + An impulse that gives rise to sensations of pain. + Nociceptive Stimulus + + + + + Nociceptive Impulse + SY + NCI + + + + + Nociceptive Stimulus + PT + NCI + + + + + An impulse that gives rise to sensations of pain. + NCI + + + + + + + + + C21124 + Organ or Tissue Function + Multicellular Process + C1513731 + Multicellular_Process + Multicellular Process + A biologic function or process involving coordinated groups or populations of single cell types, mixed cell types, or tissues. + Multicellular Process + + + + + Multicellular Process + PT + NCI + + + + + A biologic function or process involving coordinated groups or populations of single cell types, mixed cell types, or tissues. + NCI + + + + + + + + + + + + + + + C21128 + Cell Function + Histogenic Process + C0178679 + Histogenesis + Histiogenic Process + Histogenesis + Histogenic Process + Tissue Development Process + A multicellular process involved in the formation of new, more mature, or differentiated cells or tissues. (NCI) + Histogenic Process + + + + + Histiogenic Process + SY + NCI + + + + + Histogenesis + SY + NCI + + + + + Histogenic Process + PT + NCI + + + + + Tissue Development Process + SY + NCI + + + + + A multicellular process involved in the formation of new, more mature, or differentiated cells or tissues. (NCI) + NCI + + + + + + + + + + + + + + + C21143 + Cell Function + Myelopoiesis + C0525006 + Myelopoiesis + Myelopoiesis + The hematopoietic process that refers to the production of myelocytes. + Myelopoiesis + + + + + Myelopoiesis + PT + NCI + + + + + The hematopoietic process that refers to the production of myelocytes. + NCI + + + + + + + + + C21147 + Organ or Tissue Function + Developmental Process + C1511806 + Developmental_Process + Developmental Process + A process that promotes the formation of new, more mature, or differentiated tissues, organs, or organ systems. May be, and often is, part of general development, but is not restricted to occur only during general development. (NCI) + Developmental Process + + + + + Developmental Process + PT + NCI + + + + + A process that promotes the formation of new, more mature, or differentiated tissues, organs, or organ systems. May be, and often is, part of general development, but is not restricted to occur only during general development. (NCI) + NCI + + + + + + + + + + + + + + + C21519 + Molecular Function + Complement Activation + C0009528 + Complement_Activation + Complement Activation + Any physiologic process in which a protease directs the cleavage of complement components C4, C2, or factor B which then form the C3 and C5 convertases for the classical and lectin pathways, respectively. This process is involved in direct lysis of target cells, immune adherence and phagocytosis of pathogens, and recruitment and activation of immunocompetent cells. + Complement Activation + + + + + Complement Activation + PT + NCI + + + + + Any physiologic process in which a protease directs the cleavage of complement components C4, C2, or factor B which then form the C3 and C5 convertases for the classical and lectin pathways, respectively. This process is involved in direct lysis of target cells, immune adherence and phagocytosis of pathogens, and recruitment and activation of immunocompetent cells. + NCI + + + + + + + + + C21591 + Molecular Function + G Protein-Coupled Receptor Signaling + C1517377 + G_Protein-Coupled_Receptor_Signaling + G Protein Coupled Receptor Signaling + G Protein-Coupled Receptor Signaling + G-Protein Coupled Receptor Signaling + G-Protein-Coupled Receptor Signaling + GPCR Signaling + GPR Signaling + A cellular process that initiates with the binding of a G protein-associated transmembrane receptor to its cognate ligand,and results in a specific cellular response. This process is involved in signaling related to neurotranmission, immune responses, and cellular metabolism, differentiation and proliferation. + G Protein-Coupled Receptor Signaling + + + + + G Protein Coupled Receptor Signaling + SY + NCI + + + + + G Protein-Coupled Receptor Signaling + PT + NCI + + + + + G-Protein Coupled Receptor Signaling + SY + NCI + + + + + G-Protein-Coupled Receptor Signaling + SY + NCI + + + + + GPCR Signaling + SY + NCI + + + + + GPR Signaling + SY + NCI + + + + + A cellular process that initiates with the binding of a G protein-associated transmembrane receptor to its cognate ligand,and results in a specific cellular response. This process is involved in signaling related to neurotranmission, immune responses, and cellular metabolism, differentiation and proliferation. + NCI + + + + + + + + + C25976 + Molecular Function + Cytokine Signaling + C1511617 + Cytokine_Signaling + Cytokine Signal Transduction + Cytokine Signaling + Any environment-to-cell cummunication that involves cytokines. This process is involved in immune function. + Cytokine Signaling + + + + + Cytokine Signal Transduction + SY + NCI + + + + + Cytokine Signaling + PT + NCI + + + + + Any environment-to-cell cummunication that involves cytokines. This process is involved in immune function. + NCI + + + + + + + + + C26011 + Organ or Tissue Function + Antiviral Response + C1155328 + Antiviral_Response + Anti-Viral Response + Antiviral Response + An Antiviral Response is an induced humoral or cell-mediated reaction of the immune system to a viral antigen or infection. + Antiviral Response + + + + + Anti-Viral Response + SY + NCI + + + + + Antiviral Response + PT + NCI + + + + + An Antiviral Response is an induced humoral or cell-mediated reaction of the immune system to a viral antigen or infection. + NCI + + + + + + + + + C26012 + Organ or Tissue Function + Antibacterial Response + C1516002 + Antibacterial_Response + Anti-Bacterial Response + Antibacterial Response + An Antibacterial Response is an induced humoral or cell-mediated reaction of the immune system to a bacterial antigen or infection. + Antibacterial Response + + + + + Anti-Bacterial Response + SY + NCI + + + + + Antibacterial Response + PT + NCI + + + + + An Antibacterial Response is an induced humoral or cell-mediated reaction of the immune system to a bacterial antigen or infection. + NCI + + + + + + + + + C26044 + Molecular Function + Negative Regulation of Angiogenesis + C1510884 + Angiogenic_Inhibition + Angiogenesis Inhibition + Angiogenic Inhibition + Negative Regulation of Angiogenesis + Processes and mechanisms that block angiogenesis. + Negative Regulation of Angiogenesis + + + + + Angiogenesis Inhibition + SY + NCI + + + + + Angiogenic Inhibition + SY + NCI + + + + + Negative Regulation of Angiogenesis + PT + NCI + + + + + Processes and mechanisms that block angiogenesis. + NCI + + + + + + + + + + + + + + + C26080 + Cell Function + Granulopoiesis + C0302090 + Granulopoiesis + Granulopoiesis + The hematopoietic process that refers to the production of granulocytes. + Granulopoiesis + + + + + Granulopoiesis + PT + NCI + + + + + The hematopoietic process that refers to the production of granulocytes. + NCI + + + + + + + + + C26161 + Organ or Tissue Function + Nervous System Development + C0598282 + Nervous_System_Development + Nervous System Development + Human Nervous System Development begins by differentiation of gastrula ectodermal cells into the neural plate, induced by signals from the mesoderm. Further development of this primordium forms the neural crest and neural tube. Neural crest cells become the peripheral nervous system while the neural tube forms the central nervous system. Cells in both structures differentiate into various glial cells and immature neurons that migrate; differentiate axons, dendrites, and synapses; and mature. + Nervous System Development + + + + + Nervous System Development + PT + NCI + + + + + Human Nervous System Development begins by differentiation of gastrula ectodermal cells into the neural plate, induced by signals from the mesoderm. Further development of this primordium forms the neural crest and neural tube. Neural crest cells become the peripheral nervous system while the neural tube forms the central nervous system. Cells in both structures differentiate into various glial cells and immature neurons that migrate; differentiate axons, dendrites, and synapses; and mature. + NCI + + + + + + + + + + + + + + + C26280 + Cell Function + Immune Cell Activation Process + C1155000 + Immune_Cell_Activation + Immune Cell Activation + Immune Cell Activation Process + Immune Cell Activation involves cell interaction and cell signaling mechanisms that recognize or respond to the presence of foreign antigen and that induce responsive cells of the immune system to synthesize and secrete defensive products, to proliferate, to differentiate, or to attack the sources of foreign antigens. + Immune Cell Activation Process + + + + + Immune Cell Activation + SY + NCI + + + + + Immune Cell Activation Process + PT + NCI + + + + + Immune Cell Activation involves cell interaction and cell signaling mechanisms that recognize or respond to the presence of foreign antigen and that induce responsive cells of the immune system to synthesize and secrete defensive products, to proliferate, to differentiate, or to attack the sources of foreign antigens. + NCI + + + + + + + + + C26281 + Cell Function + Neutrophil Activation + C0242599 + Neutrophil_Activation + Neutrophil Activation + Neutrophil Activation involves cell interaction and cell signaling mechanisms that recognize or respond to the presence of foreign antigen and that stimulate phagocytosis, degranulation, or generation of reactive oxygen products by neutrophils to destroy invading pathogens or to induce acute inflammatory reactions. + Neutrophil Activation + + + + + Neutrophil Activation + PT + NCI + + + + + Neutrophil Activation involves cell interaction and cell signaling mechanisms that recognize or respond to the presence of foreign antigen and that stimulate phagocytosis, degranulation, or generation of reactive oxygen products by neutrophils to destroy invading pathogens or to induce acute inflammatory reactions. + NCI + + + + + + + + + C26440 + Mental Process + Conation + CL448501 + Conation + Conation + The conscious tendency to act, usually an aspect of mental process. + Conation + + + + + Conation + PT + NCI + + + + + The conscious tendency to act, usually an aspect of mental process. + NCI + + + + + + + + + C26555 + Molecular Function + Generation of Antibody Diversity + C1517502 + Generation_of_Antibody_Diversity + Generation of Antibody Diversity + Generation of Antibody Diversity during B-lymphocyte development results from a cascade of temporally ordered random gene shuffling translocations by a recombinase that join any one of multiple alternative discrete V, D, and J (heavy chain) or V and J (light chain) antibody gene variable region DNA coding segments that produce in each B-lymphocyte an antibody with a unique antigen binding region composed of a heavy and a light protein chain. In addition, splicing inaccuracies or insertion of additional nucleotides at the segment junctions generate further junctional diversity and somatic hypermutation of V regions, as B-lymphocytes proliferate, create better fitting antigen-binding sites. + Generation of Antibody Diversity + + + + + Generation of Antibody Diversity + PT + NCI + + + + + Generation of Antibody Diversity during B-lymphocyte development results from a cascade of temporally ordered random gene shuffling translocations by a recombinase that join any one of multiple alternative discrete V, D, and J (heavy chain) or V and J (light chain) antibody gene variable region DNA coding segments that produce in each B-lymphocyte an antibody with a unique antigen binding region composed of a heavy and a light protein chain. In addition, splicing inaccuracies or insertion of additional nucleotides at the segment junctions generate further junctional diversity and somatic hypermutation of V regions, as B-lymphocytes proliferate, create better fitting antigen-binding sites. + NCI + + + + + + + + + C28294 + Activity + Nutrition + C1442959 + NICHD + The taking in and use of food and other nourishing material by the body. Nutrition is a 3-part process. First, food or drink is consumed. Second, the body breaks down the food or drink into nutrients. Third, the nutrients travel through the bloodstream to different parts of the body where they are used as "fuel" and for many other purposes. To give the body proper nutrition, a person has to eat and drink enough of the foods that contain key nutrients. + Nutrition + Nutrition + nutrition + That which is consumed to fuel necessary life processes of an organism. + Nutrition + + + + + The taking in and use of food and other nourishing material by the body. Nutrition is a 3-part process. First, food or drink is consumed. Second, the body breaks down the food or drink into nutrients. Third, the nutrients travel through the bloodstream to different parts of the body where they are used as "fuel" and for many other purposes. To give the body proper nutrition, a person has to eat and drink enough of the foods that contain key nutrients. + NCI-GLOSS + + + + + Nutrition + PT + NCI + + + + + Nutrition + PT + NICHD + + + + + nutrition + PT + NCI-GLOSS + CDR0000044698 + + + + + That which is consumed to fuel necessary life processes of an organism. + NCI + + + + + + + + + C28491 + Cell Function + Cellular Infiltration + C1516369 + Cellular_Infiltration + Cellular Infiltration + Normal or pathologic migration and accumulation of cells within tissues. + Cellular Infiltration + + + + + Cellular Infiltration + PT + NCI + + + + + Normal or pathologic migration and accumulation of cells within tissues. + NCI + + + + + + + + + + + + + + + + + + + + + + + + + + + C28495 + Mental Process + Motivation + C0026605 + Motivation + Motivation + Motive + The psychological feature that arouses an organism to action toward a desired goal; the reason for the action; that which gives purpose and direction to behavior. + Motivation + + + + + Motivation + PT + NCI + + + + + Motive + SY + NCI + + + + + The psychological feature that arouses an organism to action toward a desired goal; the reason for the action; that which gives purpose and direction to behavior. + NCI + + + + + + + + + C28631 + Organ or Tissue Function + Antitumor Response + C1516031 + Antitumor_Response + Antitumor Response + An antitumor response involves destruction of cancer tumor cells primarily by activated T-cells induced to react to antigens recognized as foreign and expressed by the transformed cells. + Antitumor Response + + + + + Antitumor Response + PT + NCI + + + + + An antitumor response involves destruction of cancer tumor cells primarily by activated T-cells induced to react to antigens recognized as foreign and expressed by the transformed cells. + NCI + + + + + + + + + C28754 + Cell Function + Innate Bone Remodeling + C1512778 + Innate_Bone_Remodeling + Biological Bone Remodeling + Innate Bone Remodeling + Normal Bone Remodeling + Innate Bone Remodeling takes place in the adult skeleton at discrete foci. The continuous turnover of bone matrix and mineral that involves first, an increase in bone resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). This process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of two contrasting events, bone resorption and bone formation, results in many of the metabolic bone diseases, such as OSTEOPOROSIS. + Innate Bone Remodeling + + + + + Biological Bone Remodeling + SY + NCI + + + + + Innate Bone Remodeling + PT + NCI + + + + + Normal Bone Remodeling + SY + NCI + + + + + Innate Bone Remodeling takes place in the adult skeleton at discrete foci. The continuous turnover of bone matrix and mineral that involves first, an increase in bone resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). This process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of two contrasting events, bone resorption and bone formation, results in many of the metabolic bone diseases, such as OSTEOPOROSIS. + NCI + + + + + + + + + C30085 + Cell Function + Muscle Contraction + C0026820 + Muscle_Contraction + Contractile + Muscle Cell Contraction + Muscle Contraction + The process where thick (myosin) and thin (actin) filaments slide against each other to produce a shortening or tensing of the muscle cell or fiber. + Muscle Contraction + + + + + Contractile + AD + NCI + + + + + Muscle Cell Contraction + SY + NCI + + + + + Muscle Contraction + PT + NCI + + + + + The process where thick (myosin) and thin (actin) filaments slide against each other to produce a shortening or tensing of the muscle cell or fiber. + NCI + + + + + + + + + C30095 + Cell Function + Cardiac Muscle Contraction + C1516294 + Cardiac_Muscle_Contraction + Cardiac Muscle Contraction + Driven primarily by voltage-gated Ca+2 action potentials originating in sinoatrial pace-maker cells, Cardiac Muscle Contraction involves shortening of the gap junction-linked nonsyncytial striated heart myocytes in the atrial and ventricular chambers that forces movement of the blood through the circulatory system. + Cardiac Muscle Contraction + + + + + Cardiac Muscle Contraction + PT + NCI + + + + + Driven primarily by voltage-gated Ca+2 action potentials originating in sinoatrial pace-maker cells, Cardiac Muscle Contraction involves shortening of the gap junction-linked nonsyncytial striated heart myocytes in the atrial and ventricular chambers that forces movement of the blood through the circulatory system. + NCI + + + + + + + + + C3475 + Organ or Tissue Function + Bone Remodeling + C0085268 + Bone_Remodeling + Bone Remodeling + A concomitant process in which old bone is resorbed and new bone is formed. Bone remodeling occurs primarily in bone and involves two types of cells, osteoblasts and osteoclasts. Osteoblasts synthesize bone matrix and form new bone while osteoclasts digest mineral matrix and old bone. + Bone Remodeling + + + + + Bone Remodeling + PT + NCI + + + + + A concomitant process in which old bone is resorbed and new bone is formed. Bone remodeling occurs primarily in bone and involves two types of cells, osteoblasts and osteoclasts. Osteoblasts synthesize bone matrix and form new bone while osteoclasts digest mineral matrix and old bone. + NCI + + + + + + + + + C36731 + Cell + Gaucher Cell + C0333837 + Guacher_s_Cell + Gaucher Cell + Gaucher's Cell + Gaucher Cell + + + + + Gaucher Cell + PT + NCI + + + + + Gaucher's Cell + SY + NCI + + + + + + + + + C36745 + Cell + Abnormal Epithelial Cell + C1510721 + Abnormal_Epithelial_Cell + Abnormal Epithelial Cell + An epithelial cell that occurs in human disease or in models of human disease. + Abnormal Epithelial Cell + + + + + Abnormal Epithelial Cell + PT + NCI + + + + + An epithelial cell that occurs in human disease or in models of human disease. + NCI + + + + + + + + + + C36746 + Cell + Dyskeratotic Keratinocyte + C1512099 + Dyskeratotic_Keratinocyte + Dyskeratotic Keratinocyte + Dyskeratotic Keratinocyte + + + + + Dyskeratotic Keratinocyte + PT + NCI + + + + + + + + + C36747 + Cell + Acantholytic Keratinocyte + C1510753 + Acantholytic_Keratinocyte + Acantholytic Keratinocyte + Acantholytic Keratinocyte + + + + + Acantholytic Keratinocyte + PT + NCI + + + + + + + + + C36751 + Cell + Balloon Epithelial Cell + C1511043 + Balloon_Epithelial_Cell + Balloon Epithelial Cell + Balloon Epithelial Cell + + + + + Balloon Epithelial Cell + PT + NCI + + + + + + + + + C36764 + Cell + Abnormal Glandular Cell + C1510724 + Abnormal_Glandular_Cell + Abnormal Glandular Cell + Abnormal Glandular Cell + + + + + Abnormal Glandular Cell + PT + NCI + + + + + + + + + C36766 + Cell + Abnormal Keratinocyte + C1510728 + Abnormal_Keratinocyte + Abnormal Keratinocyte + Abnormal Keratinocyte + + + + + Abnormal Keratinocyte + PT + NCI + + + + + + + + + C36772 + Cell + Abnormal Squamous Cell + C1510734 + Abnormal_Squamous_Cell + Abnormal Squamous Cell + Abnormal Squamous Cell + + + + + Abnormal Squamous Cell + PT + NCI + + + + + + + + + + C36785 + Cell + Atypical Reparative Cell + C1510963 + Atypical_Reparative_Cell + ARC + Atypical Reparative Cell + Atypical Reparative Cell + + + + + ARC + AB + NCI + + + + + Atypical Reparative Cell + PT + NCI + + + + + + + + + C36787 + Cell + Atypical Parabasal Cell + C1510962 + Atypical_Parabasal_Cell + Atypical Parabasal Cell + Atypical Parabasal Cell + + + + + Atypical Parabasal Cell + PT + NCI + + + + + + + + + C36808 + Cell + Koilocytotic Squamous Cell + C1517678 + Koilocytotic_Squamous_Cell + Koilocyte + Koilocytotic Squamous Cell + Koilocytotic Squamous Cell + + + + + Koilocyte + SY + NCI + + + + + Koilocytotic Squamous Cell + PT + NCI + + + + + + + + + C36809 + Cell + Reactive Epithelial Cell + C1514736 + Reactive_Epithelial_Cell + Reactive Epithelial Cell + Reactive Epithelial Cell + + + + + Reactive Epithelial Cell + PT + NCI + + + + + + + + + + C36810 + Cell + Reactive Squamous Cell + C1514741 + Reactive_Squamous_Cell + Reactive Squamous Cell + Reactive Squamous Cell + + + + + Reactive Squamous Cell + PT + NCI + + + + + + + + + + C36811 + Cell + Reactive Glandular Cell + C1514738 + Reactive_Glandular_Cell + Reactive Glandular Cell + Reactive Glandular Cell + + + + + Reactive Glandular Cell + PT + NCI + + + + + + + + + C36832 + Cell + Abnormal Macrophage + C1265916 + Abnormal_Macrophage + Abnormal Macrophage + Abnormal Macrophage + + + + + Abnormal Macrophage + PT + NCI + + + + + + + + + C36843 + Cell + Abnormal Connective and Soft Tissue Cell + C1510716 + Abnormal_Connective_and_Soft_Tissue_Cell + Abnormal Connective and Soft Tissue Cell + Abnormal Connective and Soft Tissue Cell + + + + + Abnormal Connective and Soft Tissue Cell + PT + NCI + + + + + + + + + C36847 + Cell + Hemosiderin-Laden Macrophage + C0333633 + Hemosiderin-Laden_Macrophage + Hemosiderin-Laden Macrophage + Hemosiderin-Laden Macrophage + + + + + Hemosiderin-Laden Macrophage + PT + NCI + + + + + + + + + C36883 + Cell + Atypical Ductal Epithelial Cell + C1516091 + Atypical_Ductal_Epithelial_Cell + Atypical Ductal Epithelial Cell + Atypical Ductal Epithelial Cell + + + + + Atypical Ductal Epithelial Cell + PT + NCI + + + + + + + + + C36885 + Cell + Atypical Lobular Epithelial Cell + C1510958 + Atypical_Lobular_Epithelial_Cell + Atypical Lobular Epithelial Cell + Atypical Lobular Epithelial Cell + + + + + Atypical Lobular Epithelial Cell + PT + NCI + + + + + + + + + + C36912 + Cell + Atypical Glandular Cell + C1455888 + A term used to describe abnormal cells that come from inside the cervix or from the lining of the uterus. These abnormal cells are found in a small number of Pap smears (a procedure used to detect cervical cancer) and may be a sign of more serious lesions or cancer. + Atypical_Glandular_Cell + AGC + Atypical Glandular Cell + Atypical Glandular Cell, NOS + Atypical Glandular Cell, Not Otherwise Specified + atypical glandular cell + An abnormal endocervical or endometrial cell found in a cervical smear, not further characterized as neoplastic or non-neoplastic. It is often associated with clinically significant uterine lesions. + Atypical Glandular Cell + + + + + A term used to describe abnormal cells that come from inside the cervix or from the lining of the uterus. These abnormal cells are found in a small number of Pap smears (a procedure used to detect cervical cancer) and may be a sign of more serious lesions or cancer. + NCI-GLOSS + + + + + AGC + PT + NCI-GLOSS + CDR0000659608 + + + + + Atypical Glandular Cell + PT + NCI + + + + + Atypical Glandular Cell, NOS + SY + NCI + + + + + Atypical Glandular Cell, Not Otherwise Specified + SY + NCI + + + + + atypical glandular cell + PT + NCI-GLOSS + CDR0000659607 + + + + + An abnormal endocervical or endometrial cell found in a cervical smear, not further characterized as neoplastic or non-neoplastic. It is often associated with clinically significant uterine lesions. + NCI + + + + + + + + + + C36913 + Cell + Atypical Squamous Cell + C1510965 + Atypical_Squamous_Cell + Atypical Squamous Cell + Atypical Squamous Cell + + + + + Atypical Squamous Cell + PT + NCI + + + + + + + + + C36914 + Cell + Atypical Epithelial Cell + C1516093 + Atypical_Epithelial_Cell + Atypical Epithelial Cell + Atypical Epithelial Cell + + + + + Atypical Epithelial Cell + PT + NCI + + + + + + + + + C37086 + Cell + Abnormal Endothelial Cell + C1510719 + Abnormal_Endothelial_Cell + Abnormal Endothelial Cell + Abnormal Endothelial Cell + + + + + Abnormal Endothelial Cell + PT + NCI + + + + + + + + + C37087 + Cell + Atypical Endothelial Cell + C1516092 + Atypical_Endothelial_Cell + Atypical Endothelial Cell + Atypical Endothelial Cell + + + + + Atypical Endothelial Cell + PT + NCI + + + + + + + + + C37255 + Cell + Atypical Squamous Cell, cannot exclude a High Grade Lesion + C1510966 + Atypical_Squamous_Cell_cannot_exclude_a_High_Grade_Lesion + ASC-H + Atypical Squamous Cell, cannot exclude a High Grade Lesion + Atypical Squamous Cell, cannot exclude a High Grade Lesion + + + + + ASC-H + AB + NCI + + + + + Atypical Squamous Cell, cannot exclude a High Grade Lesion + PT + NCI + + + + + + + + + C37929 + Conceptual Entity + Consciousness + C0234421 + Consciousness + Conscious + Consciousness + The state of being alert, oriented, and responsive to the environment. + Consciousness + + + + + Conscious + AD + NCI + + + + + Consciousness + PT + NCI + + + + + The state of being alert, oriented, and responsive to the environment. + NCI + + + + + + + + + C37992 + Mental Process + Memory + C0025260 + Memory + Memory + The power of retaining and recalling past experience, something that is remembered. + Memory + + + + + Memory + PT + NCI + + + + + The power of retaining and recalling past experience, something that is remembered. + NCI + + + + + + + + + C38533 + Organism Function + Sight + C0042789 + Sight + Ocular + Sight + Vision + The faculty of vision, the perception of objects by the eye. + Sight + + + + + Ocular + SY + NCI + + + + + Sight + PT + NCI + + + + + Sight + SY + caDSR + + + + + Vision + SY + NCI + + + + + The faculty of vision, the perception of objects by the eye. + NCI + + + + + + + + + C38535 + Organism Function + Touch + C0702221 + Touch + Touch + The faculty of touch, the sensation produced by pressure receptors in the skin. + Touch + + + + + Touch + PT + NCI + + + + + The faculty of touch, the sensation produced by pressure receptors in the skin. + NCI + + + + + + + + + C39665 + Cell + Tzanck Cell + C1519737 + Tzanck_Cell + Acantholytic Rounded Squamous Cell + Tzanck Cell + Tzanck Cell + + + + + Acantholytic Rounded Squamous Cell + SY + NCI + + + + + Tzanck Cell + PT + NCI + + + + + + + + + C39667 + Cell + Dyskeratotic Cell + C1512098 + Dyskeratotic_Cell + Dyskeratotic Cell + Dyskeratotic Cell + + + + + Dyskeratotic Cell + PT + NCI + + + + + + + + + C40579 + Physiologic Function + Growth Factor Inhibition + C1512280 + Growth_Factor_Inhibition + Growth Factor Inhibition + Growth Factor Inhibition involves interference with, or restraint of, the activities of extracellular signaling molecules (ligands) involved in the control of target cell proliferation, survival, and differentiation. Inhibition may involve interference with growth factor binding to receptors. + Growth Factor Inhibition + + + + + Growth Factor Inhibition + PT + NCI + + + + + Growth Factor Inhibition involves interference with, or restraint of, the activities of extracellular signaling molecules (ligands) involved in the control of target cell proliferation, survival, and differentiation. Inhibition may involve interference with growth factor binding to receptors. + NCI + + + + + + + + + C40584 + Physiologic Function + Cytokine Signaling Process + C1511613 + Cytokine_Activation + Cytokine Activation + Cytokine Signaling Process + Any process which promotes expression of cytokine proteins, their subsequent secretion, binding to their cognate receptors or intracellular signaling, and results in functional responses in the immune system. This process is involved in regulating active populations of specific immune cell types, as well as coordinating systemic responses to pathogenic infection. + Cytokine Signaling Process + + + + + Cytokine Activation + SY + NCI + + + + + Cytokine Signaling Process + PT + NCI + + + + + Any process which promotes expression of cytokine proteins, their subsequent secretion, binding to their cognate receptors or intracellular signaling, and results in functional responses in the immune system. This process is involved in regulating active populations of specific immune cell types, as well as coordinating systemic responses to pathogenic infection. + NCI + + + + + + + + + C40585 + Physiologic Function + Colony Stimulating Factor Signaling Process + C1516703 + Colony_Stimulating_Factor_Activation + Colony Stimulating Factor Activation + Colony Stimulating Factor Signaling Process + Any process which promotes expression of colony stimulating factors, their subsequent secretion, binding to their cognate receptors or intracellular signaling, and results in proliferation and differentiation of the target cell. This process is involved in regulating active populations of macrophages, granulocytes and myeloid cells. + Colony Stimulating Factor Signaling Process + + + + + Colony Stimulating Factor Activation + SY + NCI + + + + + Colony Stimulating Factor Signaling Process + PT + NCI + + + + + Any process which promotes expression of colony stimulating factors, their subsequent secretion, binding to their cognate receptors or intracellular signaling, and results in proliferation and differentiation of the target cell. This process is involved in regulating active populations of macrophages, granulocytes and myeloid cells. + NCI + + + + + + + + + C40586 + Physiologic Function + Interferon Signaling Process + C1512827 + Interferon_Activation + Interferon Activation + Interferon Signaling Process + Any process which promotes expression of the interferon proteins, their subsequent secretion, binding to cognate receptors or intracellular signaling, and promotes antigen presentation by T lymphocytes, interference with viral replication, and activation of NK cells and macrophages. This process is involved in modulating functions of the immune system. + Interferon Signaling Process + + + + + Interferon Activation + SY + NCI + + + + + Interferon Signaling Process + PT + NCI + + + + + Any process which promotes expression of the interferon proteins, their subsequent secretion, binding to cognate receptors or intracellular signaling, and promotes antigen presentation by T lymphocytes, interference with viral replication, and activation of NK cells and macrophages. This process is involved in modulating functions of the immune system. + NCI + + + + + + + + + C40588 + Physiologic Function + Interleukin Signaling Process + C1512853 + Interleukin_Activation + Interleukin Activation + Interleukin Signaling Process + Any process which promotes expression of the interleukin proteins, their secretion, receptor binding or intracellular signaling, and promotes proliferation and differentiation among target populations, inflammation, chemotaxis, production of antibodies and modulation of further cytokine expression. This process is involved in regulating active populations of leukocytes and coordinating systemic responses to pathogenic infection. + Interleukin Signaling Process + + + + + Interleukin Activation + SY + NCI + + + + + Interleukin Signaling Process + PT + NCI + + + + + Any process which promotes expression of the interleukin proteins, their secretion, receptor binding or intracellular signaling, and promotes proliferation and differentiation among target populations, inflammation, chemotaxis, production of antibodies and modulation of further cytokine expression. This process is involved in regulating active populations of leukocytes and coordinating systemic responses to pathogenic infection. + NCI + + + + + + + + + C40589 + Physiologic Function + Tumor Necrosis Factor Signaling Process + C1519684 + Tumor_Necrosis_Factor_Activation + Tumor Necrosis Factor Activation + Tumor Necrosis Factor Signaling Process + Any process which promotes expression of tumor necrosis factors, their subsequent secretion, binding to cognate receptors and intracellular signaling, and results in promoting insulin resistance, fever and macrophage phagocytosis, stimulating the hypothalmic-pituitary-adrenal axis and acute phase responses, and suppressing appetite. This process is involved in coordinating systemic responses to pathogenic infection. + Tumor Necrosis Factor Signaling Process + + + + + Tumor Necrosis Factor Activation + SY + NCI + + + + + Tumor Necrosis Factor Signaling Process + PT + NCI + + + + + Any process which promotes expression of tumor necrosis factors, their subsequent secretion, binding to cognate receptors and intracellular signaling, and results in promoting insulin resistance, fever and macrophage phagocytosis, stimulating the hypothalmic-pituitary-adrenal axis and acute phase responses, and suppressing appetite. This process is involved in coordinating systemic responses to pathogenic infection. + NCI + + + + + + + + + C40592 + Physiologic Function + Platelet Activating Factor Signaling Process + C1514154 + Platelet_Activating_Factor_Activation + Platelet Activating Factor Activation + Platelet Activating Factor Signaling Process + Any process which promotes degranulation of platelets and release of platelet-activating factor into the plasma, resulting in signaling through the G protein-coupled platelet-activating factor receptor and aggregation of platelets. This process is involved in platelet aggregation, inflammation and anaphylaxis. + Platelet Activating Factor Signaling Process + + + + + Platelet Activating Factor Activation + SY + NCI + + + + + Platelet Activating Factor Signaling Process + PT + NCI + + + + + Any process which promotes degranulation of platelets and release of platelet-activating factor into the plasma, resulting in signaling through the G protein-coupled platelet-activating factor receptor and aggregation of platelets. This process is involved in platelet aggregation, inflammation and anaphylaxis. + NCI + + + + + + + + + C40595 + Physiologic Function + Negative Regulation of Complement Activation + C1516746 + Complement_Suppression + Complement Suppression + Negative Regulation of Complement Activation + Any physiologic process in which the C3 and C5 convertases are disassembled or proteolytically inactivated, limiting the persistence of convertase activity. This process is involved in regulating the extent of action of the complement system. + Negative Regulation of Complement Activation + + + + + Complement Suppression + SY + NCI + + + + + Negative Regulation of Complement Activation + PT + NCI + + + + + Any physiologic process in which the C3 and C5 convertases are disassembled or proteolytically inactivated, limiting the persistence of convertase activity. This process is involved in regulating the extent of action of the complement system. + NCI + + + + + + + + + C40597 + Physiologic Function + Colony Stimulating Factor Suppression + C1516704 + Colony_Stimulating_Factor_Suppression + Colony Stimulating Factor Suppression + Negative Regulation of Colony Stimulating Factor Signaling + Any physiologic process which occurs in response to ligation of a colony stimulating factor receptor with a cognate ligand, and results in a reduced number of active signaling molecules within the target cell. This process is involved in regulating the extent of the response to receptor binding, and in regulating active populations of macrophages, granulocytes and myeloid cells. + Colony Stimulating Factor Suppression + + + + + Colony Stimulating Factor Suppression + PT + NCI + + + + + Negative Regulation of Colony Stimulating Factor Signaling + SY + NCI + + + + + Any physiologic process which occurs in response to ligation of a colony stimulating factor receptor with a cognate ligand, and results in a reduced number of active signaling molecules within the target cell. This process is involved in regulating the extent of the response to receptor binding, and in regulating active populations of macrophages, granulocytes and myeloid cells. + NCI + + + + + + + + + C40599 + Physiologic Function + Negative Regulation of Interleukin Signaling + C1512854 + Interleukin_Suppression + Interleukin Suppression + Negative Regulation of Interleukin Signaling + Any physiologic process which occurs in response to ligation of an interleukin receptor with a cognate ligand, and results in a reduced number of active signaling molecules within the target cell. This process is involved in regulating the extent of the extent of the response to receptor binding, and in regulating active populations of T, B and hemopoietic cells. + Negative Regulation of Interleukin Signaling + + + + + Interleukin Suppression + SY + NCI + + + + + Negative Regulation of Interleukin Signaling + PT + NCI + + + + + Any physiologic process which occurs in response to ligation of an interleukin receptor with a cognate ligand, and results in a reduced number of active signaling molecules within the target cell. This process is involved in regulating the extent of the extent of the response to receptor binding, and in regulating active populations of T, B and hemopoietic cells. + NCI + + + + + + + + + C40604 + Physiologic Function + Negative Regulation of Platelet Activating Factor Signaling + C1514157 + Platelet_Activating_Factor_Suppression + Negative Regulation of Platelet Activating Factor Signaling + Platelet Activating Factor Suppression + Any physiologic process which occurs in response to ligation of the platelet activating factor receptor, and results in a reduced number of active signaling molecules within the target cell. This process is involved in regulating the extent of platelet aggregation, inflammation and anaphylaxis. + Negative Regulation of Platelet Activating Factor Signaling + + + + + Negative Regulation of Platelet Activating Factor Signaling + PT + NCI + + + + + Platelet Activating Factor Suppression + SY + NCI + + + + + Any physiologic process which occurs in response to ligation of the platelet activating factor receptor, and results in a reduced number of active signaling molecules within the target cell. This process is involved in regulating the extent of platelet aggregation, inflammation and anaphylaxis. + NCI + + + + + + + + + C40695 + Phenomenon or Process + Adhesion Factor Production + C1510805 + Adhesion_Factor_Production + Adhesion Factor Production + Any cellular process that results in the elaboration of adhesion molecules on the cell surface. + Adhesion factor production can alter maintenance of tissue integration, wound healing, cellular migrations, and metastasis. + Adhesion Factor Production + + + + + Adhesion Factor Production + PT + NCI + + + + + Any cellular process that results in the elaboration of adhesion molecules on the cell surface. + NCI + + + + + + + + + C40698 + Phenomenon or Process + Adhesion Factor Suppression + C1510807 + Adhesion_Factor_Suppression + Adhesion Factor Suppression + Any cellular process that results in the reduction or loss of adhesion molecules on the cell surface. + Adhesion factor suppression may alter maintenance of tissue integration, wound healing, cellular migration, and metastasis. + Adhesion Factor Suppression + + + + + Adhesion Factor Suppression + PT + NCI + + + + + Any cellular process that results in the reduction or loss of adhesion molecules on the cell surface. + NCI + + + + + + + + + C40702 + Physiologic Function + Receptor Activation Process + C1514758 + Receptor_Activation + Receptor Activation + Receptor Activation Process + Any intercellular signaling process in which a transmembrane or intracellular receptor in the responding cell binds to a cognate ligand and initiates an intracellular response. Receptor activation is involved in numerous processes, including metabolism, immune response, sexual development, nervous system function, and regulation of circadian rhythms, mood and behavior. + Receptor Activation Process + + + + + Receptor Activation + SY + NCI + + + + + Receptor Activation Process + PT + NCI + + + + + Any intercellular signaling process in which a transmembrane or intracellular receptor in the responding cell binds to a cognate ligand and initiates an intracellular response. Receptor activation is involved in numerous processes, including metabolism, immune response, sexual development, nervous system function, and regulation of circadian rhythms, mood and behavior. + NCI + + + + + + + + + C40703 + Physiologic Function + Negative Regulation of Receptor Activation + C1514761 + Receptor_Inhibition + Negative Regulation of Receptor Activation + Receptor Inactivation + Receptor Inhibition + Any intercellular signaling process that reduces the frequency or extent of binding of a cognate ligand to an intracellular or transmembrane receptor to initiate an intracellular response. Receptor inhibition is involved in numerous processes, including metabolism, immune response, sexual development, nervous system function, and regulation of circadian rhythms, mood and behavior. + Negative Regulation of Receptor Activation + + + + + Negative Regulation of Receptor Activation + PT + NCI + + + + + Receptor Inactivation + SY + NCI + + + + + Receptor Inhibition + SY + NCI + + + + + Any intercellular signaling process that reduces the frequency or extent of binding of a cognate ligand to an intracellular or transmembrane receptor to initiate an intracellular response. Receptor inhibition is involved in numerous processes, including metabolism, immune response, sexual development, nervous system function, and regulation of circadian rhythms, mood and behavior. + NCI + + + + + + + + + C40704 + Physiologic Function + Receptor Tyrosine Kinase Inhibition + C1519725 + Tyrosine_Kinase_Receptor_Inhibition + Receptor Tyrosine Kinase Inhibition + Tyrosine Kinase Receptor Inhibition + A process that negatively regulates the intracellular catalytic activities that originate with the binding of a tyrosine kinase-associated transmembrane receptor with its cognate ligand. This process is involved in regulation of signaling related to cellular division, cellular differentiation and morphogenesis. + Receptor Tyrosine Kinase Inhibition + + + + + Receptor Tyrosine Kinase Inhibition + PT + NCI + + + + + Tyrosine Kinase Receptor Inhibition + SY + NCI + + + + + A process that negatively regulates the intracellular catalytic activities that originate with the binding of a tyrosine kinase-associated transmembrane receptor with its cognate ligand. This process is involved in regulation of signaling related to cellular division, cellular differentiation and morphogenesis. + NCI + + + + + + + + + C40708 + Phenomenon or Process + Cell Adhesion Inhibition + C1154399 + Cell_Adhesion_Inhibition + Cell Adhesion Inhibition + Any cellular process that reduces the frequency, rate or extent of cell adhesion. + Cell Adhesion Inhibition + + + + + Cell Adhesion Inhibition + PT + NCI + + + + + Any cellular process that reduces the frequency, rate or extent of cell adhesion. + NCI + + + + + + + + + + C40709 + Phenomenon or Process + Negative Regulation of Cell-Cell Adhesion + C1516323 + Cell-Cell_Adhesion_Inhibition + Cell-Cell Adhesion Inhibition + Negative Regulation of Cell-Cell Adhesion + Any cellular process that reduces the frequency, rate or extent of adhesion between cells. + Negative Regulation of Cell-Cell Adhesion + + + + + Cell-Cell Adhesion Inhibition + SY + NCI + + + + + Negative Regulation of Cell-Cell Adhesion + PT + NCI + + + + + Any cellular process that reduces the frequency, rate or extent of adhesion between cells. + NCI + + + + + + + + + + C40710 + Phenomenon or Process + Negative Regulation of Cell-Matrix Adhesion + C1516324 + Cell-Matrix_Adhesion_Inhibition + Cell-Matrix Adhesion Inhibition + Negative Regulation of Cell-Matrix Adhesion + Any cellular process that reduces the frequency, rate or extent of adhesion between cells and the underlying extracellular matrix. + Negative Regulation of Cell-Matrix Adhesion + + + + + Cell-Matrix Adhesion Inhibition + SY + NCI + + + + + Negative Regulation of Cell-Matrix Adhesion + PT + NCI + + + + + Any cellular process that reduces the frequency, rate or extent of adhesion between cells and the underlying extracellular matrix. + NCI + + + + + + + + + C40711 + Phenomenon or Process + Regulation of Platelet Aggregation Process + C1372803 + Platelet_Aggregation_Alteration + Platelet Aggregation Alteration + Regulation of Platelet Aggregation Process + Any process that modulates the rate, frequency or extent of platelet aggregation via adhesion molecules. + Regulation of Platelet Aggregation Process + + + + + Platelet Aggregation Alteration + SY + NCI + + + + + Regulation of Platelet Aggregation Process + PT + NCI + + + + + Any process that modulates the rate, frequency or extent of platelet aggregation via adhesion molecules. + NCI + + + + + + + + + C40712 + Phenomenon or Process + Positive Regulation of Platelet Aggregation Process + C1514158 + Platelet_Aggregation_Induction + Platelet Aggregation Induction + Positive Regulation of Platelet Aggregation Process + Any platelet aggregation process that increases the rate, frequency or extent of platelet aggregation. + Positive Regulation of Platelet Aggregation Process + + + + + Platelet Aggregation Induction + SY + NCI + + + + + Positive Regulation of Platelet Aggregation Process + PT + NCI + + + + + Any platelet aggregation process that increases the rate, frequency or extent of platelet aggregation. + NCI + + + + + + + + + + C40713 + Phenomenon or Process + Negative Regulation of Platelet Aggregation Process + C0919737 + Platelet_Aggregation_Inhibition + Negative Regulation of Platelet Aggregation Process + Platelet Aggregation Inhibition + Any platelet aggregation process that decreases the rate, frequency or extent of platelet aggregation. + Negative Regulation of Platelet Aggregation Process + + + + + Negative Regulation of Platelet Aggregation Process + PT + NCI + + + + + Platelet Aggregation Inhibition + SY + NCI + + + + + Any platelet aggregation process that decreases the rate, frequency or extent of platelet aggregation. + NCI + + + + + + + + + C40715 + Phenomenon or Process + Positive Regulation of Cell Death + C1516338 + Cell_Death_Induction + Cell Death Induction + Positive Regulation of Cell Death + Any process that increases the frequency, rate or extent of cell death. + Positive Regulation of Cell Death + + + + + Cell Death Induction + SY + NCI + + + + + Positive Regulation of Cell Death + PT + NCI + + + + + Any process that increases the frequency, rate or extent of cell death. + NCI + + + + + + + + + C40716 + Phenomenon or Process + Leukocyte Apoptotic Process + C1512644 + Immune_Cell_Destruction_Induction + Immune Cell Destruction Induction + Immune Cell Destruction Process + Leukocyte Apoptotic Process + Any apoptotic process that is observed in leukocytes. + Leukocyte Apoptotic Process + + + + + Immune Cell Destruction Induction + SY + NCI + + + + + Immune Cell Destruction Process + SY + NCI + + + + + Leukocyte Apoptotic Process + PT + NCI + + + + + Any apoptotic process that is observed in leukocytes. + NCI + + + + + + + + + C40717 + Phenomenon or Process + Lymphocyte Apoptotic Process + C1518060 + Lymphocyte_Destruction_Induction + Lymphocyte Apoptotic Process + Lymphocyte Destruction Induction + Lymphocyte Destruction Process + Any apoptotic process occurring in a B cell, T cell or natural killer cell. + Lymphocyte Apoptotic Process + + + + + Lymphocyte Apoptotic Process + PT + NCI + + + + + Lymphocyte Destruction Induction + SY + NCI + + + + + Lymphocyte Destruction Process + SY + NCI + + + + + Any apoptotic process occurring in a B cell, T cell or natural killer cell. + NCI + + + + + + + + + C40720 + Phenomenon or Process + Myeloid Cell Apoptotic Process + C1513788 + Myeloid_Cell_Destruction_Induction + Myeloid Cell Apoptotic Process + Myeloid Cell Destruction Induction + Myeloid Cell Destruction Process + Any apoptotic process occurring in a neutrophil, eosinophil or basophil. + Myeloid Cell Apoptotic Process + + + + + Myeloid Cell Apoptotic Process + PT + NCI + + + + + Myeloid Cell Destruction Induction + SY + NCI + + + + + Myeloid Cell Destruction Process + SY + NCI + + + + + Any apoptotic process occurring in a neutrophil, eosinophil or basophil. + NCI + + + + + + + + + C40724 + Phenomenon or Process + Positive Regulation of Cytolytic Process + C1511620 + Cytolysis_Induction + Cytolysis Induction + Cytolysis Induction Process + Positive Regulation of Cytolytic Process + Any process that increases the frequency, rate or extent of cytolysis. + Positive Regulation of Cytolytic Process + + + + + Cytolysis Induction + SY + NCI + + + + + Cytolysis Induction Process + SY + NCI + + + + + Positive Regulation of Cytolytic Process + PT + NCI + + + + + Any process that increases the frequency, rate or extent of cytolysis. + NCI + + + + + + + + + C40725 + Phenomenon or Process + Hemolytic Process + C1512402 + Hemolysis_Induction + Hemolysis Induction + Hemolytic Process + Any cytolytic process occurring in erythrocytes, resulting in the release of hemoglobin. + Hemolytic Process + + + + + Hemolysis Induction + SY + NCI + + + + + Hemolytic Process + PT + NCI + + + + + Any cytolytic process occurring in erythrocytes, resulting in the release of hemoglobin. + NCI + + + + + + + + + C40727 + Phenomenon or Process + Negative Regulation of Cell Death + C1516339 + Cell_Death_Inhibition + Cell Death Inhibition + Negative Regulation of Cell Death + Any process that decreases the frequency, rate or extent of cell death. + Negative Regulation of Cell Death + + + + + Cell Death Inhibition + SY + NCI + + + + + Negative Regulation of Cell Death + PT + NCI + + + + + Any process that decreases the frequency, rate or extent of cell death. + NCI + + + + + + + + + + C40728 + Phenomenon or Process + Negative Regulation of Immune Cell Destruction + C1512645 + Immune_Cell_Destruction_Inhibition + Immune Cell Destruction Inhibition + Negative Regulation of Immune Cell Destruction + Any process that decreases the frequency, rate or extent of apoptosis in leukocytes. + Negative Regulation of Immune Cell Destruction + + + + + Immune Cell Destruction Inhibition + SY + NCI + + + + + Negative Regulation of Immune Cell Destruction + PT + NCI + + + + + Any process that decreases the frequency, rate or extent of apoptosis in leukocytes. + NCI + + + + + + + + + + C40729 + Phenomenon or Process + Negative Regulation of Lymphocyte Apoptotic Process + C1518061 + Lymphocyte_Destruction_Inhibition + Lymphocyte Destruction Inhibition + Negative Regulation of Lymphocyte Apoptotic Process + Negative Regulation of Lymphocyte Destruction + Any process that decreases the frequency, rate or extent of apoptosis in B cells, T cells or natural killer cells. + Negative Regulation of Lymphocyte Apoptotic Process + + + + + Lymphocyte Destruction Inhibition + SY + NCI + + + + + Negative Regulation of Lymphocyte Apoptotic Process + PT + NCI + + + + + Negative Regulation of Lymphocyte Destruction + SY + NCI + + + + + Any process that decreases the frequency, rate or extent of apoptosis in B cells, T cells or natural killer cells. + NCI + + + + + + + + + + C40732 + Phenomenon or Process + Negative Regulation of Myeloid Cell Apoptotic Process + C1513789 + Myeloid_Cell_Destruction_Inhibition + Myeloid Cell Destruction Inhibition + Negative Regulation of Myeloid Cell Apoptotic Process + Negative Regulation of Myeloid Cell Destruction + Any process that decreases the frequency, rate or extent of apoptosis in neutrophils, eosinophils or basophils. + Negative Regulation of Myeloid Cell Apoptotic Process + + + + + Myeloid Cell Destruction Inhibition + SY + NCI + + + + + Negative Regulation of Myeloid Cell Apoptotic Process + PT + NCI + + + + + Negative Regulation of Myeloid Cell Destruction + SY + NCI + + + + + Any process that decreases the frequency, rate or extent of apoptosis in neutrophils, eosinophils or basophils. + NCI + + + + + + + + + C40736 + Phenomenon or Process + Negative Regulation of Hemolytic Process + C1512403 + Hemolysis_Inhibition + Hemolysis Inhibition + Negative Regulation of Hemolytic Process + Any process that decreases the frequency, rate or extent of hemolysis. + Negative Regulation of Hemolytic Process + + + + + Hemolysis Inhibition + SY + NCI + + + + + Negative Regulation of Hemolytic Process + PT + NCI + + + + + Any process that decreases the frequency, rate or extent of hemolysis. + NCI + + + + + + + + + C40739 + Physiologic Function + Hematopoiesis Induction + C1512382 + Hematopoiesis_Induction + Hematopoiesis Induction + Hematopoiesis Induction involves initiation of a process of blood formation; more specifically formation of blood cells that are all derived from hematopoietic stem cells. + Hematopoiesis Induction + + + + + Hematopoiesis Induction + PT + NCI + + + + + Hematopoiesis Induction involves initiation of a process of blood formation; more specifically formation of blood cells that are all derived from hematopoietic stem cells. + NCI + + + + + + + + + C40741 + Physiologic Function + Hematopoiesis Inhibition + C1512383 + Hematopoiesis_Inhibition + Hematopoiesis Inhibition + Hematopoiesis Inhibition involves interference or restraint of a process of blood formation; more specifically formation of blood cells that are all derived from hematopoietic stem cells. + Hematopoiesis Inhibition + + + + + Hematopoiesis Inhibition + PT + NCI + + + + + Hematopoiesis Inhibition involves interference or restraint of a process of blood formation; more specifically formation of blood cells that are all derived from hematopoietic stem cells. + NCI + + + + + + + + + C40779 + Phenomenon or Process + Induction of Cell Senescence + C1516358 + Cell_Senescence_Induction + Cell Senescence Induction + Induction of Cell Senescence + Positive Regulation of Cell Aging + Any cellular process that increases the rate, frequency or extent of cell aging. + Induction of Cell Senescence + + + + + Cell Senescence Induction + SY + NCI + + + + + Induction of Cell Senescence + PT + NCI + + + + + Positive Regulation of Cell Aging + SY + NCI + + + + + Any cellular process that increases the rate, frequency or extent of cell aging. + NCI + + + + + + + + + C40833 + Physiologic Function + Lymphocyte Activation Process + C0024262 + Lymphocyte_Activation + Lymphocyte Activation + Lymphocyte Activation Process + Lymphocyte Activation involves stimulation of the production and activity of lymphocytes. Stimulation increases the immune response to invading substances. + Lymphocyte Activation Process + + + + + Lymphocyte Activation + SY + NCI + + + + + Lymphocyte Activation Process + PT + NCI + + + + + Lymphocyte Activation involves stimulation of the production and activity of lymphocytes. Stimulation increases the immune response to invading substances. + NCI + + + + + + + + + C40839 + Physiologic Function + Myeloid Cell Activation Process + C1513787 + Myeloid_Cell_Activation + Myeloid Cell Activation + Myeloid Cell Activation Process + Myeloid Cell Activation involves stimulation of the production and activity of myeloid cells. Immature myeloid cells sample the surrounding environment for pathogens; when they contact a presentable antigen they become activated into mature dendritic cells and migrate to a lymph node where they act as antigen-presenting cells. + Myeloid Cell Activation Process + + + + + Myeloid Cell Activation + SY + NCI + + + + + Myeloid Cell Activation Process + PT + NCI + + + + + Myeloid Cell Activation involves stimulation of the production and activity of myeloid cells. Immature myeloid cells sample the surrounding environment for pathogens; when they contact a presentable antigen they become activated into mature dendritic cells and migrate to a lymph node where they act as antigen-presenting cells. + NCI + + + + + + + + + C40844 + Physiologic Function + Negative Regulation of Immune Cell Activation + C1512646 + Immune_Cell_Suppression + Immune Cell Suppression + Negative Regulation of Immune Cell Activation + Immune Cell Suppression consists of interference with, or restraint of, the activity of one or more lymphoid or myeloid cell types associated with the immune response. + Negative Regulation of Immune Cell Activation + + + + + Immune Cell Suppression + SY + NCI + + + + + Negative Regulation of Immune Cell Activation + PT + NCI + + + + + Immune Cell Suppression consists of interference with, or restraint of, the activity of one or more lymphoid or myeloid cell types associated with the immune response. + NCI + + + + + + + + + + C40846 + Physiologic Function + Negative Regulation of Lymphocyte Activation + C1518065 + Lymphocyte_Suppression + Lymphocyte Suppression + Negative Regulation of Lymphocyte Activation + Lymphocyte Suppression involves interference with, or restraint of, the production and activity of lymphocytes. Formed in lymphoid tissue, lymphocytes are white blood cells that can generally be classified as either T- or B-cells. T-lymphocytes provide cell-mediated immunity, while B-lymphocytes produce antibodies that provide humoral immunity. Suppression decreases the ability of lymphocytes to mount an immune response to invading substances. + Negative Regulation of Lymphocyte Activation + + + + + Lymphocyte Suppression + SY + NCI + + + + + Negative Regulation of Lymphocyte Activation + PT + NCI + + + + + Lymphocyte Suppression involves interference with, or restraint of, the production and activity of lymphocytes. Formed in lymphoid tissue, lymphocytes are white blood cells that can generally be classified as either T- or B-cells. T-lymphocytes provide cell-mediated immunity, while B-lymphocytes produce antibodies that provide humoral immunity. Suppression decreases the ability of lymphocytes to mount an immune response to invading substances. + NCI + + + + + + + + + C40850 + Physiologic Function + Negative Regulation of Myeloid Cell Activation + C1513790 + Myeloid_Cell_Suppression + Myeloid Cell Suppression + Negative Regulation of Myeloid Cell Activation + Myeloid Cell Suppression involves interference with, or restraint of, the production and activity of myeloid cells. + Negative Regulation of Myeloid Cell Activation + + + + + Myeloid Cell Suppression + SY + NCI + + + + + Negative Regulation of Myeloid Cell Activation + PT + NCI + + + + + Myeloid Cell Suppression involves interference with, or restraint of, the production and activity of myeloid cells. + NCI + + + + + + + + + C40854 + Physiologic Function + Platelet Activation + C0032173 + Platelet_Activation + Platelet Activation + Platelet Activation involves initiation of a set of stimulated platelet activities involved in aggregation of platelets and fibrin during blood coagulation. + Platelet Activation + + + + + Platelet Activation + PT + NCI + + + + + Platelet Activation involves initiation of a set of stimulated platelet activities involved in aggregation of platelets and fibrin during blood coagulation. + NCI + + + + + + + + + C40856 + Physiologic Function + Antiemetic Effect + C1516011 + Antiemetic_Effect + Antiemetic Effect + An Antiemetic Effect involves suppression of nausea and vomiting. Emesis is a complex process coordinated by a central emesis center located in the lateral reticular formation of the mid-brainstem. Inhibition of certain neurotransmitters (e.g., 5-HT) or their receptors located in this region inhibits emesis. + Antiemetic Effect + + + + + Antiemetic Effect + PT + NCI + + + + + An Antiemetic Effect involves suppression of nausea and vomiting. Emesis is a complex process coordinated by a central emesis center located in the lateral reticular formation of the mid-brainstem. Inhibition of certain neurotransmitters (e.g., 5-HT) or their receptors located in this region inhibits emesis. + NCI + + + + + + + + + C40857 + Physiologic Function + Negative Regulation of Inflammatory Response Process + C1516019 + Antiinflammatory_Effect + Antiinflammatory Effect + Negative Regulation of Inflammatory Response Process + An Antiinflammatory Effect involves interference with, or restraint of, local events that constitute part of innate immunity, involve increased blood supply, and infiltration and activity of leukocytes at a site of injury or disease. Inflammation is induced by release of vasodilatory, opsonizing, and chemotactic mediators that attract phagocytizing macrophages and leukocytes; dilate local blood vessels, increasing local blood flow and capillary permeability; and induce pain. + Negative Regulation of Inflammatory Response Process + + + + + Antiinflammatory Effect + SY + NCI + + + + + Negative Regulation of Inflammatory Response Process + PT + NCI + + + + + An Antiinflammatory Effect involves interference with, or restraint of, local events that constitute part of innate immunity, involve increased blood supply, and infiltration and activity of leukocytes at a site of injury or disease. Inflammation is induced by release of vasodilatory, opsonizing, and chemotactic mediators that attract phagocytizing macrophages and leukocytes; dilate local blood vessels, increasing local blood flow and capillary permeability; and induce pain. + NCI + + + + + + + + + C40858 + Physiologic Function + Antimicrobial Effect + C1516022 + Antimicrobial_Effect + Antimicrobial Effect + An Antimicrobial Effect involves interference with, or restraint of, the activities of biologic molecules and complexes, or cellular components involved in the life cycle of a microorganism, resulting in suppression of microbial growth. Mechanisms to suppress growth include inhibition of cell wall synthesis; increased cell wall permeability; protein synthesis inhibition; and inhibition of reverse transcriptase and protease. + Antimicrobial Effect + + + + + Antimicrobial Effect + PT + NCI + + + + + An Antimicrobial Effect involves interference with, or restraint of, the activities of biologic molecules and complexes, or cellular components involved in the life cycle of a microorganism, resulting in suppression of microbial growth. Mechanisms to suppress growth include inhibition of cell wall synthesis; increased cell wall permeability; protein synthesis inhibition; and inhibition of reverse transcriptase and protease. + NCI + + + + + + + + + C40859 + Physiologic Function + Antipruritic Effect + C1516026 + Antipruritic_Effect + Antipruritic Effect + An Antipruritic Effect involves suppression of an itching sensation caused by histamine stimulation of epidermal nerve endings. Inhibition of histamine or histamine release can produce an antipruritic effect. + Antipruritic Effect + + + + + Antipruritic Effect + PT + NCI + + + + + An Antipruritic Effect involves suppression of an itching sensation caused by histamine stimulation of epidermal nerve endings. Inhibition of histamine or histamine release can produce an antipruritic effect. + NCI + + + + + + + + + C40864 + Physiologic Function + Vascular Permeability Alteration + C1371588 + Vascular_Permeability_Alteration + Vascular Permeability Alteration + Vascular Permeability Alteration involves a qualitative change in the existing capacity of substances to pass from the vascular lumen, through a blood vessel wall, into surrounding tissue, or vice versa. + Vascular Permeability Alteration + + + + + Vascular Permeability Alteration + PT + NCI + + + + + Vascular Permeability Alteration involves a qualitative change in the existing capacity of substances to pass from the vascular lumen, through a blood vessel wall, into surrounding tissue, or vice versa. + NCI + + + + + + + + + C40867 + Physiologic Function + Vasodilation + C0042401 + Patient Code (Appendix B) + FDA + Widening of a blood vessel lumen due to smooth muscle relaxation in the vessel wall and leads to increased blood flow. + Vasodilation + Vasodilatation + Vasodilation + Vasodilation involves widening of a blood vessel lumen due to smooth muscle relaxation in the vessel wall and leads to increased blood flow. + IMDRF:E0517 + Vasodilation + + + + + Widening of a blood vessel lumen due to smooth muscle relaxation in the vessel wall and leads to increased blood flow. + FDA + CDRH + + + + + Vasodilatation + PT + FDA + 2127 + CDRH + + + + + Vasodilation + PT + NCI + + + + + Vasodilation involves widening of a blood vessel lumen due to smooth muscle relaxation in the vessel wall and leads to increased blood flow. + NCI + + + + + + + + + C40912 + Physiologic Function + Immunopotentiation + C1512675 + Immunopotentiation_Effect + Immunopotentiation + An Immunopotentiation Effect involves stimulation of biologic molecules and complexes, or cellular, cell, or tissue components of a normal immune response. + Immunopotentiation + + + + + Immunopotentiation + PT + NCI + + + + + An Immunopotentiation Effect involves stimulation of biologic molecules and complexes, or cellular, cell, or tissue components of a normal immune response. + NCI + + + + + + + + + C40913 + Physiologic Function + Immunosuppressive Effect + C0021080 + Immunosuppressive_Effect + Immunosuppression Effect + Immunosuppressive Effect + An Immunosuppressive Effect involves interference with, or restraint of, the function of biologic molecules and complexes, or cellular, cell, or tissue components of a normal immune response. + Immunosuppressive Effect + + + + + Immunosuppression Effect + SY + NCI + + + + + Immunosuppressive Effect + PT + NCI + + + + + An Immunosuppressive Effect involves interference with, or restraint of, the function of biologic molecules and complexes, or cellular, cell, or tissue components of a normal immune response. + NCI + + + + + + + + + C40917 + Physiologic Function + Bone Formation Inhibition + C1371286 + Bone_Formation_Inhibition + Bone Formation Inhibition + Bone Formation Inhibition involves interference with, or restraint of, synthesis by osteoblasts of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate. + Bone Formation Inhibition + + + + + Bone Formation Inhibition + PT + NCI + + + + + Bone Formation Inhibition involves interference with, or restraint of, synthesis by osteoblasts of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate. + NCI + + + + + + + + + C40918 + Physiologic Function + Bone Formation Stimulation + C1371285 + Bone_Formation_Stimulation + Bone Formation Stimulation + Bone Formation Stimulation involves initiation of synthesis by osteoblasts of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate. + Bone Formation Stimulation + + + + + Bone Formation Stimulation + PT + NCI + + + + + Bone Formation Stimulation involves initiation of synthesis by osteoblasts of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate. + NCI + + + + + + + + + C40920 + Physiologic Function + Bone Resorption Inhibition + C3537067 + Bone_Resorption_Inhibition + Bone Resorption Inhibition + Bone Resorption Inhibition involves interference with, or restraint of, absorption and removal of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate and release of bone salts (phosphorus and, especially, calcium) into the extracellular fluid by osteoclasts, activated by parathyroid hormone. + Bone Resorption Inhibition + + + + + Bone Resorption Inhibition + PT + NCI + + + + + Bone Resorption Inhibition involves interference with, or restraint of, absorption and removal of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate and release of bone salts (phosphorus and, especially, calcium) into the extracellular fluid by osteoclasts, activated by parathyroid hormone. + NCI + + + + + + + + + C40921 + Physiologic Function + Bone Resorption Stimulation + C3537066 + Bone_Resorption_Stimulation + Bone Resorption Stimulation + Bone Resorption Stimulation involves initiation of absorption and removal of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate and release of bone salts (phosphorus and, especially, calcium) into the extracellular fluid by osteoclasts, activated by parathyroid hormone. + Bone Resorption Stimulation + + + + + Bone Resorption Stimulation + PT + NCI + + + + + Bone Resorption Stimulation involves initiation of absorption and removal of the hard connective tissue that constitutes the vertebrate skeleton and consists of a matrix of collagenous fibers impregnated chiefly with calcium phosphate and calcium carbonate and release of bone salts (phosphorus and, especially, calcium) into the extracellular fluid by osteoclasts, activated by parathyroid hormone. + NCI + + + + + + + + + C40922 + Physiologic Function + Neurologic Effect + C1518287 + Neurologic_Effect + Neurologic Effect + A Neurologic Effect involves a change in the existing function of biologic molecules and complexes, or cellular, cell, or tissue components of the nervous system. + Neurologic Effect + + + + + Neurologic Effect + PT + NCI + + + + + A Neurologic Effect involves a change in the existing function of biologic molecules and complexes, or cellular, cell, or tissue components of the nervous system. + NCI + + + + + + + + + C40924 + Physiologic Function + Neuron Conduction Induction + C1518291 + Neuron_Conduction_Induction + Neuron Conduction Induction + Neuron Conduction Induction involves initiation of activities that propagate the transfer of the electrochemical action potential process along nerve fibers away from the cell body. + Neuron Conduction Induction + + + + + Neuron Conduction Induction + PT + NCI + + + + + Neuron Conduction Induction involves initiation of activities that propagate the transfer of the electrochemical action potential process along nerve fibers away from the cell body. + NCI + + + + + + + + + C40925 + Physiologic Function + Neuron Conduction Inhibition + C1518292 + Neuron_Conduction_Inhibition + Neuron Conduction Inhibition + Neuron Conduction Inhibition involves interference with, or restraint of, activities that propagate the transfer of the electrochemical action potential process along nerve fibers away from the cell body. + Neuron Conduction Inhibition + + + + + Neuron Conduction Inhibition + PT + NCI + + + + + Neuron Conduction Inhibition involves interference with, or restraint of, activities that propagate the transfer of the electrochemical action potential process along nerve fibers away from the cell body. + NCI + + + + + + + + + C40999 + Cell + Atypical Histiocyte + C1510956 + Atypical_Histiocyte + Atypical Histiocyte + Atypical Histiocyte + + + + + Atypical Histiocyte + PT + NCI + + + + + + + + + C41209 + Mental Process + Attention Concentration + C0004268 + Attention_Concentration + Attention + Attention Concentration + Concentration + The act or process of concentrating, focusing the attention and mental energy on a single object to the exclusion of others. + Attention Concentration + + + + + Attention + SY + NCI + + + + + Attention Concentration + PT + NCI + + + + + Concentration + SY + caDSR + + + + + The act or process of concentrating, focusing the attention and mental energy on a single object to the exclusion of others. + NCI + + + + + + + + + C41473 + Phenomenon or Process + Cardiovascular Alteration + C0184522 + Cardiovascular_Alteration + Cardiovascular Alteration + Cardiovascular Alteration involves a change in the existing function of biologic molecules and complexes, or cellular, cell, or tissue components of the heart and vascular system by which blood is pumped and circulated through the body to provide tissues with oxygen and nutrients and to remove waste products. + Cardiovascular Alteration + + + + + Cardiovascular Alteration + PT + NCI + + + + + Cardiovascular Alteration involves a change in the existing function of biologic molecules and complexes, or cellular, cell, or tissue components of the heart and vascular system by which blood is pumped and circulated through the body to provide tissues with oxygen and nutrients and to remove waste products. + NCI + + + + + + + + + C41475 + Phenomenon or Process + Testosterone Secretion Process + C1515331 + Testosterone_Secretion_Induction + Testosterone Secretion + Testosterone Secretion Induction + Testosterone Secretion Process + Testosterone Secretion Induction consists of initiation of activities involved in release into the bloodstream by testicular interstitial (Leydig's) cells of the major androgenic steroid hormone (testosterone) produced in response to adenohypophyseal luteinizing hormone that regulates gonadotropic secretion; Wolffian duct differentiation into epididymis, vas deferens, and seminal vesicle; spermatogenesis after peripheral conversion to dihydrotestosterone by 5a-reductase; and skeletal muscle and bone tissue. Alteration of positive or negative feedback mechanisms can affect hormone release. + Testosterone Secretion Process + + + + + Testosterone Secretion + SY + NCI + + + + + Testosterone Secretion Induction + SY + NCI + + + + + Testosterone Secretion Process + PT + NCI + + + + + Testosterone Secretion Induction consists of initiation of activities involved in release into the bloodstream by testicular interstitial (Leydig's) cells of the major androgenic steroid hormone (testosterone) produced in response to adenohypophyseal luteinizing hormone that regulates gonadotropic secretion; Wolffian duct differentiation into epididymis, vas deferens, and seminal vesicle; spermatogenesis after peripheral conversion to dihydrotestosterone by 5a-reductase; and skeletal muscle and bone tissue. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41480 + Phenomenon or Process + Musculoskeletal Process + C1513770 + Musculoskeletal_Process + Musculoskeletal Process + A Musculoskeletal Process consists of a function of cellular, cell, or tissue components of the organ system comprised of muscle, bone, and cartilage. + Musculoskeletal Process + + + + + Musculoskeletal Process + PT + NCI + + + + + A Musculoskeletal Process consists of a function of cellular, cell, or tissue components of the organ system comprised of muscle, bone, and cartilage. + NCI + + + + + + + + + C41486 + Phenomenon or Process + Thyroid Hormone Secretion Inhibition + C1519511 + Thyroid_Hormone_Secretion_Inhibition + Thyroid Hormone Secretion Inhibition + Thyroid Hormone Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by thyroid gland follicular cells of closely related iodine-containing triiodothyronine and thyroxine (thyroid hormones) formed from thyroglobulin that increase the rate of cell metabolism and are essential for central nervous system maturation. Alteration of positive or negative feedback mechanisms can affect hormone release. + Thyroid Hormone Secretion Inhibition + + + + + Thyroid Hormone Secretion Inhibition + PT + NCI + + + + + Thyroid Hormone Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by thyroid gland follicular cells of closely related iodine-containing triiodothyronine and thyroxine (thyroid hormones) formed from thyroglobulin that increase the rate of cell metabolism and are essential for central nervous system maturation. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41492 + Phenomenon or Process + Endocrine System Process + C1516848 + Endocrine_System_Process + Endocrine System Process + An Endocrine System Process consists of functions of cellular, cell, or tissue components of glands that release hormones into the circulatory system. + Endocrine System Process + + + + + Endocrine System Process + PT + NCI + + + + + An Endocrine System Process consists of functions of cellular, cell, or tissue components of glands that release hormones into the circulatory system. + NCI + + + + + + + + + C41493 + Phenomenon or Process + Endocrine Secretory Process + C1516844 + Endocrine_Secretory_Induction + Endocrine Secretory Induction + Endocrine Secretory Process + Endocrine Secretory Induction involves stimulation of hormone release into the bloodstream from endocrine glands. Alteration of positive or negative feedback mechanisms can induce hormone release. + Endocrine Secretory Process + + + + + Endocrine Secretory Induction + SY + NCI + + + + + Endocrine Secretory Process + PT + NCI + + + + + Endocrine Secretory Induction involves stimulation of hormone release into the bloodstream from endocrine glands. Alteration of positive or negative feedback mechanisms can induce hormone release. + NCI + + + + + + + + + C41494 + Phenomenon or Process + Endocrine Secretory Inhibition + C1516845 + Endocrine_Secretory_Inhibition + Endocrine Secretory Inhibition + Endocrine Secretory Inhibition involves interference with, or restraint of, hormone release into the bloodstream from endocrine glands. Alteration of positive or negative feedback mechanisms can inhibit hormone release. + Endocrine Secretory Inhibition + + + + + Endocrine Secretory Inhibition + PT + NCI + + + + + Endocrine Secretory Inhibition involves interference with, or restraint of, hormone release into the bloodstream from endocrine glands. Alteration of positive or negative feedback mechanisms can inhibit hormone release. + NCI + + + + + + + + + C41495 + Phenomenon or Process + Thyroid Hormone Secretion Process + C1519510 + Thyroid_Hormone_Secretion_Induction + Thyroid Hormone Secretion + Thyroid Hormone Secretion Induction + Thyroid Hormone Secretion Process + Thyroid Hormone Secretion Induction consists of initiation of activities involved in release into the bloodstream by thyroid gland follicular cells of closely related iodine-containing triiodothyronine and thyroxine (thyroid hormones) formed from thyroglobulin that increase the rate of cell metabolism and are essential for central nervous system maturation. Alteration of positive or negative feedback mechanisms can affect hormone release. + Thyroid Hormone Secretion Process + + + + + Thyroid Hormone Secretion + SY + NCI + + + + + Thyroid Hormone Secretion Induction + SY + NCI + + + + + Thyroid Hormone Secretion Process + PT + NCI + + + + + Thyroid Hormone Secretion Induction consists of initiation of activities involved in release into the bloodstream by thyroid gland follicular cells of closely related iodine-containing triiodothyronine and thyroxine (thyroid hormones) formed from thyroglobulin that increase the rate of cell metabolism and are essential for central nervous system maturation. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41496 + Phenomenon or Process + Testosterone Secretion Inhibition + C1515332 + Testosterone_Secretion_Inhibition + Testosterone Secretion Inhibition + Testosterone Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by testicular interstitial (Leydig's) cells of the major androgenic steroid hormone (testosterone) produced in response to adenohypophyseal luteinizing hormone that regulates gonadotropic secretion; Wolffian duct differentiation into epididymis, vas deferens, and seminal vesicle; spermatogenesis after peripheral conversion to dihydrotestosterone by 5a-reductase; and skeletal muscle and bone tissue. Alteration of positive or negative feedback mechanisms can affect hormone release. + Testosterone Secretion Inhibition + + + + + Testosterone Secretion Inhibition + PT + NCI + + + + + Testosterone Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by testicular interstitial (Leydig's) cells of the major androgenic steroid hormone (testosterone) produced in response to adenohypophyseal luteinizing hormone that regulates gonadotropic secretion; Wolffian duct differentiation into epididymis, vas deferens, and seminal vesicle; spermatogenesis after peripheral conversion to dihydrotestosterone by 5a-reductase; and skeletal muscle and bone tissue. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41498 + Phenomenon or Process + Progesterone Secretion Inhibition + C1514473 + Progesterone_Secretion_Inhibition + Progesterone Secretion Inhibition + Progesterone Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by the corpus luteum and placenta of a steroid estrogen antagonist (progesterone) that prevents follicular development and promotes proliferation of uterine mucosa and blastocyst implantation. Alteration of positive or negative feedback mechanisms can affect hormone release. + Progesterone Secretion Inhibition + + + + + Progesterone Secretion Inhibition + PT + NCI + + + + + Progesterone Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by the corpus luteum and placenta of a steroid estrogen antagonist (progesterone) that prevents follicular development and promotes proliferation of uterine mucosa and blastocyst implantation. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41499 + Phenomenon or Process + Progesterone Secretion Process + C1514472 + Progesterone_Secretion_Induction + Progesterone Secretion + Progesterone Secretion Induction + Progesterone Secretion Process + Progesterone Secretion consists of the activities involved in release into the bloodstream by the corpus luteum and placenta of a steroid estrogen antagonist (progesterone) that prevents follicular development and promotes proliferation of uterine mucosa and blastocyst implantation. Alteration of positive or negative feedback mechanisms can affect hormone release. + Progesterone Secretion Process + + + + + Progesterone Secretion + SY + NCI + + + + + Progesterone Secretion Induction + SY + NCI + + + + + Progesterone Secretion Process + PT + NCI + + + + + Progesterone Secretion consists of the activities involved in release into the bloodstream by the corpus luteum and placenta of a steroid estrogen antagonist (progesterone) that prevents follicular development and promotes proliferation of uterine mucosa and blastocyst implantation. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41502 + Phenomenon or Process + Mineralocorticoid Secretion Inhibition + C1513310 + Mineralocorticoid_Secretion_Inhibition + Mineralocorticoid Secretion Inhibition + Mineralocorticoid Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream of a class of C21 corticosteroids (mineralocorticoids) involved in regulation of electrolyte homeostasis (sodium retention and potassium loss) and water balance (retention) through effects on epithelial ion transport. Alteration of positive or negative feedback mechanisms can affect hormone release. + Mineralocorticoid Secretion Inhibition + + + + + Mineralocorticoid Secretion Inhibition + PT + NCI + + + + + Mineralocorticoid Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream of a class of C21 corticosteroids (mineralocorticoids) involved in regulation of electrolyte homeostasis (sodium retention and potassium loss) and water balance (retention) through effects on epithelial ion transport. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41503 + Phenomenon or Process + Mineralocorticoid Secretion Process + C1513309 + Mineralocorticoid_Secretion_Induction + Mineralocorticoid Secretion Induction + Mineralocorticoid Secretion Process + Mineralocorticoid Secretion Induction consists of initiation of activities involved in release into the bloodstream of a class of C21 corticosteroids (mineralocorticoids) involved in regulation of electrolyte homeostasis (sodium retention and potassium loss) and water balance (retention) through effects on epithelial ion transport. Alteration of positive or negative feedback mechanisms can affect hormone release. + Mineralocorticoid Secretion Process + + + + + Mineralocorticoid Secretion Induction + SY + NCI + + + + + Mineralocorticoid Secretion Process + PT + NCI + + + + + Mineralocorticoid Secretion Induction consists of initiation of activities involved in release into the bloodstream of a class of C21 corticosteroids (mineralocorticoids) involved in regulation of electrolyte homeostasis (sodium retention and potassium loss) and water balance (retention) through effects on epithelial ion transport. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41504 + Phenomenon or Process + Melatonin Secretion Inhibition + C1513103 + Melatonin_Secretion_Inhibition + Melatonin Secretion Inhibition + Melatonin Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream from the pineal gland of a hormone (melatonin) implicated in regulation of sleep, mood, puberty, and ovarian cycles. + Melatonin Secretion Inhibition + + + + + Melatonin Secretion Inhibition + PT + NCI + + + + + Melatonin Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream from the pineal gland of a hormone (melatonin) implicated in regulation of sleep, mood, puberty, and ovarian cycles. + NCI + + + + + + + + + C41505 + Phenomenon or Process + Glucocorticoid Secretion Inhibition + C1512205 + Glucocorticoid_Secretion_Inhibition + Glucocorticoid Secretion Inhibition + Glucocorticoid Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by the adrenal cortex of a class of steroid substances (glucocorticoids) that affect fat, protein, and carbohydrate metabolism (gluconeogenesis, liver glycogen deposition, elevation of blood sugar); inhibit corticotropin secretion; possess anti-inflammatory activity; and play a role in arterial blood pressure, connective tissue response to injury, reduction of circulating lymphocytes, and central nervous system function. Alteration of positive or negative feedback mechanisms can affect hormone release. + Glucocorticoid Secretion Inhibition + + + + + Glucocorticoid Secretion Inhibition + PT + NCI + + + + + Glucocorticoid Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by the adrenal cortex of a class of steroid substances (glucocorticoids) that affect fat, protein, and carbohydrate metabolism (gluconeogenesis, liver glycogen deposition, elevation of blood sugar); inhibit corticotropin secretion; possess anti-inflammatory activity; and play a role in arterial blood pressure, connective tissue response to injury, reduction of circulating lymphocytes, and central nervous system function. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41506 + Phenomenon or Process + Estrogen Secretion Inhibition + C1516976 + Estrogen_Secretion_Inhibition + Estrogen Secretion Inhibition + Estrogen Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by the ovaries of a class of steroid substances (estrogens) that have a specific regulatory effect on the activity of cells involved in development and maintenance of secondary female sex characteristics and control of the cyclical changes in the reproductive cycle, as well as pregnancy maintenance and an anabolic effect on protein metabolism and water retention. Alteration of positive or negative feedback mechanisms can affect hormone release. + Estrogen Secretion Inhibition + + + + + Estrogen Secretion Inhibition + PT + NCI + + + + + Estrogen Secretion Inhibition consists of interference with, or restraint of, activities involved in release into the bloodstream by the ovaries of a class of steroid substances (estrogens) that have a specific regulatory effect on the activity of cells involved in development and maintenance of secondary female sex characteristics and control of the cyclical changes in the reproductive cycle, as well as pregnancy maintenance and an anabolic effect on protein metabolism and water retention. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41507 + Phenomenon or Process + Estrogen Secretion Process + C1516975 + Estrogen_Secretion_Induction + Estrogen Secretion + Estrogen Secretion Induction + Estrogen Secretion Process + Estrogen Secretion Induction consists of the initiation of activities involved in release into the bloodstream by the ovaries of a class of steroid substances (estrogens) that have a specific regulatory effect on the activity of cells involved in development and maintenance of secondary female sex characteristics and control of the cyclical changes in the reproductive cycle, as well as pregnancy maintenance and an anabolic effect on protein metabolism and water retention. Alteration of positive or negative feedback mechanisms can affect hormone release. + Estrogen Secretion Process + + + + + Estrogen Secretion + SY + NCI + + + + + Estrogen Secretion Induction + SY + NCI + + + + + Estrogen Secretion Process + PT + NCI + + + + + Estrogen Secretion Induction consists of the initiation of activities involved in release into the bloodstream by the ovaries of a class of steroid substances (estrogens) that have a specific regulatory effect on the activity of cells involved in development and maintenance of secondary female sex characteristics and control of the cyclical changes in the reproductive cycle, as well as pregnancy maintenance and an anabolic effect on protein metabolism and water retention. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41510 + Phenomenon or Process + Circulatory Process + C1516559 + Circulatory_Process + Circulation + Circulatory Process + A Circulatory Process consists of functions of cellular, cell, or tissue components of the heart and vessels by which blood and lymph is circulated through the body. + Circulatory Process + + + + + Circulation + SY + NCI + + + + + Circulatory Process + PT + NCI + + + + + A Circulatory Process consists of functions of cellular, cell, or tissue components of the heart and vessels by which blood and lymph is circulated through the body. + NCI + + + + + + + + + C41514 + Phenomenon or Process + Cell Adhesion Process + C0007577 + The close adherence (bonding) to adjoining cell surfaces. + Cell_Adhesion_Process + Cell Adhesion + Cell Adhesion Process + Cellular Adhesion + cellular adhesion + A cellular process initiated by cell adhesion molecules which results in the attachment of a cell to either another cell or to an underlying substrate such as the extracellular matrix. + Cell Adhesion Process + + + + + The close adherence (bonding) to adjoining cell surfaces. + NCI-GLOSS + + + + + Cell Adhesion + SY + NCI + + + + + Cell Adhesion Process + PT + NCI + + + + + Cellular Adhesion + SY + NCI + + + + + cellular adhesion + PT + NCI-GLOSS + CDR0000046480 + + + + + A cellular process initiated by cell adhesion molecules which results in the attachment of a cell to either another cell or to an underlying substrate such as the extracellular matrix. + NCI + + + + + + + + + C41515 + Phenomenon or Process + Cell Death Process + C0007587 + Cell_Death_Process + Cell Death + Cell Death Process + The cellular process resulting in permanent cessation of all vital functions of a cell. + Cell Death Process + + + + + Cell Death + SY + NCI + + + + + Cell Death Process + PT + NCI + + + + + The cellular process resulting in permanent cessation of all vital functions of a cell. + NCI + + + + + + + + + C41516 + Phenomenon or Process + Negative Regulation of Cytolytic Process + C1511621 + Cytolysis_Inhibition + Cytolysis Inhibition + Negative Regulation of Cytolytic Process + Any process that decreases the frequency, rate or extent of cytolysis. + Negative Regulation of Cytolytic Process + + + + + Cytolysis Inhibition + SY + NCI + + + + + Negative Regulation of Cytolytic Process + PT + NCI + + + + + Any process that decreases the frequency, rate or extent of cytolysis. + NCI + + + + + + + + + C41519 + Phenomenon or Process + Hormone Activity Induction + C1512493 + Hormone_Activity_Induction + Hormone Activity Induction + Hormone Activity Induction involves initiation of the biological function of a biochemical substance (typically secreted by an endocrine gland) having a selective regulatory effect on the activity of a specific cell type(s) or organ(s). + Hormone Activity Induction + + + + + Hormone Activity Induction + PT + NCI + + + + + Hormone Activity Induction involves initiation of the biological function of a biochemical substance (typically secreted by an endocrine gland) having a selective regulatory effect on the activity of a specific cell type(s) or organ(s). + NCI + + + + + + + + + C41520 + Phenomenon or Process + Hormone Activity Inhibition + C1512494 + Hormone_Activity_Inhibition + Hormone Activity Inhibition + Hormone Activity Inhibition involves interference with, or restraint of, the biological function of a biochemical substance (typically secreted by an endocrine gland) having a selective regulatory effect on the activity of a specific cell type(s) or organ(s). + Hormone Activity Inhibition + + + + + Hormone Activity Inhibition + PT + NCI + + + + + Hormone Activity Inhibition involves interference with, or restraint of, the biological function of a biochemical substance (typically secreted by an endocrine gland) having a selective regulatory effect on the activity of a specific cell type(s) or organ(s). + NCI + + + + + + + + + C41521 + Phenomenon or Process + Neurotransmitter Activity Inhibition + C1518303 + Neurotransmitter_Activity_Inhibition + Neurotransmitter Activity Inhibition + Neurotransmitter Activity Inhibition involves interference with, such as receptor binding, decreased production, neuronal release, or increased re-uptake, or restraint of the biological function of endogenous signaling molecules secreted by neurons that have specific regulatory effects on the activity of ion channels or second messenger systems in target effector cells. + Neurotransmitter Activity Inhibition + + + + + Neurotransmitter Activity Inhibition + PT + NCI + + + + + Neurotransmitter Activity Inhibition involves interference with, such as receptor binding, decreased production, neuronal release, or increased re-uptake, or restraint of the biological function of endogenous signaling molecules secreted by neurons that have specific regulatory effects on the activity of ion channels or second messenger systems in target effector cells. + NCI + + + + + + + + + C41522 + Phenomenon or Process + Neurotransmitter Activity Induction + C1518302 + Neurotransmitter_Activity_Induction + Neurotransmitter Activity Induction + Neurotransmitter Activity Induction involves initiation of the biological function, through increased production, neuronal release, or decreased re-uptake, of endogenous signaling molecules secreted by neurons that have specific regulatory effects on the activity of ion channels or second messenger systems in target effector cells. + Neurotransmitter Activity Induction + + + + + Neurotransmitter Activity Induction + PT + NCI + + + + + Neurotransmitter Activity Induction involves initiation of the biological function, through increased production, neuronal release, or decreased re-uptake, of endogenous signaling molecules secreted by neurons that have specific regulatory effects on the activity of ion channels or second messenger systems in target effector cells. + NCI + + + + + + + + + C41523 + Phenomenon or Process + Adrenal Hormone Activity Inhibition + C1515892 + Adrenal_Hormone_Activity_Inhibition + Adrenal Hormone Activity Inhibition + Adrenal Hormone Activity Inhibition involves interference with, such as receptor binding, or restraint of the biological function of biochemical substances secreted by the adrenal gland that have a specific regulatory effect on electrolyte balance, blood pressure, inflammation, blood sugar balance, and immune system control. + Adrenal Hormone Activity Inhibition + + + + + Adrenal Hormone Activity Inhibition + PT + NCI + + + + + Adrenal Hormone Activity Inhibition involves interference with, such as receptor binding, or restraint of the biological function of biochemical substances secreted by the adrenal gland that have a specific regulatory effect on electrolyte balance, blood pressure, inflammation, blood sugar balance, and immune system control. + NCI + + + + + + + + + C41526 + Phenomenon or Process + Adrenal Hormone Activity Induction + C1515891 + Adrenal_Hormone_Activity_Induction + Adrenal Hormone Activity Induction + Adrenal Hormone Activity Induction involves initiation of the biological function of biochemical substances secreted by the adrenal gland that have a specific regulatory effect on electrolyte balance, blood pressure, inflammation, blood sugar balance, and immune system control. + Adrenal Hormone Activity Induction + + + + + Adrenal Hormone Activity Induction + PT + NCI + + + + + Adrenal Hormone Activity Induction involves initiation of the biological function of biochemical substances secreted by the adrenal gland that have a specific regulatory effect on electrolyte balance, blood pressure, inflammation, blood sugar balance, and immune system control. + NCI + + + + + + + + + C41528 + Phenomenon or Process + Negative Regulation of Histamine Release + C1512466 + Histamine_Activity_Inhibition + Histamine Activity Inhibition + Negative Regulation of Histamine Release + Any process that reduces the release of the biogenic amine and neurotransmitter histamine. Histamine activity is reduced by inhibition of histamine synthesis or destruction of histamine-releasing neurons in the brain. This process is involved in suppression of allergies and induction of sleep. + Negative Regulation of Histamine Release + + + + + Histamine Activity Inhibition + SY + NCI + + + + + Negative Regulation of Histamine Release + PT + NCI + + + + + Any process that reduces the release of the biogenic amine and neurotransmitter histamine. Histamine activity is reduced by inhibition of histamine synthesis or destruction of histamine-releasing neurons in the brain. This process is involved in suppression of allergies and induction of sleep. + NCI + + + + + + + + + C41530 + Phenomenon or Process + Negative Regulation of Serotonin Release + C1519258 + Serotonin_Activity_Inhibition + Negative Regulation of Serotonin Release + Serotonin Activity Inhibition + Any process which reduces the steady-state level or inhibits the release of the monoamine neurotransmitter serotonin, resulting in diminished or abbreviated neurotransmission. Some antidepressants act by selectively enhancing reuptake of serotonin from synapses, thus reducing neurotransmission. This process is involved in numerous functions, including regulation of mood, appetite, sleep, muscle contraction, and some cognitive functions including memory and learning. + Negative Regulation of Serotonin Release + + + + + Negative Regulation of Serotonin Release + PT + NCI + + + + + Serotonin Activity Inhibition + SY + NCI + + + + + Any process which reduces the steady-state level or inhibits the release of the monoamine neurotransmitter serotonin, resulting in diminished or abbreviated neurotransmission. Some antidepressants act by selectively enhancing reuptake of serotonin from synapses, thus reducing neurotransmission. This process is involved in numerous functions, including regulation of mood, appetite, sleep, muscle contraction, and some cognitive functions including memory and learning. + NCI + + + + + + + + + C41531 + Phenomenon or Process + Positive Regulation of Histamine Release + C1512465 + Histamine_Activity_Induction + Histamine Activity Induction + Positive Regulation of Histamine Release + Any process in which the biogenic amine and neurotransmitter histamine is released, typically from mast cells, basophils, enterochromaffin-like cells and the brain. Histamine activity can be upregulated in the presence of certain amines, alkaloids and antibiotics and by degranulation of mast cells and basophils. This process is involved in immune system disorders and allergies. + Positive Regulation of Histamine Release + + + + + Histamine Activity Induction + SY + NCI + + + + + Positive Regulation of Histamine Release + PT + NCI + + + + + Any process in which the biogenic amine and neurotransmitter histamine is released, typically from mast cells, basophils, enterochromaffin-like cells and the brain. Histamine activity can be upregulated in the presence of certain amines, alkaloids and antibiotics and by degranulation of mast cells and basophils. This process is involved in immune system disorders and allergies. + NCI + + + + + + + + + C41533 + Phenomenon or Process + Positive Regulation of Serotonin Release + C1519257 + Serotonin_Activity_Induction + Positive Regulation of Serotonin Release + Serotonin Activity Induction + Any process in which the monoamine neurotransmitter serotonin is released or retained in the synaptic cleft, resulting in induced or sustained neurotransmission. Serotonin release can be upregulated in the presence of the empathogen MDMA. Monoamine oxidase inhibitors similarly increase steady state levels of serotonin in the brain by reducing its degradation within synapses. This process is involved in numerous functions, including regulation of mood, appetite, sleep, muscle contraction, and some cognitive functions including memory and learning. + Positive Regulation of Serotonin Release + + + + + Positive Regulation of Serotonin Release + PT + NCI + + + + + Serotonin Activity Induction + SY + NCI + + + + + Any process in which the monoamine neurotransmitter serotonin is released or retained in the synaptic cleft, resulting in induced or sustained neurotransmission. Serotonin release can be upregulated in the presence of the empathogen MDMA. Monoamine oxidase inhibitors similarly increase steady state levels of serotonin in the brain by reducing its degradation within synapses. This process is involved in numerous functions, including regulation of mood, appetite, sleep, muscle contraction, and some cognitive functions including memory and learning. + NCI + + + + + + + + + C41559 + Phenomenon or Process + Glucocorticoid Secretion Process + C1512204 + Glucocorticoid_Secretion_Induction + Glucocorticoid Secretion Induction + Glucocorticoid Secretion Process + Glucocorticoid Secretion Induction consists of initiation of activities involved in release into the bloodstream by the adrenal cortex of a class of steroid substances (glucocorticoids) that affect fat, protein, and carbohydrate metabolism (gluconeogenesis, liver glycogen deposition, elevation of blood sugar); inhibit corticotropin secretion; possess anti-inflammatory activity; and play a role in arterial blood pressure, connective tissue response to injury, reduction of circulating lymphocytes, and central nervous system function. Alteration of positive or negative feedback mechanisms can affect hormone release. + Glucocorticoid Secretion Process + + + + + Glucocorticoid Secretion Induction + SY + NCI + + + + + Glucocorticoid Secretion Process + PT + NCI + + + + + Glucocorticoid Secretion Induction consists of initiation of activities involved in release into the bloodstream by the adrenal cortex of a class of steroid substances (glucocorticoids) that affect fat, protein, and carbohydrate metabolism (gluconeogenesis, liver glycogen deposition, elevation of blood sugar); inhibit corticotropin secretion; possess anti-inflammatory activity; and play a role in arterial blood pressure, connective tissue response to injury, reduction of circulating lymphocytes, and central nervous system function. Alteration of positive or negative feedback mechanisms can affect hormone release. + NCI + + + + + + + + + C41560 + Phenomenon or Process + Melatonin Secretion Process + C1513102 + Melatonin_Secretion_Induction + Melatonin Secretion Induction + Melatonin Secretion Process + Melatonin Secretion Induction involves initiation of activities involved in release into the bloodstream from the pineal gland of a hormone (melatonin) implicated in regulation of sleep, mood, puberty, and ovarian cycles. + Melatonin Secretion Process + + + + + Melatonin Secretion Induction + SY + NCI + + + + + Melatonin Secretion Process + PT + NCI + + + + + Melatonin Secretion Induction involves initiation of activities involved in release into the bloodstream from the pineal gland of a hormone (melatonin) implicated in regulation of sleep, mood, puberty, and ovarian cycles. + NCI + + + + + + + + + C41567 + Phenomenon or Process + Antigen Targeting + C1516015 + Antigen_Targeting + Antigen Targeting + Antigen Targeting involves specific and high affinity non-covalent interaction (binding) of an antibody reagent through intermolecular physical forces of attraction and spatial complementarity with a soluble or particulate substance (antigen) that induces an immune response. Using the keen specificity of antigen recognition by antibodies, targeting selectively localizes antibody-associated reagents to antigen sites for therapeutic or diagnostic effect. + Antigen Targeting + + + + + Antigen Targeting + PT + NCI + + + + + Antigen Targeting involves specific and high affinity non-covalent interaction (binding) of an antibody reagent through intermolecular physical forces of attraction and spatial complementarity with a soluble or particulate substance (antigen) that induces an immune response. Using the keen specificity of antigen recognition by antibodies, targeting selectively localizes antibody-associated reagents to antigen sites for therapeutic or diagnostic effect. + NCI + + + + + + + + + C41572 + Phenomenon or Process + Complement-Dependent Cytotoxicity + C1516743 + Complement-Dependent_Cytotoxicity + Complement-Dependent Cytotoxicity + Activated by cell-surface bound antibody, by immune complexes, or by microbial membrane carbohydrate, Complement-Dependent Cytotoxicity involves complex cascades (classical or properdin pathway) of sequentially interacting serum proteins (some serine proteases), their receptors, and related regulatory proteins that generate Membrane Attack Complex, which creates target cell pores and lysis. + Complement-Dependent Cytotoxicity + + + + + Complement-Dependent Cytotoxicity + PT + NCI + + + + + Activated by cell-surface bound antibody, by immune complexes, or by microbial membrane carbohydrate, Complement-Dependent Cytotoxicity involves complex cascades (classical or properdin pathway) of sequentially interacting serum proteins (some serine proteases), their receptors, and related regulatory proteins that generate Membrane Attack Complex, which creates target cell pores and lysis. + NCI + + + + + + + + + C41585 + Phenomenon or Process + Integrin Inhibition + C1512811 + Integrin_Inhibition + Integrin Inhibition + Integrin Inhibition involves interference with, or restraint of, the activities of a family of noncovalent heterodimeric transmembrane glycoprotein signal transduction receptors for fibronectin, laminin, and other adhesive extracellular matrix glycoproteins, complement, and other cells. Different alpha and beta complexes vary in ligand-specificity and the intracellular domains interact with cytoskeleton. + Integrin Inhibition + + + + + Integrin Inhibition + PT + NCI + + + + + Integrin Inhibition involves interference with, or restraint of, the activities of a family of noncovalent heterodimeric transmembrane glycoprotein signal transduction receptors for fibronectin, laminin, and other adhesive extracellular matrix glycoproteins, complement, and other cells. Different alpha and beta complexes vary in ligand-specificity and the intracellular domains interact with cytoskeleton. + NCI + + + + + + + + + C42597 + Molecular Function + Epitope Spreading + C1707940 + Epitope_Spreading + Epitope Spreading + A normal feature of responses to infectious agents that allows recognition of multiple antigenic targets, Epitope Spreading involves non-cross-reactive epitopes, distinct from the inducing epitope, becoming major targets of an ongoing immune response. Epitope spreading (ES) involves an increased presentation of cryptic epitopes on one protein (intermolecular ES) or dominant epitopes on neighboring molecules (intramolecular ES). The result is an increase in antibody repertoire diversify, resulting in an enhanced overall immune response. Conversely, epitope spreading is the primary immunopathogenic event in autoimmune diseases. + Epitope Spreading + + + + + Epitope Spreading + PT + NCI + + + + + A normal feature of responses to infectious agents that allows recognition of multiple antigenic targets, Epitope Spreading involves non-cross-reactive epitopes, distinct from the inducing epitope, becoming major targets of an ongoing immune response. Epitope spreading (ES) involves an increased presentation of cryptic epitopes on one protein (intermolecular ES) or dominant epitopes on neighboring molecules (intramolecular ES). The result is an increase in antibody repertoire diversify, resulting in an enhanced overall immune response. Conversely, epitope spreading is the primary immunopathogenic event in autoimmune diseases. + NCI + + + + + + + + + C42785 + Phenomenon or Process + Caspase-Dependent Apoptosis + C1707312 + Caspase-Dependent_Apoptosis + Caspase-Dependent Apoptosis + Any apoptotic process that involves pathways that activate intracellular proteolytic caspases. + Caspase-Dependent Apoptosis + + + + + Caspase-Dependent Apoptosis + PT + NCI + + + + + Any apoptotic process that involves pathways that activate intracellular proteolytic caspases. + NCI + + + + + + + + + C42786 + Phenomenon or Process + Caspase-Independent Apoptosis + C1707313 + Caspase-Independent_Apoptosis + Caspase-Independent Apoptosis + Any apoptotic process that does not involve pathways that activate intracellular proteolytic caspases. + Caspase-Independent Apoptosis + + + + + Caspase-Independent Apoptosis + PT + NCI + + + + + Any apoptotic process that does not involve pathways that activate intracellular proteolytic caspases. + NCI + + + + + + + + + C42788 + Molecular Function + Receptor Down Regulation + C0949469 + Receptor_Down_Regulation + Receptor Down Regulation + A multicellular process that regulates the number of transmembrane receptors, by means of increased internalization or decreased expression of the transmembrane receptor. This process is involved in dampening the response to extracellular signals. + Receptor Down Regulation + + + + + Receptor Down Regulation + PT + NCI + + + + + A multicellular process that regulates the number of transmembrane receptors, by means of increased internalization or decreased expression of the transmembrane receptor. This process is involved in dampening the response to extracellular signals. + NCI + + + + + + + + + C42789 + Molecular Function + Tyrosine Kinase-Associated Receptor Down-Regulation + C1709853 + Receptor_Tyrosine_Kinase_Down_Regulation + Receptor Tyrosine Kinase Down Regulation + Tyrosine Kinase-Associated Receptor Down-Regulation + A multicellular process that regulates the number of tyrosine kinase-associated transmembrane receptors, by means of increased internalization or decreased expression of the transmembrane receptor. This process is involved in dampening the response to extracellular signals. + Tyrosine Kinase-Associated Receptor Down-Regulation + + + + + Receptor Tyrosine Kinase Down Regulation + SY + NCI + + + + + Tyrosine Kinase-Associated Receptor Down-Regulation + PT + NCI + + + + + A multicellular process that regulates the number of tyrosine kinase-associated transmembrane receptors, by means of increased internalization or decreased expression of the transmembrane receptor. This process is involved in dampening the response to extracellular signals. + NCI + + + + + + + + + C43367 + Conceptual Entity + Confidence + C1704726 + Confidence + Confidence + A feeling of trust (in someone or something). + Confidence + + + + + Confidence + PT + NCI + + + + + A feeling of trust (in someone or something). + NCI + + + + + + + + + C45546 + Molecular Function + Retinoic Acid Receptor Activation + C1709932 + Retinoic_Acid_Receptor_Activation + Retinoic Acid Receptor Activation + Any environment-to-cell communication in which the ligand retinoic acid binds to intracellular retinoic acid receptors. This process is involved in embryonic developmental patterning. + Retinoic Acid Receptor Activation + + + + + Retinoic Acid Receptor Activation + PT + NCI + + + + + Any environment-to-cell communication in which the ligand retinoic acid binds to intracellular retinoic acid receptors. This process is involved in embryonic developmental patterning. + NCI + + + + + + + + + C45547 + Molecular Function + Cytokine Receptor Activation + C1707601 + Cytokine_Receptor_Activation + Cytokine Receptor Activation + Any interaction between a cognate ligand and any of a series of cytokine receptors. Activation of cytokine receptors is involved in regulation of the immune system, cell proliferation, cell death, as well as other multicellular processes. + Cytokine Receptor Activation + + + + + Cytokine Receptor Activation + PT + NCI + + + + + Any interaction between a cognate ligand and any of a series of cytokine receptors. Activation of cytokine receptors is involved in regulation of the immune system, cell proliferation, cell death, as well as other multicellular processes. + NCI + + + + + + + + + C45548 + Molecular Function + Antigen Sensitization + C1706823 + Antigen_Sensitization + Antigen Sensitization + Antigen Sensitization is a process of immunization with an antigen preparation that renders an immune-response involving generation of antibodies against the specific antigen(s) injected. + Antigen Sensitization + + + + + Antigen Sensitization + PT + NCI + + + + + Antigen Sensitization is a process of immunization with an antigen preparation that renders an immune-response involving generation of antibodies against the specific antigen(s) injected. + NCI + + + + + + + + + C45549 + Molecular Function + Receptor Desensitization + C1709852 + Receptor_Desensitization + Desensitization + Receptor Desensitization + A multicellular process that regulates the extent of response to a stimulus either by modulation of active receptors or inhibition of intracellular catalytic activities that are initiated by receptor activation. + Receptor Desensitization + + + + + Desensitization + SY + NCI + + + + + Receptor Desensitization + PT + NCI + + + + + A multicellular process that regulates the extent of response to a stimulus either by modulation of active receptors or inhibition of intracellular catalytic activities that are initiated by receptor activation. + NCI + + + + + + + + + C45839 + Phenomenon or Process + Anoikis + C0872097 + Suspension-Induced_Apoptosis + Anoikis + Detachment-Induced Cell Death + Suspension-Induced Apoptosis + Any apoptotic process triggered by inadequate or inappropriate adherence to substrate, such as may occur after disruption of the interactions between normal epithelial cells and the extracellular matrix. + Anoikis + + + + + Anoikis + PT + NCI + + + + + Detachment-Induced Cell Death + SY + NCI + + + + + Suspension-Induced Apoptosis + SY + NCI + + + + + Any apoptotic process triggered by inadequate or inappropriate adherence to substrate, such as may occur after disruption of the interactions between normal epithelial cells and the extracellular matrix. + NCI + + + + + + + + + C51035 + Phenomenon or Process + Mechanism of Cell Death + C1708951 + Mechanism_of_Cell_Death + Mechanism of Cell Death + A biological process that results in permanent cessation of all vital functions of a cell. + Mechanism of Cell Death + + + + + Mechanism of Cell Death + PT + NCI + + + + + A biological process that results in permanent cessation of all vital functions of a cell. + NCI + Gene Ontology + + + + + + + + + C51037 + Phenomenon or Process + Regulation of Cell Death Process + C1711228 + Regulation_of_Cell_Death + Regulation of Cell Death + Regulation of Cell Death Process + A process that is involved in modulating the rate or frequency of cell death. + Regulation of Cell Death Process + + + + + Regulation of Cell Death + SY + NCI + + + + + Regulation of Cell Death Process + PT + NCI + + + + + A process that is involved in modulating the rate or frequency of cell death. + NCI + Gene Ontology + + + + + + + + + C54070 + Mental Process + Awareness + C0004448 + Awareness + Aware + Awareness + Knowing that something exists, or having knowledge or experience of a particular thing; having special interest in or experience of something and so being well informed of what is happening in that subject at the present time. + Awareness + + + + + Aware + SY + NCI + + + + + Awareness + PT + NCI + + + + + Knowing that something exists, or having knowledge or experience of a particular thing; having special interest in or experience of something and so being well informed of what is happening in that subject at the present time. + NCI + dictionary.cambridge.org + + + + + + + + + C54103 + Cell + Abnormal Germ Cell + C1706683 + Abnormal_Germ_Cell + Abnormal Germ Cell + Abnormal Germ Cell + + + + + Abnormal Germ Cell + PT + NCI + + + + + + + + + + + + + + + C54226 + Mental Process + Thinking + C0039869 + Thinking + Thinking + Thought + Thoughts + Mental activity, not predominantly perceptual, by which one apprehends some aspect of an object or situation based on past learning and experience. + Thinking + + + + + Thinking + PT + NCI + + + + + Thought + SY + NCI + + + + + Thoughts + SY + NCI + + + + + Mental activity, not predominantly perceptual, by which one apprehends some aspect of an object or situation based on past learning and experience. + NCI + On-line Medical Dictionary + + + + + + + + + C54266 + Mental Process + Emotion + C0013987 + Emotion + Emotion + Emotional + Emotions + That aspect of consciousness devoted to affect or feeling; a strong feeling, aroused mental state, or intense state of drive or unrest directed toward a definite object, with physiological, somatic, and behavioral components. + Emotion + + + + + Emotion + PT + NCI + + + + + Emotional + AD + NCI + + + + + Emotions + SY + NCI + + + + + That aspect of consciousness devoted to affect or feeling; a strong feeling, aroused mental state, or intense state of drive or unrest directed toward a definite object, with physiological, somatic, and behavioral components. + NCI + + + + + + + + + + + + + + + C54268 + Mental Process + Dreaming + C0013117 + Dreaming + Dream + Dreaming + Dreams + A mental phenomenon occurring during sleep in which images, emotions, and thoughts are experienced with a sense of reality; occurs during REM sleep. + Dreaming + + + + + Dream + SY + NCI + + + + + Dreaming + PT + NCI + + + + + Dreams + SY + NCI + + + + + A mental phenomenon occurring during sleep in which images, emotions, and thoughts are experienced with a sense of reality; occurs during REM sleep. + NCI + + + + + + + + + C60730 + Conceptual Entity + Interest + C0543488 + Interest + Interest + A state of curiosity or concern about or attention to something. + Interest + + + + + Interest + PT + NCI + + + + + A state of curiosity or concern about or attention to something. + NCI + + + + + + + + + C60804 + Cell + Small Cuboidal Cell Resembling Fetal Hepatocyte + C1883046 + Small_Cuboidal_Cell_Resembling_Fetal_Hepatocyte + Small Cuboidal Cell Resembling Fetal Hepatocyte + Small Cuboidal Cell Resembling Fetal Hepatocyte + + + + + Small Cuboidal Cell Resembling Fetal Hepatocyte + PT + NCI + + + + + + + + + C61457 + Physiologic Function + Thrombolysis + C0520997 + The process of breaking up a thrombus (blood clot) that is blocking blood flow. The blood clot may be dissolved using drugs delivered through a catheter (tube) into the clot. + Thrombolysis + Thrombolysis + Thrombolytic + thrombolysis + The process of breaking up and dissolving blood clots. + Thrombolysis + + + + + The process of breaking up a thrombus (blood clot) that is blocking blood flow. The blood clot may be dissolved using drugs delivered through a catheter (tube) into the clot. + NCI-GLOSS + + + + + Thrombolysis + PT + NCI + + + + + Thrombolytic + AD + NCI + + + + + thrombolysis + PT + NCI-GLOSS + CDR0000476063 + + + + + The process of breaking up and dissolving blood clots. + NCI + + + + + + + + + C61553 + Phenomenon or Process + Cytolytic Process + C1536403 + In biology, lysis refers to the breakdown of a cell caused by damage to its plasma (outer) membrane. It can be caused by chemical or physical means (for example, strong detergents or high-energy sound waves) or by infection with a strain virus that can lyse cells. + Cytolysis + Cytolysis + Cytolytic Process + lysis + Any cell death process resulting from rupture of cell membranes and loss of cytoplasm. + Cytolytic Process + + + + + In biology, lysis refers to the breakdown of a cell caused by damage to its plasma (outer) membrane. It can be caused by chemical or physical means (for example, strong detergents or high-energy sound waves) or by infection with a strain virus that can lyse cells. + NCI-GLOSS + + + + + Cytolysis + SY + NCI + + + + + Cytolytic Process + PT + NCI + + + + + lysis + PT + NCI-GLOSS + CDR0000044606 + + + + + Any cell death process resulting from rupture of cell membranes and loss of cytoplasm. + NCI + + + + + + + + + + + + + + + C62109 + Organ or Tissue Function + Diastole + C0012000 + Diastole + Diastole + Diastolic + The widening of the chambers of the heart between two contractions when the chambers fill with blood. + Diastole + + + + + Diastole + PT + NCI + + + + + Diastolic + AD + NCI + + + + + The widening of the chambers of the heart between two contractions when the chambers fill with blood. + NCI + + + + + + + + + + + + + + + C62110 + Organ or Tissue Function + Systole + C0039155 + Systole + Systole + Systolic + The contraction of the chambers of the heart (especially the ventricles) to drive blood into the aorta and pulmonary artery. + Systole + + + + + Systole + PT + NCI + + + + + Systolic + AD + NCI + + + + + The contraction of the chambers of the heart (especially the ventricles) to drive blood into the aorta and pulmonary artery. + NCI + + + + + + + + + C62183 + Organism Function + Articulation + C0234830 + Articulation + Articulation + Movements of the mouth and airway that produce speech; the act of vocal expression. + Articulation + + + + + Articulation + PT + NCI + + + + + Movements of the mouth and airway that produce speech; the act of vocal expression. + NCI + + + + + + + + + C62184 + Mental Process + Dissatisfaction + C0870433 + Dissatisfaction + Dissatisfaction + Dissatisfied + The feeling of being displeased and discontent. + Dissatisfaction + + + + + Dissatisfaction + PT + NCI + + + + + Dissatisfied + AD + NCI + + + + + The feeling of being displeased and discontent. + NCI + + + + + + + + + C62185 + Mental Process + Satisfaction + C0242428 + Satisfaction + Satisfaction + Satisfied + The feeling of being pleased and content. + Satisfaction + + + + + Satisfaction + PT + NCI + + + + + Satisfied + AD + NCI + + + + + The feeling of being pleased and content. + NCI + + + + + + + + + C62186 + Mental Process + Self-conscious + C1882997 + Self-conscious + Self-conscious + Excessively and uncomfortably conscious of your appearance or behavior. + Self-conscious + + + + + Self-conscious + PT + NCI + + + + + Excessively and uncomfortably conscious of your appearance or behavior. + NCI + + + + + + + + + C62187 + Mental Process + Embarrassment + C0679112 + Embarrassment + Embarrassment + An unpleasant emotional state experienced upon having an inadequacy, guilt, or socially unacceptable act or trait witnessed by or revealed to others. + Embarrassment + + + + + Embarrassment + PT + NCI + + + + + An unpleasant emotional state experienced upon having an inadequacy, guilt, or socially unacceptable act or trait witnessed by or revealed to others. + NCI + + + + + + + + + C62655 + Biologic Function + Bioluminescence + C0162404 + Bioluminescence + Bioluminescence + The production of light by certain living organisms, including fireflies and phytoplankton, by the conversion of chemical to radiant energy. + Bioluminescence + + + + + Bioluminescence + PT + NCI + + + + + The production of light by certain living organisms, including fireflies and phytoplankton, by the conversion of chemical to radiant energy. + NCI + + + + + + + + + C6527 + Physiologic Function + Alloimmunization + C0948201 + MedDRA + NICHD + An immune system response to foreign human substances. + Alloimmunization + Alloimmunization + Alloimmunisation + Alloimmunization + An immune response to foreign (donor) antigens. + Alloimmunization + + + + + An immune system response to foreign human substances. + NICHD + + + + + Alloimmunization + Has Synonym + LLT + 10054308 + MedDRA + 18.1 + + + + + Alloimmunisation + SY + NICHD + + + + + Alloimmunization + PT + NCI + + + + + Alloimmunization + PT + NICHD + + + + + An immune response to foreign (donor) antigens. + NCI + + + + + + + + + C71427 + Cell Function + Autophagy + Autophagy + C0004391 + CTRP + A normal process in which a cell destroys proteins and other substances in its cytoplasm (the fluid inside the cell membrane but outside the nucleus), which may lead to cell death. Autophagy may prevent normal cells from developing into cancer cells, but it may also protect cancer cells by destroying anticancer drugs or substances taken up by them. + Autophagy + Autophagocytosis + Autophagy + autophagy + Autophagy is a biological process that involves the lysosomal degradation of intracellular components using it a cell's own machinery. This process can play a role in cellular defense, embryonic development, and cell growth. + Autophagy + + + + + A normal process in which a cell destroys proteins and other substances in its cytoplasm (the fluid inside the cell membrane but outside the nucleus), which may lead to cell death. Autophagy may prevent normal cells from developing into cancer cells, but it may also protect cancer cells by destroying anticancer drugs or substances taken up by them. + NCI-GLOSS + + + + + Autophagocytosis + SY + NCI + + + + + Autophagy + DN + CTRP + + + + + Autophagy + PT + NCI + + + + + autophagy + PT + NCI-GLOSS + CDR0000561319 + + + + + Autophagy is a biological process that involves the lysosomal degradation of intracellular components using it a cell's own machinery. This process can play a role in cellular defense, embryonic development, and cell growth. + NCI + + + + + + + + + C71733 + Phenomenon or Process + Biological Absorption + C2347023 + CDISC-GLOSS + The process by which medications reach the blood stream when administered other than intravenously, for example, through nasal membranes. See also ADME (pharmacokinetics). + The process of taking nutrients from the digestive system into the blood so they can be used in the body. + Biological_Absorption + Absorption + Biological Absorption + absorption + The process of penetration of a substance into a living organism. This process could involve specialized and/or non-specialized mechanisms, active transport or passive movement, and carrier system(s). The common routes of absorption in mammals include the organs of the respiratory and gastrointestinal systems, and the skin. + Biological Absorption + + + + + The process by which medications reach the blood stream when administered other than intravenously, for example, through nasal membranes. See also ADME (pharmacokinetics). + CDISC-GLOSS + + + + + The process of taking nutrients from the digestive system into the blood so they can be used in the body. + NCI-GLOSS + + + + + Absorption + SY + NCI + + + + + Biological Absorption + PT + NCI + + + + + absorption + PT + CDISC-GLOSS + + + + + absorption + SY + NCI-GLOSS + CDR0000463702 + + + + + The process of penetration of a substance into a living organism. This process could involve specialized and/or non-specialized mechanisms, active transport or passive movement, and carrier system(s). The common routes of absorption in mammals include the organs of the respiratory and gastrointestinal systems, and the skin. + NCI + + + + + + + + + C72670 + Mental Process + Happiness + C0018592 + Happiness + Happiness + Happy + The feeling of being pleased and content. + Happiness + + + + + Happiness + PT + NCI + + + + + Happy + AD + NCI + + + + + The feeling of being pleased and content. + NCI + + + + + + + + + C72882 + Mental Process + Reluctance + C2347948 + Reluctance + Reluctance + Reluctant + A certain degree of unwillingness. + Reluctance + + + + + Reluctance + PT + NCI + + + + + Reluctant + AD + NCI + + + + + A certain degree of unwillingness. + NCI + + + + + + + + + C72883 + Mental Process + Mood + C0026516 + Mood + Mood + A relatively temporary state of feeling. + Mood + + + + + Mood + PT + NCI + + + + + Mood + SY + caDSR + + + + + A relatively temporary state of feeling. + NCI + + + + + + + + + C72885 + Mental Process + Outlook + C0004271 + Outlook + Attitude + Outlook + A habitual or characteristic mental attitude that determines how a person will interpret and respond to situations. + Outlook + + + + + Attitude + SY + NCI + + + + + Outlook + PT + NCI + + + + + A habitual or characteristic mental attitude that determines how a person will interpret and respond to situations. + NCI + + + + + + + + + C73431 + Mental Process + Shame + C0036938 + Shame + Shame + A painful emotion resulting from a feeling of inadequacy, embarrassment, or guilt. + Shame + + + + + Shame + PT + NCI + + + + + A painful emotion resulting from a feeling of inadequacy, embarrassment, or guilt. + NCI + + + + + + + + + C73497 + Organism Function + Balance + C0014653 + Balance + Balance + The maintenance of a stable, upright body position. + Balance + + + + + Balance + PT + NCI + + + + + The maintenance of a stable, upright body position. + NCI + + + + + + + + + C73506 + Mental Process + Anger + C0002957 + MedDRA + NICHD + An emotional state characterized by marked annoyance or hostility. + Anger + Anger + Anger + An emotional state characterized by marked annoyance or hostility. + Anger + + + + + An emotional state characterized by marked annoyance or hostility. + NICHD + + + + + Anger + Has Synonym + LLT + 10002368 + MedDRA + 18.1 + + + + + Anger + PT + NCI + + + + + Anger + PT + NICHD + + + + + An emotional state characterized by marked annoyance or hostility. + NCI + + + + + + + + + C73508 + Mental Process + Affection + C0871641 + Affection + Affection + A positive feeling of liking. + Affection + + + + + Affection + PT + NCI + + + + + A positive feeling of liking. + NCI + WordNet + + + + + + + + + C73509 + Mental Process + Love + C0024028 + Love + Love + A strong positive emotion of affection and attraction. + Love + + + + + Love + PT + NCI + + + + + A strong positive emotion of affection and attraction. + NCI + + + + + + + + + C73510 + Mental Process + Humiliation + C0683285 + Humiliation + Humiliation + A feeling of extreme embarrassment. + Humiliation + + + + + Humiliation + PT + NCI + + + + + A feeling of extreme embarrassment. + NCI + + + + + + + + + C73522 + Mental Process + Sexual Arousal + C0233972 + Sexual_Arousal + Sexual Arousal + Heightened urges of sexual desires in preparation for sexual behavior. + Sexual Arousal + + + + + Sexual Arousal + PT + NCI + + + + + Heightened urges of sexual desires in preparation for sexual behavior. + NCI + + + + + + + + + C74531 + Mental Process + Hopelessness + C3845527 + Hopelessness + Feeling of Hopelessness + Hopeless + Hopelessness + The despair you feel when you have abandoned hope of comfort or success. + Hopelessness + + + + + Feeling of Hopelessness + SY + NCI + + + + + Hopeless + AD + NCI + + + + + Hopelessness + PT + NCI + + + + + The despair you feel when you have abandoned hope of comfort or success. + NCI + + + + + + + + + C74532 + Mental Process + Nervousness + C0027769 + Nervousness + Feeling of Nervousness + Nervous + Nervousness + An uneasy psychological state; the anxious feeling you have when you have the jitters. + Nervousness + + + + + Feeling of Nervousness + SY + NCI + + + + + Nervous + AD + NCI + + + + + Nervousness + PT + NCI + + + + + An uneasy psychological state; the anxious feeling you have when you have the jitters. + NCI + + + + + + + + + C74534 + Mental Process + Sadness + C3536794 + MedDRA + NICHD + An emotional state characterized by feelings of unhappiness or grief. + Sadness + Feeling sad + Feeling of Sadness + Sad + Sad Mood + Sadness + Feelings of grief or unhappiness. + Sadness + + + + + An emotional state characterized by feelings of unhappiness or grief. + NICHD + + + + + Feeling sad + Has Synonym + LLT + 10016364 + MedDRA + 18.1 + + + + + Feeling of Sadness + SY + NCI + + + + + Sad + AD + NCI + + + + + Sad Mood + SY + caDSR + + + + + Sadness + PT + NCI + + + + + Sadness + PT + NICHD + + + + + Feelings of grief or unhappiness. + NCI + + + + + + + + + C74535 + Mental Process + Worthlessness + C0855235 + Worthlessness + Feeling of Worthlessness + Worthless + Worthlessness + Feelings of being unimportant or useless. + Worthlessness + + + + + Feeling of Worthlessness + SY + NCI + + + + + Worthless + AD + NCI + + + + + Worthlessness + PT + NCI + + + + + Feelings of being unimportant or useless. + NCI + + + + + + + + + C77821 + Mental Process + Orientation + C0029266 + Orientation_Awareness + Orientation + A person's awareness of self with regard to time, place, and personal relationships. + Orientation + + + + + Orientation + PT + NCI + + + + + A person's awareness of self with regard to time, place, and personal relationships. + NCI + + + + + + + + + C77960 + Mental Process + Fear + C0015726 + Fear + Fear + Fearful + Fearfulness + A feeling of apprehension that one may be in danger. + Fear + + + + + Fear + PT + NCI + + + + + Fearful + AD + NCI + + + + + Fearfulness + SY + NCI + + + + + A feeling of apprehension that one may be in danger. + NCI + + + + + + + + + C77961 + Mental Process + Joy + CL449058 + Joy + Enjoyed + Enjoyment + Feeling of Joy + Joy + Joyful + A feeling of delight. + Joy + + + + + Enjoyed + AD + NCI + + + + + Enjoyment + SY + NCI + + + + + Feeling of Joy + SY + NCI + + + + + Joy + PT + NCI + + + + + Joyful + AD + NCI + + + + + A feeling of delight. + NCI + + + + + + + + + C77962 + Mental Process + Hope + C0392347 + Hope + Hope + Hopeful + Hopefulness + A feeling of optimism that one will attain a desired outcome. + Hope + + + + + Hope + PT + NCI + + + + + Hopeful + AD + NCI + + + + + Hopefulness + SY + NCI + + + + + A feeling of optimism that one will attain a desired outcome. + NCI + + + + + + + + + C77965 + Mental Process + Feelings + C1527305 + Feelings + Feeling + Feelings + Emotional sensations. + Feelings + + + + + Feeling + SY + NCI + + + + + Feelings + PT + NCI + + + + + Emotional sensations. + NCI + + + + + + + + + C77966 + Mental Process + Irritation + C0022107 + A disorder characterized by an abnormal responsiveness to stimuli or physiological arousal; may be in response to pain, fright, a drug, an emotional situation or a medical condition. + Irritation_Emotion + Irritability + Irritation + Feelings of annoyance, impatience, and anger. + Irritation + + + + + A disorder characterized by an abnormal responsiveness to stimuli or physiological arousal; may be in response to pain, fright, a drug, an emotional situation or a medical condition. + CTCAE + + + + + Irritability + PT + CTCAE + + + + + Irritability + SY + NCI + + + + + Irritation + PT + NCI + + + + + Feelings of annoyance, impatience, and anger. + NCI + + + + + + + + + C77969 + Mental Process + Like + C0870814 + Like + Like + A feeling of fondness for a person or thing. + Like + + + + + Like + PT + NCI + + + + + A feeling of fondness for a person or thing. + NCI + + + + + + + + + C78654 + Phenomenon or Process + Grip + C0220843 + Grip + Grasp + Grip + The ability to hold or grasp. + Grip + + + + + Grasp + SY + NCI + + + + + Grip + PT + NCI + + + + + The ability to hold or grasp. + NCI + + + + + + + + + C81269 + Organism Function + Motor Development + C0870919 + NICHD + Motor_Development + Motor Development + The evolution of physical movement over an individual's lifespan. + Motor Development + + + + + Motor Development + PT + NCI + + + + + Motor Development + PT + NICHD + + + + + The evolution of physical movement over an individual's lifespan. + NCI + + + + + + + + + C82956 + Organ or Tissue Function + Odontogenesis + C0028877 + Odontogenesis + Odontogenesis + The process of tooth development. + Odontogenesis + + + + + Odontogenesis + PT + NCI + + + + + The process of tooth development. + NCI + + + + + + + + + C83011 + Cell + Ground Glass Hepatocyte + C0598786 + Ground_Glass_Hepatocyte + Ground Glass Cell + Ground Glass Hepatocyte + An abnormally large hepatocyte with eosinophilic or pale, glassy cytoplasm and peripherally displaced nucleus. This appearance is due to hyperplasia of the smooth endoplasmic reticulum. + Ground Glass Hepatocyte + + + + + Ground Glass Cell + SY + NCI + + + + + Ground Glass Hepatocyte + PT + NCI + + + + + An abnormally large hepatocyte with eosinophilic or pale, glassy cytoplasm and peripherally displaced nucleus. This appearance is due to hyperplasia of the smooth endoplasmic reticulum. + NCI + + + + + + + + + C86022 + Mental Process + Comprehension + C0162340 + Comprehension + Understanding + An ability to understand the meaning or importance of something (or the knowledge acquired as a result). + Comprehension + + + + + Comprehension + PT + NCI + + + + + Understanding + SY + NCI + + + + + An ability to understand the meaning or importance of something (or the knowledge acquired as a result). + NCI + + + + + + + + + C86064 + Mental Process + Despondency + C0392375 + Despondency + A state of emotional depression which may result in a negative outlook on life. + Despondency + + + + + Despondency + PT + NCI + + + + + A state of emotional depression which may result in a negative outlook on life. + NCI + + + + + + + + + C86579 + Organ or Tissue Function + Placentation + C0032058 + Placentation + The formation of the placenta in the uterus. + Placentation + + + + + Placentation + PT + NCI + + + + + The formation of the placenta in the uterus. + NCI + + + + + + + + + C86580 + Mental Process + Pleasure + C0679105 + Pleasure + An emotion associated with feeling good. + Pleasure + + + + + Pleasure + PT + NCI + + + + + An emotion associated with feeling good. + NCI + + + + + + + + + C86584 + Mental Process + Reasoning + C0684328 + Reasoning + Thinking that is coherent and logical. + Reasoning + + + + + Reasoning + PT + NCI + + + + + Thinking that is coherent and logical. + NCI + + + + + + + + + C86585 + Mental Process + Recognition + C0524637 + Recognition + The act of seeing something as familiar. + Recognition + + + + + Recognition + PT + NCI + + + + + The act of seeing something as familiar. + NCI + + + + + + + + + C86911 + Mental Process + Somatization + C0149779 + Somatization + The conversion of mental experiences or states into physical symptoms. + Somatization + + + + + Somatization + PT + NCI + + + + + The conversion of mental experiences or states into physical symptoms. + NCI + + + + + + + + + C86941 + Mental Process + Worry + CL449055 + Worry + Mental distress resulting from concern for something impending or anticipated. + Worry + + + + + Worry + PT + NCI + + + + + Mental distress resulting from concern for something impending or anticipated. + NCI + + + + + + + + + C86946 + Mental Process + Mental Blocking + C0233660 + Blocking + Mental Block + Mental Blocking + Difficulty in recollection, or interruption of a train of thought or speech, due to emotional factors. + Mental Blocking + + + + + Blocking + SY + NCI + + + + + Mental Block + SY + NCI + + + + + Mental Blocking + PT + NCI + + + + + Difficulty in recollection, or interruption of a train of thought or speech, due to emotional factors. + NCI + + + + + + + + + C87177 + Organism Function + Color Vision + C0086032 + Color Vision + The ability to perceive differences in color. + Color Vision + + + + + Color Vision + PT + NCI + + + + + The ability to perceive differences in color. + NCI + + + + + + + + + C88416 + Mental Process + Verbal Memory + C0561770 + Verbal Memory + The ability to store and recall linguistic information. + Verbal Memory + + + + + Verbal Memory + PT + NCI + + + + + The ability to store and recall linguistic information. + NCI + + + + + + + + + C88417 + Mental Process + Visual Memory + C0542316 + Visual Memory + The ability to store and recall visual information. + Visual Memory + + + + + Visual Memory + PT + NCI + + + + + The ability to store and recall visual information. + NCI + + + + + + + + + C88418 + Mental Process + Working Memory + C0025265 + Working Memory + Short term memory related to the storage, processing and recall of information required for the accomplishment of immediate cognitive tasks. + Working Memory + + + + + Working Memory + PT + NCI + + + + + Short term memory related to the storage, processing and recall of information required for the accomplishment of immediate cognitive tasks. + NCI + + + + + + + + + C88419 + Mental Process + Executive Function + C0935584 + Executive Function + A set of mental processes that controls and manages the cognitive functions. + Executive Function + + + + + Executive Function + PT + NCI + + + + + A set of mental processes that controls and manages the cognitive functions. + NCI + + + + + + + + + C88420 + Organ or Tissue Function + Gross Motor Skill + C0678858 + Gross Motor Skill + The ability to use large muscle groups for gross body movements. This developmental skill begins in infancy and early childhood. + Gross Motor Skill + + + + + Gross Motor Skill + PT + NCI + + + + + The ability to use large muscle groups for gross body movements. This developmental skill begins in infancy and early childhood. + NCI + + + + + + + + + C89275 + Mental Process + Comfort + C1331418 + Comfort + Ease + A feeling of freedom from constraint or embarrassment; feeling relaxed and natural. + Comfort + + + + + Comfort + PT + NCI + + + + + Ease + SY + NCI + + + + + A feeling of freedom from constraint or embarrassment; feeling relaxed and natural. + NCI + + + + + + + + + C92160 + Phenomenon or Process + Activation of Membrane Attack Complex + CL449111 + Activation of Membrane Attack Complex + A series of reactions that result in formation of a pore, composed of complement proteins C5b, C6, C7, C8, and C9, in the membrane of a pathogenic cell. The pore allows free diffusion of molecules into and out of the cell and reduces cell viability. + Activation of Membrane Attack Complex + + + + + Activation of Membrane Attack Complex + PT + NCI + + + + + A series of reactions that result in formation of a pore, composed of complement proteins C5b, C6, C7, C8, and C9, in the membrane of a pathogenic cell. The pore allows free diffusion of molecules into and out of the cell and reduces cell viability. + NCI + + + + + + + + + C92166 + Cell or Molecular Dysfunction + Clonal Deletion + C0206123 + Clonal Deletion + Processes that result in the removal of B and T lymphocytes which have specificity for self antigens. + Clonal Deletion + + + + + Clonal Deletion + PT + NCI + + + + + Processes that result in the removal of B and T lymphocytes which have specificity for self antigens. + NCI + + + + + + + + + C93211 + Mental Process + Acculturation + C0000943 + Acculturation + The process of adopting the traits or social patterns of a different population group. + Acculturation + + + + + Acculturation + PT + NCI + + + + + The process of adopting the traits or social patterns of a different population group. + NCI + + + + + + + + + C94544 + Organism Function + Dental Attrition + C0004277 + Attrition + Dental Attrition + The loss of tooth structure by mechanical forces from opposing teeth. + Dental Attrition + + + + + Attrition + SY + NCI + + + + + Dental Attrition + PT + NCI + + + + + The loss of tooth structure by mechanical forces from opposing teeth. + NCI + + + + + + + + + C94593 + Mental Process + Optimism + C0237428 + The tendency to believe that there is good in everything and to have positive thoughts about most things that happen. + Optimism + optimism + Optimism + + + + + The tendency to believe that there is good in everything and to have positive thoughts about most things that happen. + NCI-GLOSS + + + + + Optimism + PT + NCI + + + + + optimism + PT + NCI-GLOSS + CDR0000640063 + + + + + + + + + C94869 + Organ or Tissue Function + Cerebral Blood Flow + C0428714 + CBF + Cerebral Blood Flow + Perfusion of blood through the cerebrum. + Cerebral Blood Flow + + + + + CBF + AB + NCI + + + + + Cerebral Blood Flow + PT + NCI + + + + + Perfusion of blood through the cerebrum. + NCI + Dr. Joseph A. Thie + + + + + + + + + C94939 + Organ or Tissue Function + Myocardial Blood Flow + C2986786 + MBF + Myocardial Blood Flow + Perfusion of blood through the myocardium. + Myocardial Blood Flow + + + + + MBF + AB + NCI + + + + + Myocardial Blood Flow + PT + NCI + + + + + Perfusion of blood through the myocardium. + NCI + Dr. Joseph A. Thie + + + + + + + + + C95492 + Mental Process + Calm + CL449160 + Calm + A feeling of freedom from agitation or excitement. + Calm + + + + + Calm + PT + NCI + + + + + A feeling of freedom from agitation or excitement. + NCI + + + + + + + + + C95494 + Mental Process + Content + C0423896 + Content + Contentment + A feeling of satisfaction with things as they are. + Content + + + + + Content + PT + NCI + + + + + Contentment + SY + NCI + + + + + A feeling of satisfaction with things as they are. + NCI + + + + + + + + + C95495 + Mental Process + Indecision + CL449162 + Indecision + Indecisive + A feeling of doubt concerning two or more possible alternatives or courses of action. + Indecision + + + + + Indecision + PT + NCI + + + + + Indecisive + SY + NCI + + + + + A feeling of doubt concerning two or more possible alternatives or courses of action. + NCI + + + + + + + + + C95496 + Mental Process + Jittery + C2987186 + Jittery + A feeling of nervous unease. + Jittery + + + + + Jittery + PT + NCI + + + + + A feeling of nervous unease. + NCI + + + + + + + + + C95497 + Mental Process + Pleasant + C2987187 + Pleasant + Pleasant Feeling + Feeling friendly, kind, or good-natured. + Pleasant + + + + + Pleasant + PT + NCI + + + + + Pleasant Feeling + SY + NCI + + + + + Feeling friendly, kind, or good-natured. + NCI + + + + + + + + + C95498 + Mental Process + Secure + C3146231 + Secure + Secure Feeling + Feeling untroubled by fear, doubt, or vulnerability. + Secure + + + + + Secure + PT + NCI + + + + + Secure Feeling + SY + NCI + + + + + Feeling untroubled by fear, doubt, or vulnerability. + NCI + + + + + + + + + + C95499 + Mental Process + Self-confidence + C0237529 + Self-confidence + A feeling of trust in yourself and your abilities. + Self-confidence + + + + + Self-confidence + PT + NCI + + + + + A feeling of trust in yourself and your abilities. + NCI + + + + + + + + + C95500 + Mental Process + Steady + C0205361 + Steady + Not subject to change, especially in behavior. + Steady + + + + + Steady + PT + NCI + + + + + Not subject to change, especially in behavior. + NCI + + + + + + + + + C95501 + Mental Process + Strain + C2987481 + Strain + A feeling of difficulty that causes worry or emotional tension. + Strain + + + + + Strain + PT + NCI + + + + + A feeling of difficulty that causes worry or emotional tension. + NCI + + + + + + + + + C95502 + Mental Process + Tension + C0235108 + Tense + Tense Feeling + Tension + A feeling of mental or emotional strain or suspense. + Tension + + + + + Tense + SY + NCI + + + + + Tense Feeling + SY + NCI + + + + + Tension + PT + NCI + + + + + A feeling of mental or emotional strain or suspense. + NCI + + + + + + + + + C95503 + Mental Process + Upset + C3887804 + Upset + A feeling of worry and unhappiness. + Upset + + + + + Upset + PT + NCI + + + + + A feeling of worry and unhappiness. + NCI + + + + + + + + + C95555 + Mental Process + Guilt + C0018379 + Feeling Guilty + Guilt + Guilty + A feeling of shame and sorrow based on the belief of having done something wrong or failing an obligation. + Guilt + + + + + Feeling Guilty + SY + NCI + + + + + Guilt + PT + NCI + + + + + Guilty + SY + NCI + + + + + A feeling of shame and sorrow based on the belief of having done something wrong or failing an obligation. + NCI + + + + + + + + + C95745 + Mental Process + Helplessness + C0150063 + Helpless + Helplessness + A feeling of being unable to control yourself or your circumstances. + Helplessness + + + + + Helpless + AD + NCI + + + + + Helplessness + PT + NCI + + + + + A feeling of being unable to control yourself or your circumstances. + NCI + + + + + + + + + C96323 + Molecular Function + Positive Regulation of Angiogenesis + C1160253 + Positive Regulation of Angiogenesis + Promotion of Angiogenesis + Up-Regulation of Angiogenesis + Upregulation of Angiogenesis + A process or mechanism that promotes, initiates or sustains angiogenesis. + Positive Regulation of Angiogenesis + + + + + Positive Regulation of Angiogenesis + PT + NCI + + + + + Promotion of Angiogenesis + SY + NCI + + + + + Up-Regulation of Angiogenesis + SY + NCI + + + + + Upregulation of Angiogenesis + SY + NCI + + + + + A process or mechanism that promotes, initiates or sustains angiogenesis. + NCI + + + + + + + + + + + + + + + C96825 + Cell Function + Megakaryopoiesis + CL449218 + Megakaryocytopoiesis + Megakaryopoiesis + A hematopoietic process that refers to the production of megakaryocytes in the bone marrow. + Megakaryopoiesis + + + + + Megakaryocytopoiesis + SY + NCI + + + + + Megakaryopoiesis + PT + NCI + + + + + A hematopoietic process that refers to the production of megakaryocytes in the bone marrow. + NCI + + + + + + + + + + + + + + + C96829 + Cell Function + Leukocyte Differentiation + C1817973 + Leukocyte Differentiation + The biological process that refers to the maturation of leukocytes. + Leukocyte Differentiation + + + + + Leukocyte Differentiation + PT + NCI + + + + + The biological process that refers to the maturation of leukocytes. + NCI + + + + + + + + + + + + + + + C96831 + Cell Function + Granulocyte Differentiation + C1326082 + Granulocyte Differentiation + The biological process that refers to the maturation of granulocytes. + Granulocyte Differentiation + + + + + Granulocyte Differentiation + PT + NCI + + + + + The biological process that refers to the maturation of granulocytes. + NCI + + + + + + + + + + + + + + + C96832 + Cell Function + Myeloid Cell Differentiation + C1622499 + Myeloid Cell Differentiation + The biological process that refers to the maturation of myelocytes. + Myeloid Cell Differentiation + + + + + Myeloid Cell Differentiation + PT + NCI + + + + + The biological process that refers to the maturation of myelocytes. + NCI + + + + + + + + + + + + + + + C96833 + Cell Function + Erythrocyte Differentiation + C1159942 + Erythrocyte Differentiation + A biological process that refers to the maturation of erythrocytes. + Erythrocyte Differentiation + + + + + Erythrocyte Differentiation + PT + NCI + + + + + A biological process that refers to the maturation of erythrocytes. + NCI + + + + + + + + + + + + + + + C96834 + Cell Function + Thrombocyte Differentiation + C3273068 + Thrombocyte Differentiation + A biological process that refers to the maturation of thrombocytes. + Thrombocyte Differentiation + + + + + Thrombocyte Differentiation + PT + NCI + + + + + A biological process that refers to the maturation of thrombocytes. + NCI + + + + + + + + + C99493 + Mental Process + Cognitive Flexibility + C2370892 + Cognitive Flexibility + The ability to restructure knowledge and change behavioral responses depending on the context of a situation. + Cognitive Flexibility + + + + + Cognitive Flexibility + PT + NCI + + + + + The ability to restructure knowledge and change behavioral responses depending on the context of a situation. + NCI + + + + + + + + + C99494 + Mental Process + Delayed Reward Discounting + C3274767 + Delayed Reward Discounting + A form of impulsivity related to the increased perceived value of immediate gratification as compared to a larger future reward. The more remote the future reward, the lower its perceived present value (the more it is discounted) and the less likely it is to be chosen. + Delayed Reward Discounting + + + + + Delayed Reward Discounting + PT + NCI + + + + + A form of impulsivity related to the increased perceived value of immediate gratification as compared to a larger future reward. The more remote the future reward, the lower its perceived present value (the more it is discounted) and the less likely it is to be chosen. + NCI + + + + + + + + + CNO Test Class + + + + + + + + + CNO test value + + + + + + + + + Leukocyte Apoptotic Test Class + + + + + + + + + Leukocyte Test Class + + + + + + + + + NCIT Test Value + + + + + + + + + New Thesaurus of Cells + + + + + + + + + OGMS Test Class + + + + + + + + + Test Class for NCIT + + + + + + + + + Thesaurus Test Value + + + + + + + + + test OGMS value + + + + + + + + realization + + + + + + + + + This class is based on the assumption that models can represented as particular assemblies of components that can be either specific to the different level of description (cellular, synaptic and network) or generic. + definition based on element from NCI Thesaurus: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Element_Part + model component + model element + a generically dependent continuant that is a constituent part of a model + + + + + + + + A property representing a two or three character abbreviation that indicates the nature of each FULL_SYN term associated with a concept. (e.g., PT=Preferred Term; SY=Synonym) + + + + + A property representing a two or three character abbreviation that indicates the nature of each FULL_SYN term associated with a concept. (e.g., PT=Preferred Term; SY=Synonym) + NCI + Hahn-Dantona, Elizabeth + 2018-11-07 + + + A property representing the organization that is the supplier or owner of each FULL_SYN term. + + + + + A property representing the organization that is the supplier or owner of each FULL_SYN term. + NCI + Hahn-Dantona, Elizabeth + 2018-11-07 + + + + + + + diff --git a/test/data/ontology_files/ogms_test.owl b/test/data/ontology_files/ogms_test.owl new file mode 100644 index 00000000..43a32429 --- /dev/null +++ b/test/data/ontology_files/ogms_test.owl @@ -0,0 +1,4382 @@ + + + + + The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. + +OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + Ontology for General Medical Science + Sivaram Arabandi + 2021-08-19 + Albert Goldfain + 2009-08-07 + Alan Ruttenberg + The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + +The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl + +The OGMS developer site is https://github.com/OGMS/ogms + +If you are interested in participating in the development of OGMS, please send email to baeverma + Werner Ceusters + Brian Aevermann + Jie Zheng + Bill Hogan + Lindsay Cowell + Cornelius Rosse + Richard Scheuermann + http://creativecommons.org/licenses/by/4.0/ + Anand Kumar + Daniel Merico + Barry Smith + + + + + + + + + + + + + + + + + + + Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. + Really of interest to developers only + BFO OWL specification label + + + + + + + + + Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 + Person:Alan Ruttenberg + Really of interest to developers only + BFO CLIF specification label + + + + + + + + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred term + + + + + + + + example of usage + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + definition source + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + + curator note + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + + + + + + + + ontology term requester + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + + + + + + + + is denotator type + Relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + Use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + has ID digit count + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + + + + + + + + has ID range allocated + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + + + + + + + + has ID policy for + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + + + + + + + + has ID prefix + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + is allocated id range + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + Add as annotation triples in the granting ontology + is allocated id range + + + + + + + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + + + + + + + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + scheduled for obsoletion on or after + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + + + + + + + + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + + continuant + Continuant + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + + + + + occurrent + Occurrent + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + + + + + + + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + + + + + + + s-region + SpatialRegion + BFO 2 Reference: Spatial regions do not participate in processes. + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + spatial region + + + + + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + + per discussion with Barry Smith + + + + + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + + + + + + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + + + + + + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + + + + + + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + + + + + + + + + + + + t-region + TemporalRegion + Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional + A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) + All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) + Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) + (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] + (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] + (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] + + temporal region + + + + + Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional + + per discussion with Barry Smith + + + + + A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) + + + + + + All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) + + + + + + Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) + + + + + + (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] + + + + + + (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] + + + + + + (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] + + + + + + + + + + + 2d-s-region + TwoDimensionalSpatialRegion + an infinitely thin plane in space. + the surface of a sphere-shaped part of space + A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) + (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] + + two-dimensional spatial region + + + + + A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) + + + + + + (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] + + + + + + + + + + st-region + SpatiotemporalRegion + the spatiotemporal region occupied by a human life + the spatiotemporal region occupied by a process of cellular meiosis. + the spatiotemporal region occupied by the development of a cancer tumor + A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) + All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) + Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) + Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) + Every spatiotemporal region occupies_spatiotemporal_region itself. + Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) + (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] + (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] + (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] + (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] + (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] + + spatiotemporal region + + + + + A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) + + + + + + All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) + + + + + + Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) + + + + + + Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) + + + + + + Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) + + + + + + (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] + + + + + + (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] + + + + + + (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] + + + + + + (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] + + + + + + (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + + + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + + + + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + + + + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + + + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + + + + 0d-s-region + ZeroDimensionalSpatialRegion + A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) + (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] + + zero-dimensional spatial region + + + + + A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) + + + + + + (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] + + + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + quality + + + + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + + + + + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + + + + + + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + + + + + + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + + + + + + + + + fiat-object-part + FiatObjectPart + or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 + the FMA:regional parts of an intact human body. + the Western hemisphere of the Earth + the division of the brain into regions + the division of the planet into hemispheres + the dorsal and ventral surfaces of the body + the upper and lower lobes of the left lung + BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions + b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) + (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] + + fiat object part + + + + + b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) + + + + + + (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] + + + + + + + + + + + 1d-s-region + OneDimensionalSpatialRegion + an edge of a cube-shaped portion of space. + A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) + (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] + + one-dimensional spatial region + + + + + A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) + + + + + + (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] + + + + + + + + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + object aggregate + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + + + + + + + + + 3d-s-region + ThreeDimensionalSpatialRegion + a cube-shaped region of space + a sphere-shaped region of space, + A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) + (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] + + three-dimensional spatial region + + + + + A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) + + + + + + (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] + + + + + + + + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + site + + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + + + + + + + + + object + Object + atom + cell + cells and organisms + engineered artifacts + grain of sand + molecule + organelle + organism + planet + solid portions of matter + star + BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. + BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). + BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 + BFO 2 Reference: an object is a maximal causally unified material entity + BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 + b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) + + object + + + + + b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + function + Function + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + function + + + + + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + + + + + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + + + + + + + + + p-boundary + ProcessBoundary + the boundary between the 2nd and 3rd year of your life. + p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) + Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) + (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] + (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] + + process boundary + + + + + p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) + + + + + + Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) + + + + + + (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] + + + + + + (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] + + + + + + + + + + + 1d-t-region + OneDimensionalTemporalRegion + the temporal region during which a process occurs. + BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). + A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) + (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] + + one-dimensional temporal region + + + + + A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) + + + + + + (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] + + + + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + + + cf-boundary + ContinuantFiatBoundary + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. + BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 + Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. + Every continuant fiat boundary is located at some spatial region at every time at which it exists + (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] + + continuant fiat boundary + + + + + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + + + + + + Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. + + + + + + (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] + + + + + + + + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity + + + + + + + + + + + 1d-cf-boundary + OneDimensionalContinuantFiatBoundary + The Equator + all geopolitical boundaries + all lines of latitude and longitude + the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. + the median sulcus of your tongue + a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) + (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] + + one-dimensional continuant fiat boundary + + + + + a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) + + + + + + (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] + + + + + + + + + + + process-profile + ProcessProfile + On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels + One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. + The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. + b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) + b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) + (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] + (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] + + process profile + + + + + b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) + + + + + + b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) + + + + + + (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] + + + + + + (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] + + + + + + + + + + r-quality + RelationalQuality + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + a marriage bond, an instance of requited love, an obligation between one person and another. + b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) + (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] + + relational quality + + + + + b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) + + + + + + (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] + + + + + + + + + + 2d-cf-boundary + TwoDimensionalContinuantFiatBoundary + a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) + (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] + + two-dimensional continuant fiat boundary + + + + + a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) + + + + + + (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] + + + + + + + + + + 0d-cf-boundary + ZeroDimensionalContinuantFiatBoundary + the geographic North Pole + the point of origin of some spatial coordinate system. + the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet + zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. + a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) + (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] + + zero-dimensional continuant fiat boundary + + + + + zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. + + requested by Melanie Courtot + + + + + + a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) + + + + + + (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] + + + + + + + + + + 0d-t-region + ZeroDimensionalTemporalRegion + a temporal region that is occupied by a process boundary + right now + the moment at which a child is born + the moment at which a finger is detached in an industrial accident + the moment of death. + temporal instant. + A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) + (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] + + zero-dimensional temporal region + + + + + A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) + + + + + + (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] + + + + + + + + + + history + History + A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) + + history + + + + + A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) + + + + + + + + + + data item + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + + data item + + + + + + + + + information content entity + A generically dependent continuant that is about some thing. + + information content entity + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + + directive information entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + denotator type + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + ontology module + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module + + + + + + + + + base ontology module + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + base ontology module + + + + + + + + + + editors ontology module + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + editors ontology module + + + + + + + + + main release ontology module + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + main release ontology module + + + + + + + + + bridge ontology module + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + bridge ontology module + + + + + + + + + + import ontology module + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + import ontology module + + + + + + + + + + subset ontology module + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + subset ontology module + + + + + + + + + + + curation subset ontology module + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + curation subset ontology module + + + + + + + + + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module + + + + + + + + + single layer ontology module + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + single layer subset ontology module + + + + + + + + + exclusion subset ontology module + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + exclusion subset ontology module + + + + + + + + + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module + + + + + + + + + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module + + + + + + + + + + reasoned ontology module + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + reasoned ontology module + + + + + + + + + + generated ontology module + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + generated ontology module + + + + + + + + + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module + + + + + + + + + + + + taxonomic bridge ontology module + taxonomic bridge ontology module + + + + + + + + + ontology module subsetted by expressivity + ontology module subsetted by expressivity + + + + + + + + + obo basic subset ontology module + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + obo basic subset ontology module + + + + + + + + + + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile + + + + + + + + + EL++ ontology module + EL++ ontology module + + + + + + + + + An infection that is clinically abnormal. + + infectious disorder + + + + + + + + + A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. + + infection + + + + + + + + + An infection resulting from a transmission process that unfolds in a hospital. + + hospital-acquired infection + + + + + + + + + A process that realizes a plan which is the concretization of a plan specification. + + planned process + + + + + + + + + a part of an occurrence of a disease process which is associated with position in the normal progression of the disease + + disease stage + + + + + + + + + A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T10:18:02Z + clinical finding + + + + + + + + + A series of statements representing health-relevant qualities of a patient and of a patient's family. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T10:18:59Z + clinical history + + + + + + + + + A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T10:20:20Z + clinical picture + + + + + + + + + A representation of an image that supports an inference to an assertion about some quality of a patient. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T10:21:10Z + image finding + + + + + + + + + A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T10:21:58Z + laboratory finding + + + + + + + + + A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T10:22:44Z + preclinical finding + + + + + + + + + A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant. + note: defined class + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-11-18T11:02:10Z +Updated: 2020-07-06 + symptom + + + + + + + + + A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:12:33Z + manifestation of a disease + + + + + + + + + A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T11:13:49Z + phenotype + + + + + + + + + The class sign has been replaced by three seperate classes which reflect the different types of signs possible. + obsolete_sign + true + + + + + + + + + A manifestation of a disease that is detectable in a clinical history taking or physical examination. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:15:43Z + clinical manifestation of a disease + + + + + + + + + A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:16:50Z + preclinical manifestation of a disease + + + + + + + + + A clinically abnormal phenotype. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:18:05Z + clinical phenotype + + + + + + + + + A clinically abnormal phenotype that is characteristic of a single disease. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:18:39Z + disease phenotype + + + + + + + + + A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:19:17Z + vital sign + + + + + + + + + A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:20:25Z + predisposition to disease of type X + + + + + + + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:21:20Z + disease + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:22:01Z + homeostasis + + + + + + + + + A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:23:07Z + genetic predisposition to disease of type X + + + + + + + + + A disease whose physical basis is an acquired genetic disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:24:05Z + acquired genetic disease + + + + + + + + + A disease whose physical basis is a constitutional genetic disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:24:59Z + constitutional genetic disease + + + + + + + + + Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:26:44Z + abnormal homeostasis + + + + + + + + + Homeostasis of a type that is not clinically abnormal. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:27:28Z + normal homeostasis + + + + + + + + + A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:36:24Z + configuration + + + + + + + + + A configuration which deviates in some way from a canonical configuration for a particular organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:36:58Z + pathological physical configuration + + + + + + + + + A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:39:44Z + disorder + + + + + + + + + A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:40:27Z + epigenetic disorder + + + + + + + + + A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:41:14Z + genetic disorder + + + + + + + + + A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:43:09Z + acquired genetic disorder + + + + + + + + + A genetic disorder inherited during conception that is part of all cells in the organism. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:43:44Z + constitutional genetic disorder + + + + + + + + + A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:49:16Z + clinical history taking + + + + + + + + + A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:49:49Z + clinical laboratory test + + + + + + + + + A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2010-07-19T11:50:18Z + physical examination + + + + + + + + + A process in an organism that leads to a subsequent disorder. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:53:07Z + etiological process + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:53:49Z + bodily process + + + + + + + + + A bodily process that is clinically abnormal. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:54:29Z + pathological bodily process + + + + + + + + + The totality of all processes through which a given disease instance is realized. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:55:44Z + disease course + + + + + + + + + A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:56:26Z + +10212020 + +for definition use: +http://purl.obolibrary.org/obo/PATO_0001863 + chronic disease course + + + + + + + + + A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:57:09Z + progressive disease course + + + + + + + + + A disease course that terminates in a return to normal homeostasis. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T11:57:44Z + transient disease course + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:58:22Z + _undefined primitive term + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T11:59:24Z + clinically abnormal + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T12:00:09Z + physical basis + + + + + + + + + Albert Goldfain + creation date: 2009-06-23T12:00:39Z + realization + + + + + + + + + The representation of a conclusion of a diagnostic process. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-23T12:42:23Z + diagnosis + + + + + + + + + A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population. + Albert Goldfain + http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf + creation date: 2009-06-26T10:31:34Z + normal value + + + + + + + + + TODO: Define, relate to disorder, and place in the OGMS hierarchy. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:14:59Z + pathological formation + + + + + + + + + An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:14:05Z + pathological anatomical structure + + + + + + + + + TODO: Define, relate to disorder, and place in the OGMS hierarchy. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:15:17Z + portion of pathological body substance + + + + + + + + + A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:17:07Z + pathological transformation + + + + + + + + + A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:17:24Z + pathological derivation + + + + + + + + + TODO: Define. + Albert Goldfain + http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf + creation date: 2009-07-13T02:17:47Z + pathological invasion + + + + + + + + + TODO: Define. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=26 + creation date: 2009-11-24T04:51:11Z + physical examination finding + + + + + + + + + An aggregate of organisms of the same type. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=33 + creation date: 2009-11-24T04:51:11Z + organism population + + + + + + + + + A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage. + Albert Goldfain + http://www.referent-tracking.com/RTU/sendfile/?file=painTokyo1_27_2011.pdf + creation date: 2009-11-24T04:51:11Z + pain + + + + + + + + + A pattern of signs and symptoms that typically co-occur. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=32 + creation date: 2009-11-24T04:51:11Z + syndrome + + + + + + + + + An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=3 + creation date: 2010-01-25T04:51:11Z + extended organism + + + + + + + + + A communication from a patient about something they perceive as being abnormal about their body or life. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=12 + creation date: 2010-01-25T04:51:11Z + patient symptom report + + + + + + + + + A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism. + Albert Goldfain + congenital malformation + http://code.google.com/p/ogms/issues/detail?id=28 + creation date: 2010-03-31T04:51:11Z + congenital disorder + + + + + + + + + A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=35 + creation date: 2010-03-31T04:51:11Z + treatment + + + + + + + + + A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=35 + creation date: 2010-03-31T04:51:11Z + convalescence + + + + + + + + + A process which has as parts all the processes in which a given organism is participant. + Albert Goldfain +Richard Scheuermann +Sagar Jain + http://code.google.com/p/ogms/issues/detail?id=38 + creation date: 2010-03-31T04:51:11Z + +EDIT: 10 NOV 2015 + life course + + + + + + + + + A hypothesis about some future part of a disease course. + Albert Goldfain + http://code.google.com/p/ogms/issues/detail?id=35 + creation date: 2010-03-31T12:42:23Z + prognosis + + + + + + + + + A disease course with an acute onset + Albert Goldfain + http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 + creation date: 2010-07-19T11:57:44Z + +10212020 + +for definition use + +http://purl.obolibrary.org/obo/PATO_0000389 + acute disease course + + + + + + + + + A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling. + Albert Goldfain +Richard Scheuermann +Sagar Jain + http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 + creation date: 2010-07-19T11:57:44Z + +Updated: 10 NOV 2015 + inflammatory process + + + + + + + + + A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient + Albert Goldfain +Sagar Jain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z +editor date: 2017-04-18 + health care process + + + + + + + + + A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z + health care encounter + + + + + + + + + TODO + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z + 09/16/2020 +Is this same as admission? +Is this the same as inpatient encounter? + hospitalization + + + + + + + + + TODO + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z + outpatient encounter + + + + + + + + + A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night. + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z + inpatient encounter + + + + + + + + + A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention. + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 + creation date: 2011-02-21T09:57:44Z + emergency department encounter + + + + + + + + + A disorder that involves some structural damage that is immediately caused by a catastrophic external force. + At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. + +Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level. + Albert Goldfain +Sagar Jain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 + +OGMS call adoption- 16 SEPT 2015 +https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit + creation date: 2011-09-20T09:57:44Z +edited date: 30 SEPT 2015 + injury + + + + + + + + + A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder. + Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question. + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e + creation date: 2011-09-20T09:57:44Z + disease prophylaxis + + + + + + + + + A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output). + Albert Goldfain + http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e + creation date: 2011-09-20T09:57:44Z + diagnostic process + + + + + + + + + A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease. + A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course. + Albert Goldfain +Richard Scheuermann +Sagar Jain + recurrent + http://code.google.com/p/ogms/issues/detail?id=73 + 10 NOV 2015 + relapse + + + + + + + + + A disease stage which is characterized by the lack of a manifestation of a disease + A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased. + Albert Goldfain +Richard Scheuermann +Sagar Jain + http://code.google.com/p/ogms/issues/detail?id=73 + 10 NOV 2015 + remission + + + + + + + + + A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient. + 2017-04-18 + Sagar Jain + ancillary health care process + + + + + + + + + A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + creation: 16MAY2017 + Sagar Jain + health care process assay + + + + + + + + + A health care process which results in physical changes in a specified input material + creation: 16MAY2017 + Sagar Jain + health care process biomaterial transformation + + + + + + + + + A health care process that produces output from input data + creation: 16MAY2017 + Sagar Jain + health care process data transformation + + + + + + + + + A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process. + Creation date: 2018-11-27 + prophylactic treatment + + + + + + + + + A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process. + Creation data: 2018-11-27 + therapeutic procedure + + + + + + + + + A therapeutic procedure that uses synthetic or naturally-occurring chemicals + creation date: 2018-11-27 + chemotherapy procedure + + + + + + + + + A therapeutic procedure that uses immune system derived entities. + creation date: 2018-11-27 + immunotherapy procedure + + + + + + + + + A therapeutic procedure that uses physical conditioning + creation date: 2018-11-27 + physical therapy procedure + + + + + + + + + A therapeutic procedure that uses radiation. + creation date: 2018-11-27 + radiation therapy procedure + + + + + + + + + A disease stage characterized by the lack of symptoms associated with a given disease + creation date: 2018-11-27 + asymptomatic + + + + + + + + + A disease stage that marks the beginning of a disease + creation date 2018-11-27 + onset + + + + + + + + + A disease stage with a rapid unfolding of signs and symptoms + creation date 2018-11-27 + acute onset + + + + + + + + + A remission which is characterized by a prolonged lack of all manifestations of a disease + complete remission + + + + + + + + + A remission which is characterized by a prolonged lack of some manifestations of a disease + partial remission + + + + + + + + + A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist + creation date: 2018-11-27 + recovered from disease + + + + + + + + + A data item that is about a patient and is the specified output of a health care process assay or diagnostic process + creation date: 2018-11-27 + clinical data item + + + + + + + + + A health care encounter that is regularly scheduled for the purpose of health monitoring. + routine clinical visit + routine health care encounter + + + + + + + + + A health care encounter that is scheduled for the purpose of assessing a known set of specific issues + follow-up clinical visit + follow-up health care encounter + + + + + + + + + A congenital disorder arising as a result of an infectious process + congenital infection + + + + + + + + + A congenital disorder arising as a result of a drug exposure causing an anatomical abnormality + drug induced congenital malformation + + + + + + + + + A pathological bodily process that occurs in the fetus during fetal development + congenital process + + + + + + + + + An abnormal material entity that is part of a patient and hypothesized to be clinically relevant. + Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension + physical sign + + + + + + + + + The process in which an allergic disease unfolds. + allergic disease process + + + + + + + + + The process in which cancer unfolds + cancer process + + + + + + + + + The process in which an autoimmune disease unfolds. + autoimmune disease process + + + + + + + + + progression stage + + + + + + + + + cancer progression stage + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ). + cancer progression stage 0 + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass. + cancer progression stage I + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass. + cancer progression stage II + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes. + cancer progression stage III + + + + + + + + + A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes. + cancer progression stage IV + + + + + + + + + The process in which an infectious disease unfolds + infectious disease process + + + + + + + + + An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant. + processual sign + + + + + + + + + An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant. + Example: the color of a rash; the shape of a melanoma + qualitative sign + + + + + + + + + A therapeutic procedure in which a body part is transferred into a organism + transplantation + + + + + + + + + A transplantation in which the body part is a non-fluid tissue + solid organ transplant + + + + + + + + + A transplantation in which the body part is a bodily fluid + transfusion + + + + + + + + + A disorder of some macroscopic part of a tissue + tissue disorder + + + + + + + + + A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass + neoplasm + + + + + + + + + A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease. + Originally OBIB_0000026 + medication role + + + + + + + + + Leukocyte Test Class + + + + + + + + + cno test value + + + + + + + + + ncit test value + + + + + + + + + thesaurus test value + + + + + + + + + This class is based on the assumption that models can represented as particular assemblies of components that can be either specific to the different level of description (cellular, synaptic and network) or generic. + definition based on element from NCI Thesaurus: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Element_Part + model component + model element + a generically dependent continuant that is a constituent part of a model + + + + + + + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + + obsolete_core + true + + + + + + + + + placeholder removed + placeholder removed + + + + + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/data/ontology_files/vario_test.obo b/test/data/ontology_files/vario_test.obo new file mode 100644 index 00000000..2157b55c --- /dev/null +++ b/test/data/ontology_files/vario_test.obo @@ -0,0 +1,3444 @@ +format-version: 1.2 +date: 23:11:2018 15:56 +saved-by: med-mnv +auto-generated-by: OBO-Edit 2.3.1 +default-namespace: variation_ontology +remark: A Variation Ontology +ontology: vario +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"\")\n) + +[Term] +id: VariO:0001 +name: variation +def: "Alteration in DNA, RNA or protein." [VariO:mv] + +[Term] +id: VariO:0002 +name: variation affecting protein +def: "Effects of a variation on protein level." [VariO:mv] +is_a: VariO:0001 ! variation + +[Term] +id: VariO:0003 +name: variation affecting protein function +def: "Effect of variation on protein function." [VariO:mv] +is_a: VariO:0002 ! variation affecting protein + +[Term] +id: VariO:0004 +name: effect on protein movement +def: "Effect of variation on the movement of a protein along filament of a polymeric molecule." [VariO:mv] +is_a: VariO:0003 ! variation affecting protein function + +[Term] +id: VariO:0005 +name: effect on protein storage +def: "Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions." [VariO:mv] +is_a: VariO:0003 ! variation affecting protein function + +[Term] +id: VariO:0006 +name: effect on structural protein +def: "Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems." [VariO:mv] +is_a: VariO:0003 ! variation affecting protein function + +[Term] +id: VariO:0007 +name: effect on protein recognition +def: "Effect of variation on selective non-covalent interaction of protein." [VariO:mv] +is_a: VariO:0003 ! variation affecting protein function + +[Term] +id: VariO:0008 +name: effect on catalytic protein function +def: "Effect of variation on catalytic function of protein." [VariO:mv] +is_a: VariO:0003 ! variation affecting protein function + +[Term] +id: VariO:0009 +name: effect on transport function of protein +def: "Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane." [VariO:mv] +is_a: VariO:0003 ! variation affecting protein function + +[Term] +id: VariO:0010 +name: effect on RNA abundance +def: "Variation affecting abundance of produced RNA molecules." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property + +[Term] +id: VariO:0011 +name: effect on protein information transfer +def: "Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs." [VariO:mv] +is_a: VariO:0003 ! variation affecting protein function + +[Term] +id: VariO:0012 +name: protein variation type +def: "Type of protein variation. Describes origin and classification of a variant." [VariO:mv] +is_a: VariO:0002 ! variation affecting protein + +[Term] +id: VariO:0013 +name: protein variation of genetic origin +def: "Protein variation that has genetic origin." [VariO:mv] +is_a: VariO:0323 ! protein variation origin + +[Term] +id: VariO:0014 +name: amino acid deletion +def: "Removal of one or more continuous amino acids from protein." [VariO:mv] +is_a: VariO:0325 ! protein variation classification + +[Term] +id: VariO:0015 +name: protein truncation +def: "Shortening of protein sequence from terminus." [VariO:mv] +is_a: VariO:0014 ! amino acid deletion + +[Term] +id: VariO:0016 +name: sequence retaining amino acid deletion +def: "Deletion of one or more amino acids from a protein, without affecting the sequence after deletion." [VariO:mv] +is_a: VariO:0014 ! amino acid deletion + +[Term] +id: VariO:0017 +name: nonsynonymous variation +def: "mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid." [Vario:mv] +is_a: VariO:0232 ! variation attribute +created_by: med-mnv +creation_date: 2015-06-04T13:23:24Z + +[Term] +id: VariO:0018 +name: amino acid insertion +def: "Addition of one or more amino acids to protein sequence." [VariO:mv] +is_a: VariO:0325 ! protein variation classification + +[Term] +id: VariO:0019 +name: amphigoric amino acid insertion +def: "Insertion of one or more amino acids to protein with sequence completely changed after the insertion position. Caused by insertion of number of RNA nucleotides not divisible by three leading to frame shift of mRNA reading frame." [VariO:mv] +is_a: VariO:0018 ! amino acid insertion + +[Term] +id: VariO:0020 +name: sequence retaining amino acid insertion +def: "Insertion of one or more amino acids to the protein without affecting the sequence after insertion." [VariO:mv] +is_a: VariO:0018 ! amino acid insertion + +[Term] +id: VariO:0021 +name: amino acid substitution +def: "Substitution of an amino acid in protein." [VariO:mv] +xref: SO:0001606 +is_a: VariO:0325 ! protein variation classification + +[Term] +id: VariO:0022 +name: amino acid indel +def: "A complex protein variation consisting of both amino acid insertion(s) and deletion(s)." [VariO:mv] +is_a: VariO:0325 ! protein variation classification + +[Term] +id: VariO:0023 +name: amphigoric amino acid indel +def: "Amino acid indel with sequence completely changed after the indel position. Caused by indel of number of RNA nucleotides not divisible by three leading to frameshift of reading frame." [VariO:mv] +is_a: VariO:0022 ! amino acid indel +created_by: Mauno Vihinen +creation_date: 2013-03-06T10:59:41Z + +[Term] +id: VariO:0024 +name: variation emerging at protein level +def: "Protein variation that does not have genetic origin being modified at protein level." [VariO:mv] +is_a: VariO:0323 ! protein variation origin + +[Term] +id: VariO:0025 +name: epigenetic protein variation +def: "Heritable protein variation of non-genetic origin." [VariO:mv] +is_a: VariO:0024 ! variation emerging at protein level + +[Term] +id: VariO:0026 +name: protein structural inheritance +def: "Inheritance of protein or protein complex structure without involvement of genetic information." [VariO:mv] +is_a: VariO:0025 ! epigenetic protein variation + +[Term] +id: VariO:0027 +name: proteinaceous infection +def: "Protein conformation change induced by structurally modified protein." [VariO:mv] +is_a: VariO:0025 ! epigenetic protein variation + +[Term] +id: VariO:0028 +name: post translational modification +def: "Protein molecule chemically modified after translation." [VariO:mv] +is_a: VariO:0024 ! variation emerging at protein level + +[Term] +id: VariO:0029 +name: sequence retaining amino acid indel +def: "Amino acid indel without affecting the sequence after the indel position." [VariO:mv] +is_a: VariO:0022 ! amino acid indel +created_by: Mauno Vihinen +creation_date: 2013-03-06T11:04:21Z + +[Term] +id: VariO:0030 +name: in-frame indel +def: "RNA indel not affecting reading frame after indel position." [VariO:mv] +is_a: VariO:0311 ! RNA indel +created_by: Mauno Vihinen +creation_date: 2013-06-14T10:03:57Z + +[Term] +id: VariO:0031 +name: out-of-frame indel +def: "RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame." [VariO:mv] +is_a: VariO:0311 ! RNA indel +created_by: Mauno Vihinen +creation_date: 2013-06-14T10:03:57Z + +[Term] +id: VariO:0032 +name: variation affecting protein property +def: "Variation affecting characteristic property of protein." [VariO:mv] +is_a: VariO:0002 ! variation affecting protein + +[Term] +id: VariO:0033 +name: effect on protein subcellular localization +def: "Effect of variation on the targeting of a protein within a cell or cellular compartment." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0034 +name: effect on protein stability +def: "Effect of variation on stability of protein." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0035 +name: effect on protein solubility +def: "Effect of variation on the potential of protein to dissolve in a liquid." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0036 +name: effect on protein inclusion body formation +def: "Variation affecting the formation of particles of aggregated proteins." [VariO:mv] +xref: GO:0016234 +is_a: VariO:0035 ! effect on protein solubility + +[Term] +id: VariO:0037 +name: covariant position +def: "Variation at a covarying sequence position." [VariO:mv] +is_a: VariO:0233 ! conservation +created_by: Mauno Vihinen +creation_date: 2014-01-16T14:03:51Z + +[Term] +id: VariO:0038 +name: effect on protein aggregation +def: "Variation affecting protein aggregation tendency." [VariO:mv] +is_a: VariO:0035 ! effect on protein solubility + +[Term] +id: VariO:0039 +name: protein function change +def: "Type of protein function affecting variation." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0040 +name: protein gain of function +def: "Effect of variation causing new or enhanced protein activity." [VariO:mv] +is_a: VariO:0039 ! protein function change + +[Term] +id: VariO:0041 +name: neomorphic protein variation +def: "Variation generates new protein function." [VariO:mv] +is_a: VariO:0040 ! protein gain of function + +[Term] +id: VariO:0042 +name: antimorphic protein variation +def: "Dominant variation that acts to opposite direction than the normal protein." [VariO:mv] +synonym: "dominant negative protein variation" EXACT [] +is_a: VariO:0040 ! protein gain of function + +[Term] +id: VariO:0043 +name: protein loss of function +def: "Effect of variation reducing or abolishing protein activity." [VariO:mv] +is_a: VariO:0039 ! protein function change + +[Term] +id: VariO:0044 +name: effect on protein accessibility +def: "Effect of variation to the accessibility of protein region to solvent." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0045 +name: variation exposing buried region +def: "Variation exposing buried region." [VariO:mv] +is_a: VariO:0044 ! effect on protein accessibility + +[Term] +id: VariO:0046 +name: variation burying exposed region +def: "Variation leading to burying of exposed region." [VariO:mv] +is_a: VariO:0044 ! effect on protein accessibility + +[Term] +id: VariO:0047 +name: association of protein variation to pathogenicity +def: "Implication of a protein variant to pathogenicity." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0048 +name: effect on protein charge +def: "Effect of variation on charge in protein." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0049 +name: effect on protein electrostatics +def: "Variation affecting electrostatics of the protein surface." [VariO:mv] +is_a: VariO:0048 ! effect on protein charge + +[Term] +id: VariO:0050 +name: effect on protein isoelectric point +def: "Variation changing protein isoelectric point." [VariO:mv] +is_a: VariO:0048 ! effect on protein charge + +[Term] +id: VariO:0051 +name: effect on protein degradation +def: "Effect of variation on degradation of protein." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0052 +name: effect on protein abundance +def: "Variation affecting abundance of produced protein molecules." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0053 +name: effect on protein activity +def: "Effect of variation on activity of protein." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0054 +name: effect on protein affinity +def: "Effect of variation on protein affinity to binding molecule(s)." [VariO:mv] +is_a: VariO:0053 ! effect on protein activity + +[Term] +id: VariO:0055 +name: effect on protein specificity +def: "Effect of variation on substrate binding specificity of protein." [VariO:mv] +is_a: VariO:0053 ! effect on protein activity + +[Term] +id: VariO:0056 +name: effect on enzyme reaction kinetics +def: "Effect of variation to enzyme reaction kinetics." [VariO:mv] +is_a: VariO:0435 ! effect on protein reaction kinetics + +[Term] +id: VariO:0057 +name: conservation of protein variation site +def: "Conservation of the variant site in related protein sequences." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0058 +name: effect on protein interaction +def: "Effect of variation on the interaction of protein with its partner." [VariO:mv] +is_a: VariO:0032 ! variation affecting protein property + +[Term] +id: VariO:0059 +name: effect on protein contact energy +def: "Effect of variation on contact energy between interacting molecules." [VariO:mv] +is_a: VariO:0058 ! effect on protein interaction + +[Term] +id: VariO:0060 +name: variation affecting protein structure +def: "Variation affecting structure of protein." [VariO:mv] +is_a: VariO:0002 ! variation affecting protein + +[Term] +id: VariO:0061 +name: epigenetic protein modification +def: "Hereditary protein structure modification of non-genetic origin." [VariO:mv] +is_a: VariO:0060 ! variation affecting protein structure + +[Term] +id: VariO:0062 +name: prion formation +def: "Variation affecting the formation of infectious protein having misfolded structure." [VariO:mv] +is_a: VariO:0061 ! epigenetic protein modification + +[Term] +id: VariO:0063 +name: epigenetic protein complex structure +def: "Variation affecting heritable protein complex structure." [VariO:mv] +is_a: VariO:0061 ! epigenetic protein modification + +[Term] +id: VariO:0064 +name: effect on protein 3D structure +def: "Variation affecting protein three dimensional structure." [VariO:mv] +is_a: VariO:0060 ! variation affecting protein structure + +[Term] +id: VariO:0065 +name: effect on protein dynamics +def: "Variation affecting dynamics in protein structure." [VariO:mv] +is_a: VariO:0064 ! effect on protein 3D structure + +[Term] +id: VariO:0066 +name: effect on structural flexibility +def: "Variation affecting protein structural flexibility." [VariO:mv] +is_a: VariO:0065 ! effect on protein dynamics + +[Term] +id: VariO:0067 +name: effect on induced fit +def: "Variation affecting induced fit of protein binding to its partner." [VariO:mv] +is_a: VariO:0065 ! effect on protein dynamics + +[Term] +id: VariO:0068 +name: effect on structural disorder +def: "Variation affecting protein structural disorder." [VariO:mv] +is_a: VariO:0065 ! effect on protein dynamics + +[Term] +id: VariO:0069 +name: effect on allosteric site +def: "Variation in affecting protein allosteric site." [VariO:mv] +is_a: VariO:0065 ! effect on protein dynamics + +[Term] +id: VariO:0070 +name: effect on protein tertiary structure +def: "Variation affecting protein three dimensional structure." [VariO:mv] +is_a: VariO:0064 ! effect on protein 3D structure + +[Term] +id: VariO:0071 +name: effect on protein folding rate +def: "Variation affecting rate of protein folding." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0072 +name: extrachromosomal DNA affected +def: "Variation effect on nonchromosomal DNA." [VariO:mv] +is_a: VariO:0159 ! affected DNA level +created_by: Mauno Vihinen +creation_date: 2012-11-09T14:16:30Z + +[Term] +id: VariO:0073 +name: effect to protein fold +def: "Variation affecting protein tertiary structure." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0074 +name: protein conformational change +def: "Variation changing protein conformation." [VariO:mv] +is_a: VariO:0073 ! effect to protein fold + +[Term] +id: VariO:0075 +name: global protein conformation change +def: "Variation causing large overall protein conformational change." [VariO:mv] +is_a: VariO:0074 ! protein conformational change + +[Term] +id: VariO:0076 +name: local protein conformation change +def: "Variation causing local and minor conformational change." [VariO:mv] +is_a: VariO:0074 ! protein conformational change + +[Term] +id: VariO:0077 +name: changed domain orientation +def: "Variation affecting protein structure due to alteration to domain orientation." [VariO:mv] +is_a: VariO:0073 ! effect to protein fold + +[Term] +id: VariO:0078 +name: effect on protein disulphide formation +def: "Variation affecting formation of intramolecular disulphide bonds." [VariO:mv] +is_a: VariO:0073 ! effect to protein fold + +[Term] +id: VariO:0079 +name: effect on protein secondary structural element +def: "Variation affecting protein secondary structural element of local ordered structure." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0080 +name: effect on protein helix +def: "Variation affecting secondary structure conformation where the peptide backbone forms a coil." [VariO:mv] +is_a: VariO:0079 ! effect on protein secondary structural element + +[Term] +id: VariO:0081 +name: effect on left handed protein helix +def: "Variation affecting protein left handed helix turning anticlockwise." [VariO:mv] +is_a: VariO:0080 ! effect on protein helix + +[Term] +id: VariO:0082 +name: effect on right handed protein helix +def: "Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw." [VariO:mv] +is_a: VariO:0080 ! effect on protein helix + +[Term] +id: VariO:0083 +name: effect on pi helix +def: "Variation affecting protein helix having 4.1 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [VariO:mv] +is_a: VariO:0082 ! effect on right handed protein helix + +[Term] +id: VariO:0084 +name: effect on three ten helix +def: "Variation affecting protein helix having 3 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [VariO:mv] +is_a: VariO:0082 ! effect on right handed protein helix + +[Term] +id: VariO:0085 +name: effect on alpha helix +def: "Variation affecting protein helix having 3.6 residues per turn. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [VariO:mv] +is_a: VariO:0082 ! effect on right handed protein helix + +[Term] +id: VariO:0086 +name: effect on protein beta strand +def: "Variation affecting extended protein backbone structure." [VariO:mv] +is_a: VariO:0079 ! effect on protein secondary structural element + +[Term] +id: VariO:0087 +name: effect on protein antiparallel beta strand +def: "Variation affecting beta strand forming part of antiparallel beta sheet. Hydrogen bonds are formed with another region of protein running in the opposite direction. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees)." [VariO:mv] +comment: Range. +is_a: VariO:0086 ! effect on protein beta strand + +[Term] +id: VariO:0088 +name: effect on protein parallel beta strand +def: "Variation affecting beta strand forming part of parallel beta sheet. Hydrogen bonds are formed with another region of protein running in the same direction. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees)." [VariO:mv] +comment: Range. +is_a: VariO:0086 ! effect on protein beta strand + +[Term] +id: VariO:0089 +name: effect on protein turn motif +def: "Variation affecting protein backbone turn motif." [VariO:mv] +is_a: VariO:0079 ! effect on protein secondary structural element + +[Term] +id: VariO:0090 +name: effect on protein alpha beta motif +def: "Variation affecting protein motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0091 +name: effect on protein beta turn +def: "Variation affecting protein motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which is used to sub-categorize the turns." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0092 +name: effect on protein st motif +def: "Variation affecting protein motif of five consecutive residues and two H-bonds, where residue(i) is either serine or threonine. Side chain O of residue(i) is H-bonded to the main chain NH of residue(i+2) or (i+3), and main chain CO or residue(i) is H-bonded to the main chain NH or residue(i+3) or (i+4)." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0093 +name: effect on protein st staple +def: "Variation affecting protein motif of four or five consecutive residues and one H-bond in which residue(i) is serine or threonine, the side chain OH of residue(i) is H-bonded to the main chain CO or residue(i-3) or (i-4), and phi angles of residues(i-1), (i-2) and (i-3) are negative." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0094 +name: effect on protein gamma turn +def: "Variation affecting protein turn defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0095 +name: effect on protein st turn +def: "Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is serine or threonine, the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0096 +name: effect on protein schellman loop +def: "Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0097 +name: effect on protein nest motif +def: "Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0098 +name: effect on protein niche motif +def: "Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0099 +name: effect on protein asx motif +def: "Variation affecting protein motif of five consecutive residues and two H-bonds in which: Residue(i) is aspartate or asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0100 +name: effect on protein beta bulge +def: "Variation affecting protein motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0101 +name: effect on protein asx turn +def: "Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is aspartate or asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0102 +name: effect on protein beta bulge loop +def: "Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds." [VariO:mv] +is_a: VariO:0089 ! effect on protein turn motif + +[Term] +id: VariO:0103 +name: effect on protein coil +def: "Variation affecting irregular, unstructured region of protein." [VariO:mv] +is_a: VariO:0079 ! effect on protein secondary structural element + +[Term] +id: VariO:0104 +name: effect on transmembrane polypeptide +def: "Variation altering membrane spanning protein." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0105 +name: effect on membrane protein extramembrane region +def: "Variation affecting region not traversing the lipid bilayer in a membrane protein." [VariO:mv] +is_a: VariO:0104 ! effect on transmembrane polypeptide + +[Term] +id: VariO:0106 +name: effect on membrane protein intramembrane region +def: "Variation affecting region present in the lipid bilayer in a membrane protein." [VariO:mv] +is_a: VariO:0104 ! effect on transmembrane polypeptide + +[Term] +id: VariO:0107 +name: effect on protein post translational modification +def: "Variation affecting the covalent alteration of protein amino acid by post translational process." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0108 +name: deletion of a post translational modification site +def: "Variation causing deletion of a post translational modification site." [VariO:mv] +is_a: VariO:0107 ! effect on protein post translational modification + +[Term] +id: VariO:0109 +name: effect on protein processing +def: "Variation affecting site of protein maturation by cleavage of peptide bond(s)." [VariO:mv] +is_a: VariO:0107 ! effect on protein post translational modification + +[Term] +id: VariO:0110 +name: effect on protein splicing +def: "Variation affecting post-translational removal of peptide sequences from within a protein sequence." [VariO:mv] +is_a: VariO:0109 ! effect on protein processing + +[Term] +id: VariO:0111 +name: variation generating a novel protein processing site +def: "Variation that generates a novel protein processing site." [VariO:mv] +is_a: VariO:0109 ! effect on protein processing + +[Term] +id: VariO:0112 +name: variation preventing polypeptide processing +def: "Variation causing prevention of polypeptide processing." [VariO:mv] +is_a: VariO:0109 ! effect on protein processing + +[Term] +id: VariO:0113 +name: generation of a novel post translational modification site +def: "Variation generating a novel post translational modification site." [VariO:mv] +is_a: VariO:0107 ! effect on protein post translational modification + +[Term] +id: VariO:0114 +name: effect on amino acid size +def: "Variation affecting amino acid side chain size." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0115 +name: effect on protein packing +def: "Variation affecting amino acid packing in folded protein." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0116 +name: protein cavity formation +def: "Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one." [VariO:mv] +is_a: VariO:0115 ! effect on protein packing + +[Term] +id: VariO:0117 +name: protein overpacking +def: "Variation causing over packing of amino acids due to replacement by larger amino acid side chain." [VariO:mv] +is_a: VariO:0115 ! effect on protein packing + +[Term] +id: VariO:0118 +name: effect on protein interaction site +def: "Variation affecting ligand binding amino acid(s) in protein." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0119 +name: effect on protein binding site +def: "Variation affecting region on the surface of a protein that interacts with another molecule." [VariO:mv] +is_a: VariO:0118 ! effect on protein interaction site + +[Term] +id: VariO:0120 +name: effect on protein catalytic site +def: "Variation affecting amino acid(s) in protein catalytic site." [VariO:mv] +is_a: VariO:0118 ! effect on protein interaction site + +[Term] +id: VariO:0121 +name: effect on protein quaternary structure +def: "Variation affecting three dimensional structure of a protein complex." [VariO:mv] +is_a: VariO:0064 ! effect on protein 3D structure + +[Term] +id: VariO:0122 +name: effect on protein quaternary structure forming interaction +def: "Variation affecting interaction between protein subunits in quaternary structure." [VariO:mv] +is_a: VariO:0121 ! effect on protein quaternary structure + +[Term] +id: VariO:0123 +name: complex 3D structural change +def: "Complex change of protein three dimensional structure." [VariO:mv] +is_a: VariO:0064 ! effect on protein 3D structure + +[Term] +id: VariO:0124 +name: protein elongation +def: "Variation prolonging protein chain at an end." [VariO:mv] +is_a: VariO:0070 ! effect on protein tertiary structure + +[Term] +id: VariO:0125 +name: C-terminal protein elongation +def: "Addition of one or more amino acids to protein C-terminus." [VariO:mv] +is_a: VariO:0124 ! protein elongation + +[Term] +id: VariO:0126 +name: N-terminal protein elongation +def: "Addition of one or more amino acids to protein N-terminus." [VariO:mv] +is_a: VariO:0124 ! protein elongation + +[Term] +id: VariO:0127 +name: DNA variation origin +def: "Origin of DNA variation." [VariO:mv] +is_a: VariO:0129 ! DNA variation type +created_by: Mauno Vihinen +creation_date: 2013-10-11T08:46:32Z + +[Term] +id: VariO:0128 +name: variation affecting DNA +def: "Effects of a variation on DNA level." [VariO:mv] +is_a: VariO:0001 ! variation + +[Term] +id: VariO:0129 +name: DNA variation type +def: "Type of DNA variation. Describes origin and classification of a variant." [VariO:mv] +is_a: VariO:0128 ! variation affecting DNA + +[Term] +id: VariO:0130 +name: DNA variation of genetic origin +def: "DNA variation that has genetic origin." [VariO:mv] +is_a: VariO:0127 ! DNA variation origin + +[Term] +id: VariO:0131 +name: genomic variation +def: "Variation of genomic level." [VariO:mv] +is_a: VariO:0322 ! DNA variation classification + +[Term] +id: VariO:0132 +name: chromosomal variation +def: "Variation at chromosomal level." [VariO:mv] +is_a: VariO:0322 ! DNA variation classification + +[Term] +id: VariO:0133 +name: variation of chromosome number +def: "Variation affecting chromosome number." [VariO:mv] +synonym: "aneuploidy" RELATED [] +is_a: VariO:0132 ! chromosomal variation + +[Term] +id: VariO:0134 +name: variation of chromosome structure +def: "Variation affecting structure of chromosome." [VariO:mv] +is_a: VariO:0132 ! chromosomal variation + +[Term] +id: VariO:0135 +name: DNA chain variation +def: "Variation at DNA chain." [VariO:mv] +is_a: VariO:0322 ! DNA variation classification + +[Term] +id: VariO:0136 +name: DNA substitution +def: "Substitution of a DNA nucleotide." [VariO:mv] +is_a: VariO:0135 ! DNA chain variation + +[Term] +id: VariO:0137 +name: effect on RNA tertiary structure +def: "Variation affecting RNA tertiary structure." [VariO:mv] +is_a: VariO:0338 ! variation affecting RNA structure +created_by: med-mnv +creation_date: 2018-04-26T12:45:52Z + +[Term] +id: VariO:0138 +name: variant +def: "A genetic character, organism or individual with a difference to reference state." [VariO:mv] +is_a: VariO:0232 ! variation attribute +created_by: Mauno Vihinen +creation_date: 2012-11-11T19:43:00Z + +[Term] +id: VariO:0139 +name: mutation +def: "Any process generating variation." [VariO:mv] +is_a: VariO:0232 ! variation attribute +created_by: Mauno Vihinen +creation_date: 2012-11-11T19:43:39Z + +[Term] +id: VariO:0140 +name: not changed +def: "The observed feature is not changed in relation to the wild type form." [VariO:mv] +is_a: VariO:0289 ! quantity change +created_by: Mauno Vihinen +creation_date: 2012-11-11T19:46:40Z + +[Term] +id: VariO:0141 +name: DNA deletion +def: "Removal of one or more continuous nucleotides from DNA sequence." [VariO:mv] +synonym: "nucleotide deletion" EXACT [] +is_a: VariO:0135 ! DNA chain variation + +[Term] +id: VariO:0142 +name: DNA insertion +def: "Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence." [VariO:mv] +synonym: "nucleotide insertion" EXACT [] +is_a: VariO:0135 ! DNA chain variation + +[Term] +id: VariO:0143 +name: DNA indel +def: "A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s)." [VariO:mv] +is_a: VariO:0135 ! DNA chain variation + +[Term] +id: VariO:0144 +name: DNA translocation +def: "A continuous stretch of DNA sequence moved to a new position within a chromosome." [VariO:mv] +xref: MI:0593 +xref: SO:0000199 +is_a: VariO:0135 ! DNA chain variation + +[Term] +id: VariO:0145 +name: DNA inversion +def: "A continuous stretch of DNA sequence inserted to the same position in reverse orientation." [VariO:mv] +xref: SO:1000036 +is_a: VariO:0144 ! DNA translocation + +[Term] +id: VariO:0146 +name: DNA variation of non-genetic origin +def: "DNA variation that does not have genetic origin." [VariO:mv] +is_a: VariO:0127 ! DNA variation origin + +[Term] +id: VariO:0147 +name: epigenetic DNA variation +def: "Heritable DNA variation of non-genetic origin." [VariO:mv] +is_a: VariO:0146 ! DNA variation of non-genetic origin + +[Term] +id: VariO:0148 +name: variation affecting DNA function +def: "Variation having effect on DNA function and usage." [VariO:mv] +is_a: VariO:0128 ! variation affecting DNA + +[Term] +id: VariO:0149 +name: effect on transcription +def: "Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA." [VariO:mv] +is_a: VariO:0148 ! variation affecting DNA function + +[Term] +id: VariO:0150 +name: effect on DNA information transfer +def: "Variation affecting information transfer of DNA." [VariO:mv] +is_a: VariO:0148 ! variation affecting DNA function + +[Term] +id: VariO:0151 +name: effect on DNA repair +def: "Variation affecting the process of restoring DNA after damage." [VariO:mv] +xref: GO:0006281 +xref: Wikipedia:DNA_repair +is_a: VariO:0148 ! variation affecting DNA function + +[Term] +id: VariO:0152 +name: effect on regulatory function of DNA +def: "Variation affecting regulatory function of DNA." [VariO:mv] +is_a: VariO:0148 ! variation affecting DNA function + +[Term] +id: VariO:0153 +name: chromatin variation +def: "Variation affecting chromatin." [VariO:mv] +is_a: VariO:0322 ! DNA variation classification +created_by: med-mnv +creation_date: 2018-03-05T16:05:29Z + +[Term] +id: VariO:0154 +name: effect on DNA replication +def: "Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule." [VariO:mv] +is_a: VariO:0148 ! variation affecting DNA function + +[Term] +id: VariO:0155 +name: variation affecting DNA structure +def: "Variation affecting structure of DNA." [VariO:mv] +is_a: VariO:0128 ! variation affecting DNA + +[Term] +id: VariO:0156 +name: epigenetic DNA modification +def: "Hereditary variation of DNA not affecting primary sequence." [VariO:mv] +is_a: VariO:0155 ! variation affecting DNA structure + +[Term] +id: VariO:0157 +name: epigenetic DNA methylation +def: "Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression." [VariO:mv] +is_a: VariO:0156 ! epigenetic DNA modification + +[Term] +id: VariO:0158 +name: nucleosome positioning +def: "Positioning of nucleosomes to DNA strand." [VariO:mv] +synonym: "chromatin modeling" EXACT [GO:0006338] +synonym: "chromatin remodelling" EXACT [GO:0006338] +is_a: VariO:0156 ! epigenetic DNA modification +is_a: VariO:0226 ! chromatin structure variation +relationship: part_of VariO:0156 ! epigenetic DNA modification +relationship: part_of VariO:0226 ! chromatin structure variation + +[Term] +id: VariO:0159 +name: affected DNA level +def: "Affected level of DNA." [VariO:mv] +is_a: VariO:0155 ! variation affecting DNA structure + +[Term] +id: VariO:0160 +name: DNA chain affected +def: "Variation effect on DNA level." [VariO:mv] +is_a: VariO:0159 ! affected DNA level + +[Term] +id: VariO:0161 +name: variation in intron +def: "Variation located in intron." [VariO:mv] +xref: SO:0001627 +is_a: VariO:0160 ! DNA chain affected + +[Term] +id: VariO:0162 +name: variation in exon +def: "Variation located in exon." [VariO:mv] +is_a: VariO:0160 ! DNA chain affected + +[Term] +id: VariO:0163 +name: variation at intergenic DNA +def: "Variation located in intergenic DNA." [VariO:mv] +xref: SO:0001628 +is_a: VariO:0160 ! DNA chain affected + +[Term] +id: VariO:0164 +name: chromosome affected +def: "Variation effect on chromosome level." [VariO:mv] +is_a: VariO:0159 ! affected DNA level + +[Term] +id: VariO:0165 +name: genome affected +def: "Variation effect on genome level." [VariO:mv] +is_a: VariO:0159 ! affected DNA level + +[Term] +id: VariO:0166 +name: immunological receptor gene rearrangement +def: "Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes." [VariO:mv] +is_a: VariO:0447 ! immunological recognition molecule diversification +created_by: med-mnv +creation_date: 2015-09-22T19:10:52Z + +[Term] +id: VariO:0167 +name: effect on DNA form +def: "Variation affecting DNA structural form." [VariO:mv] +is_a: VariO:0171 ! effect on DNA tertiary structure +created_by: med-mnv +creation_date: 2017-01-16T12:52:26Z + +[Term] +id: VariO:0168 +name: somatic hypermutation +def: "Immunoglobulin diversification mechanism by producing variations to antigen variable regions." [VariO:mv] +is_a: VariO:0447 ! immunological recognition molecule diversification +created_by: med-mnv +creation_date: 2015-09-22T19:12:51Z + +[Term] +id: VariO:0169 +name: class switch recombination +def: "Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain." [VariO:mv] +is_a: VariO:0447 ! immunological recognition molecule diversification +created_by: med-mnv +creation_date: 2015-09-22T19:12:51Z + +[Term] +id: VariO:0170 +name: immunological receptor gene conversion +def: "Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence." [VariO:mv] +is_a: VariO:0447 ! immunological recognition molecule diversification +created_by: med-mnv +creation_date: 2015-09-22T19:12:51Z + +[Term] +id: VariO:0171 +name: effect on DNA tertiary structure +def: "Variation affecting DNA tertiary structure." [VariO:mv] +is_a: VariO:0155 ! variation affecting DNA structure + +[Term] +id: VariO:0172 +name: artificial DNA variation +def: "Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA." [VariO:mv] +is_a: VariO:0146 ! DNA variation of non-genetic origin +created_by: Mauno Vihinen +creation_date: 2012-11-16T08:44:55Z + +[Term] +id: VariO:0173 +name: effect on nucleic acid G-quadruplex +def: "Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular." [VariO:mv] +is_a: VariO:0420 ! effect on four-stranded DNA +is_a: VariO:0426 ! effect on four-stranded RNA +relationship: part_of VariO:0420 ! effect on four-stranded DNA +relationship: part_of VariO:0426 ! effect on four-stranded RNA + +[Term] +id: VariO:0174 +name: effect on i motif +def: "Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly." [VariO:mv] +is_a: VariO:0420 ! effect on four-stranded DNA + +[Term] +id: VariO:0175 +name: effect on DNA triple helix +def: "Variation affecting DNA helix formed of three strands." [VariO:mv] +is_a: VariO:0167 ! effect on DNA form + +[Term] +id: VariO:0176 +name: chromosome variation +def: "Variation affecting chromosome." [VariO:mv] +xref: SO:0000240 +is_a: VariO:0155 ! variation affecting DNA structure + +[Term] +id: VariO:0177 +name: telomere length change +def: "Variation affecting length of telomere sequence." [VariO:mv] +is_a: VariO:0180 ! chromosome structure variation + +[Term] +id: VariO:0178 +name: telomere shortening +def: "Variation shortening length of telomere sequence." [VariO:mv] +is_a: VariO:0177 ! telomere length change + +[Term] +id: VariO:0179 +name: telomere extension +def: "Variation extending length of telomere sequence." [VariO:mv] +is_a: VariO:0177 ! telomere length change + +[Term] +id: VariO:0180 +name: chromosome structure variation +def: "Variation affecting structure of chromosome." [VariO:mv] +xref: SO:1000183 +is_a: VariO:0176 ! chromosome variation + +[Term] +id: VariO:0181 +name: isochromosome +def: "Chromosome lacking one arm with duplication of the other arm." [VariO:mv] +is_a: VariO:0180 ! chromosome structure variation + +[Term] +id: VariO:0182 +name: ring chromosome +def: "Circular chromosome with ends joined." [VariO:mv] +xref: SO:1000045 +is_a: VariO:0180 ! chromosome structure variation + +[Term] +id: VariO:0183 +name: chromosomal amplification +def: "Increase in the frequency of a chromosomal region." [VariO:mv] +is_a: VariO:0180 ! chromosome structure variation + +[Term] +id: VariO:0184 +name: interspersed repeat +def: "Copies of a chromosomal region of length greater than one scattered to genome sequence." [VariO:mv] +xref: SO:0000658 +is_a: VariO:0427 ! type of chromosomal amplification + +[Term] +id: VariO:0185 +name: tandem repeat +def: "Adjacent copies of a chromosomal region of length greater than 1." [VariO:mv] +xref: SO:0000705 +is_a: VariO:0427 ! type of chromosomal amplification + +[Term] +id: VariO:0186 +name: minisatellite +def: "Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs." [VariO:mv] +is_a: VariO:0430 ! nucleotide expansion + +[Term] +id: VariO:0187 +name: copy number variation +def: "Increase or decrease of the number of copies of a chromosomal region. Sizes of copy number variations range from about 1 kilobase to several megabases." [VariO:mv] +xref: SO:0001019 +is_a: VariO:0183 ! chromosomal amplification +is_a: VariO:0193 ! chromosomal deletion +relationship: part_of VariO:0183 ! chromosomal amplification +relationship: part_of VariO:0193 ! chromosomal deletion + +[Term] +id: VariO:0188 +name: microsatellite +def: "Tandem repetitive sequence consisting of units of two to six base pair." [VariO:mv] +is_a: VariO:0430 ! nucleotide expansion + +[Term] +id: VariO:0189 +name: trinucleotide expansion +def: "Tandem repetitive sequence consisting of three nucleotide units." [VariO:mv] +is_a: VariO:0188 ! microsatellite + +[Term] +id: VariO:0190 +name: mononucleotide expansion +def: "Tandem repetitive sequence consisting of one nucleotide type." [VariO:mv] +is_a: VariO:0188 ! microsatellite + +[Term] +id: VariO:0191 +name: tetranucleotide expansion +def: "Tandem repetitive sequence consisting of four nucleotide units." [VariO:mv] +is_a: VariO:0188 ! microsatellite + +[Term] +id: VariO:0192 +name: DNA mobile genetic element insertion +def: "Mobile genetic element incorporated into chromosome." [VariO:mv] +is_a: VariO:0183 ! chromosomal amplification + +[Term] +id: VariO:0193 +name: chromosomal deletion +def: "Deletion of chromosomal region." [VariO:mv] +is_a: VariO:0180 ! chromosome structure variation + +[Term] +id: VariO:0194 +name: interstitial deletion +def: "Deletion of chromosomal region not including terminus." [VariO:mv] +is_a: VariO:0193 ! chromosomal deletion + +[Term] +id: VariO:0195 +name: terminal deletion +def: "Deletion of chromosomal region from the end of chromosome arm." [VariO:mv] +is_a: VariO:0193 ! chromosomal deletion + +[Term] +id: VariO:0196 +name: complex chromosomal variation +def: "Chromosome structure variation with four or more breakpoints." [SO:ke, VariO:mv] +xref: SO:1000146 +is_a: VariO:0180 ! chromosome structure variation + +[Term] +id: VariO:0197 +name: chromosomal translocation +def: "Translocation of chromosomal region." [VariO:mv] +xref: SO:0000199 +is_a: VariO:0180 ! chromosome structure variation + +[Term] +id: VariO:0198 +name: intrachromosomal translocation +def: "Translocation of chromosomal region within a chromosome." [VariO:mv] +is_a: VariO:0197 ! chromosomal translocation + +[Term] +id: VariO:0199 +name: chromosomal inversion +def: "Intrachromosomal variation where a chromosomal region is inserted in reverse direction." [VariO:mv] +is_a: VariO:0198 ! intrachromosomal translocation + +[Term] +id: VariO:0200 +name: paracentric inversion +def: "Chromosomal inversion within a chromosome arm." [VariO:mv] +xref: SO:1000047 +is_a: VariO:0199 ! chromosomal inversion + +[Term] +id: VariO:0201 +name: pericentric inversion +def: "Chromosomal inversion including centromere." [VariO:mv] +xref: SO:1000046 +is_a: VariO:0199 ! chromosomal inversion + +[Term] +id: VariO:0202 +name: interchromosomal translocation +def: "Translocation of chromosomal region to another chromosome." [VariO:mv] +is_a: VariO:0197 ! chromosomal translocation + +[Term] +id: VariO:0203 +name: reciprocal chromosomal translocation +def: "Switching of chromosomal regions between nonhomologous chromosomes." [VariO:mv] +xref: SO:1000048 +is_a: VariO:0202 ! interchromosomal translocation + +[Term] +id: VariO:0204 +name: Robertsonian translocation +def: "Fusion of long arms of two acrocentric chromosomes having very short p arms." [VariO:mv] +xref: SO:1000043 +is_a: VariO:0202 ! interchromosomal translocation + +[Term] +id: VariO:0205 +name: dinucleotide expansion +def: "Tandem repetitive sequence consisting of two nucleotide units." [VariO:mv] +is_a: VariO:0188 ! microsatellite +created_by: med-mnv +creation_date: 2015-09-17T10:53:06Z + +[Term] +id: VariO:0206 +name: chromosome number variation +def: "Variation affecting the number of chromosomes." [VariO:mv] +synonym: "aneuploidy" EXACT [] +is_a: VariO:0176 ! chromosome variation + +[Term] +id: VariO:0207 +name: trisomy +def: "Three copies of a chromosome in a cell or organism." [VariO:mv] +is_a: VariO:0206 ! chromosome number variation + +[Term] +id: VariO:0208 +name: disomy +def: "Two copies of a chromosome in a cell or organism ." [VariO:mv] +is_a: VariO:0206 ! chromosome number variation + +[Term] +id: VariO:0209 +name: uniparental disomy +def: "Both copies of a chromosome or a part of it in diploid cell or organism are from one parent." [VariO:mv] +is_a: VariO:0208 ! disomy + +[Term] +id: VariO:0210 +name: isodisomy +def: "Uniparental disomy with duplication of a single chromosome from one parent." [VariO:mv] +is_a: VariO:0208 ! disomy + +[Term] +id: VariO:0211 +name: heterodisomy +def: "Pair of non-identical chromosomes inherited from one parent." [VariO:mv] +is_a: VariO:0208 ! disomy + +[Term] +id: VariO:0212 +name: nullisomy +def: "No copies of a chromosome in a cell or organism." [VariO:mv] +is_a: VariO:0206 ! chromosome number variation + +[Term] +id: VariO:0213 +name: tetrasomy +def: "Four copies of a chromosome in a cell or organism." [VariO:mv] +is_a: VariO:0206 ! chromosome number variation + +[Term] +id: VariO:0214 +name: monosomy +def: "One copy of a chromosome in a cell or organism." [VariO:mv] +is_a: VariO:0206 ! chromosome number variation + +[Term] +id: VariO:0215 +name: chromosome set number variation +def: "Variation affecting number of entire chromosome sets." [VariO:mv] +synonym: "euploidy" EXACT [] +is_a: VariO:0428 ! genome variation + +[Term] +id: VariO:0216 +name: diploidy +def: "Variation with two sets of chromosomes." [VariO:mv] +is_a: VariO:0215 ! chromosome set number variation + +[Term] +id: VariO:0217 +name: tetraploidy +def: "Variation with four sets of chromosomes." [VariO:mv] +is_a: VariO:0215 ! chromosome set number variation +created_by: Mauno +creation_date: 2011-03-04T12:19:35Z + +[Term] +id: VariO:0218 +name: polyploidy +def: "Variation with several sets of chromosomes." [VariO:mv] +is_a: VariO:0215 ! chromosome set number variation + +[Term] +id: VariO:0219 +name: autopolyploidy +def: "Variation with several sets of chromosomes originating from the same organism." [VariO:mv] +is_a: VariO:0218 ! polyploidy + +[Term] +id: VariO:0220 +name: allopolyploidy +def: "Variation with several sets of chromosomes originating from a different organism." [VariO:mv] +is_a: VariO:0218 ! polyploidy + +[Term] +id: VariO:0221 +name: nulliploidy +def: "Variation without chromosomes." [VariO:mv] +is_a: VariO:0215 ! chromosome set number variation + +[Term] +id: VariO:0222 +name: triploidy +def: "Variation with three sets of chromosomes." [VariO:mv] +is_a: VariO:0215 ! chromosome set number variation + +[Term] +id: VariO:0223 +name: pentaploidy +def: "Variation with five sets of chromosomes." [VariO:mv] +is_a: VariO:0215 ! chromosome set number variation + +[Term] +id: VariO:0224 +name: hexaploidy +def: "Variation with six sets of chromosomes." [VariO:mv] +is_a: VariO:0215 ! chromosome set number variation + +[Term] +id: VariO:0225 +name: monoploidy +def: "Variation with a single set of chromosomes." [VariO:mv] +synonym: "haploidy" EXACT [] +is_a: VariO:0215 ! chromosome set number variation + +[Term] +id: VariO:0226 +name: chromatin structure variation +def: "Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins." [VariO:mv] +is_a: VariO:0155 ! variation affecting DNA structure + +[Term] +id: VariO:0227 +name: variation affecting DNA property +def: "Variation affecting characteristic property of DNA." [VariO:mv] +is_a: VariO:0128 ! variation affecting DNA + +[Term] +id: VariO:0228 +name: protein fusion +def: "Fusion of two protein chains. Produced from fusion gene of two joined genes." [VariO:mv] +is_a: VariO:0124 ! protein elongation +created_by: Mauno Vihinen +creation_date: 2012-12-11T08:59:44Z + +[Term] +id: VariO:0229 +name: association of DNA variation to pathogenicity +def: "Implication of a DNA variant to pathogenicity." [VariO:mv] +is_a: VariO:0227 ! variation affecting DNA property + +[Term] +id: VariO:0230 +name: effect on DNA interaction +def: "Variation affecting interaction of DNA with its partner." [VariO:mv] +is_a: VariO:0227 ! variation affecting DNA property + +[Term] +id: VariO:0231 +name: conservation of DNA variation site +def: "Conservation of the variation site in related DNA sequences." [VariO:mv] +is_a: VariO:0227 ! variation affecting DNA property + +[Term] +id: VariO:0232 +name: variation attribute +def: "Attributes define and modulate terms at other levels." [VariO:mv] +is_a: VariO:0001 ! variation + +[Term] +id: VariO:0233 +name: conservation +def: "Sequence conservation attribute." [VariO:mv] +is_a: VariO:0232 ! variation attribute + +[Term] +id: VariO:0234 +name: conserved region +def: "Variation at a region of sequence similarity in multiple sequence alignment of related sequences." [VariO:mv] +is_a: VariO:0233 ! conservation + +[Term] +id: VariO:0235 +name: invariant region +def: "Variation at invariant sequence region in multiple sequence alignment of related sequences." [VariO:mv] +is_a: VariO:0233 ! conservation + +[Term] +id: VariO:0236 +name: interaction +def: "Mutual or reciprocal action or influence that happens at a given place and time between participating molecules." [src_code:NR, VariO:mv] +is_a: VariO:0232 ! variation attribute + +[Term] +id: VariO:0237 +name: genetic interaction +def: "Two genes A and B \"genetically interact\" when the phenotype generated as the result of variations in both genes (double variant ab) is unexpectedly not just a combination of the phenotypes of the two single variants a and b." [PMID:16527956, VariO:mv] +xref: MI:0208 +is_a: VariO:0236 ! interaction + +[Term] +id: VariO:0238 +name: genetic interaction defined by inequality +def: "Two genes A and B present a genetic interaction defined by inequality if the phenotypes of the two single variants a and b, the double variant ab and the wild-type can be measured quantitatively and described relative to each other by an inequality relationship." [PMID:14755292, VariO:mv] +synonym: "genetic inequality" EXACT [MI:0931] +xref: MI:0931 +is_a: VariO:0237 ! genetic interaction + +[Term] +id: VariO:0239 +name: single nonmonotonic genetic interaction defined by inequality +def: "The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g. WT > a > ab > b." [PMID:15833125] +synonym: "single nonmonotonic" EXACT [MI:0800] +synonym: "single nonmonotonic genetic interaction (sensu inequality)" EXACT [MI:0800] +xref: MI:0800 +is_a: VariO:0238 ! genetic interaction defined by inequality + +[Term] +id: VariO:0240 +name: missing protein +def: "Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism." [VariO:mv] +is_a: VariO:0325 ! protein variation classification +created_by: Mauno Vihinen +creation_date: 2012-12-11T13:07:02Z + +[Term] +id: VariO:0241 +name: RNA translocation +def: "A continuous stretch of RNA sequence moved to a new position." [VariO:mv] +is_a: VariO:0328 ! RNA variation classification +created_by: Mauno Vihinen +creation_date: 2012-12-18T16:17:33Z + +[Term] +id: VariO:0242 +name: conditional genetic interaction defined by inequality +def: "The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b variant has an effect only in the a background. A has an effect only in the b background, or the b variant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab." [PMID:15833125, VariO:mv] +synonym: "conditional" EXACT [MI:0798] +synonym: "conditional genetic interaction (sensu inequality)" EXACT [MI:0798] +xref: MI:0798 +is_a: VariO:0238 ! genetic interaction defined by inequality + +[Term] +id: VariO:0243 +name: additive genetic interaction defined by inequality +def: "Single-variant phenotype effects combine to give a double-variant effect different from the wild type and different from single variant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b." [PMID:15833125, VariO:mv] +synonym: "additive" EXACT [MI:0799] +synonym: "additive genetic interaction (sensu inequality)" EXACT [MI:0799] +xref: MI:0799 +is_a: VariO:0238 ! genetic interaction defined by inequality + +[Term] +id: VariO:0244 +name: RNA inversion +def: "A continuous stretch of RNA sequence inserted to the same position in reverse orientation." [VriO:mv] +is_a: VariO:0241 ! RNA translocation +created_by: Mauno Vihinen +creation_date: 2012-12-18T16:17:33Z + +[Term] +id: VariO:0245 +name: missing RNA +def: "Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site." [VariO:mv] +is_a: VariO:0328 ! RNA variation classification +created_by: Mauno Vihinen +creation_date: 2013-01-04T09:23:09Z + +[Term] +id: VariO:0246 +name: artificial protein variation +def: "Protein variation generated on purpose." [VariO:mv] +is_a: VariO:0024 ! variation emerging at protein level +created_by: gerard +creation_date: 2013-02-01T11:24:30Z + +[Term] +id: VariO:0247 +name: artificial RNA variation +def: "RNA variation generated on purpose." [VariO:mv] +is_a: VariO:0333 ! RNA variation of non-genetic origin +created_by: gerard +creation_date: 2013-02-01T11:27:07Z + +[Term] +id: VariO:0248 +name: positive genetic interaction +def: "The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b." [PMID:14755292, VariO:mv] +synonym: "positive gent int" EXACT [MI:0935] +xref: MI:0935 +is_a: VariO:0237 ! genetic interaction + +[Term] +id: VariO:0249 +name: double nonmonotonic genetic interaction defined by inequality +def: "The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other variant gene. E.g. WT >= ab > a >= b." [PMID:15833125, VariO:mv] +synonym: "double nonmonotonic" EXACT [MI:0801] +synonym: "double nonmonotonic genetic interaction (sensu inequality)" EXACT [MI:0801] +xref: MI:0801 +is_a: VariO:0238 ! genetic interaction defined by inequality +is_a: VariO:0248 ! positive genetic interaction + +[Term] +id: VariO:0250 +name: epistatic genetic interaction +def: "The genetic interaction between a group of genes, in which the effects of an allele of one member gene of the group hide the effects of alleles of other genes in the group." [PMID:11988766] +synonym: "epistatis" EXACT [MI:0930] +xref: MI:0930 +is_a: VariO:0248 ! positive genetic interaction + +[Term] +id: VariO:0251 +name: epistatic genetic interaction defined by inequality +def: "The phenotype resulting from genetic perturbation of A and B have different effects (in terms of direction or magnitude) on the wild-type background and the double variant has the same phenotype as either A or B (for example, A < WT < B = AB)." [PMID:15833125, VariO:mv] +synonym: "epistatic" EXACT [MI:0797] +synonym: "epistatic genetic interaction (sensu inequality)" EXACT [MI:0797] +xref: MI:0797 +is_a: VariO:0238 ! genetic interaction defined by inequality +is_a: VariO:0250 ! epistatic genetic interaction + +[Term] +id: VariO:0252 +name: asynthetic genetic interaction defined by inequality +def: "The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. E. g., WT > a = b = ab." [PMID:15833125] +synonym: "asynthetic" EXACT [MI:0795] +synonym: "asynthetic genetic interaction (sensu inequality)" EXACT [MI:0795] +xref: MI:0795 +is_a: VariO:0238 ! genetic interaction defined by inequality +is_a: VariO:0250 ! epistatic genetic interaction + +[Term] +id: VariO:0253 +name: suppressive genetic interaction defined by inequality +def: "The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor b, which itself shows no single-variant effect. E. g., WT = b = ab > a." [PMID:15833125, VariO:mv] +synonym: "suppression" EXACT [MI:0796] +synonym: "suppressive genetic interaction (sensu inequality)" EXACT [MI:0796] +xref: MI:0796 +is_a: VariO:0238 ! genetic interaction defined by inequality +is_a: VariO:0250 ! epistatic genetic interaction + +[Term] +id: VariO:0254 +name: neutral genetic interaction +def: "The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b." [PMID:14755292, VariO:mv] +synonym: "neutral gent int" EXACT [MI:0934] +xref: MI:0934 +is_a: VariO:0237 ! genetic interaction + +[Term] +id: VariO:0255 +name: noninteractive genetic interaction defined by inequality +def: "Variation that has no effect in the WT and b backgrounds, or b has no effect in the a and WT backgrounds, or both hold true. E. g., WT = a > b = ab." [PMID:15833125, VariO:mv] +synonym: "noninteractive" EXACT [MI:0932] +synonym: "noninteractive genetic interaction (sensu inequality)" EXACT [MI:0932] +xref: MI:0932 +is_a: VariO:0238 ! genetic interaction defined by inequality +is_a: VariO:0254 ! neutral genetic interaction + +[Term] +id: VariO:0256 +name: negative genetic interaction +def: "The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b." [PMID:14755292, VariO:mv] +synonym: "negative gen int" EXACT [MI:0933] +xref: MI:0933 +is_a: VariO:0237 ! genetic interaction + +[Term] +id: VariO:0257 +name: synthetic genetic interaction defined by inequality +def: "The phenotype resulting from genetic perturbation a and the phenotype resulting from genetic perturbation b have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. E. g., WT = a = b > ab." [PMID:15833125] +synonym: "synthetic" EXACT [MI:0794] +synonym: "synthetic genetic interaction (sensu inequality)" EXACT [MI:0794] +xref: MI:0794 +is_a: VariO:0238 ! genetic interaction defined by inequality +is_a: VariO:0256 ! negative genetic interaction + +[Term] +id: VariO:0258 +name: structural level of interaction +def: "Molecular structural level of interaction." [VariO:mv] +is_a: VariO:0236 ! interaction + +[Term] +id: VariO:0259 +name: intermolecular interaction +def: "Interaction between molecules." [VariO:mv] +is_a: VariO:0258 ! structural level of interaction + +[Term] +id: VariO:0260 +name: intramolecular interaction +def: "Interaction within a molecule." [VariO:mv] +is_a: VariO:0258 ! structural level of interaction + +[Term] +id: VariO:0261 +name: colocalization +def: "Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred." [PMID:14755292] +xref: MI:0403 +is_a: VariO:0236 ! interaction + +[Term] +id: VariO:0262 +name: interactor +def: "Entity participating in a physical or functional interaction." [SBO:0000336] +xref: SBO:0000336 +is_a: VariO:0236 ! interaction + +[Term] +id: VariO:0263 +name: small molecule +def: "Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [PMID:14755292] +xref: MI:0328 +is_a: VariO:0262 ! interactor + +[Term] +id: VariO:0264 +name: metal +def: "Metal atom." [CHEBI:33521] +xref: CHEBI:33521 +is_a: VariO:0263 ! small molecule + +[Term] +id: VariO:0265 +name: solvent +def: "A liquid that can dissolve other substances (solutes) without any change in their chemical composition." [CHEBI:46787] +xref: CHEBI:46787 +is_a: VariO:0263 ! small molecule + +[Term] +id: VariO:0266 +name: water +def: "An inorganic hydroxy compound that has formula H2O." [CHEBI:15377] +xref: CHEBI:15377 +is_a: VariO:0265 ! solvent + +[Term] +id: VariO:0267 +name: complex +def: "Set of interacting molecules that can be copurified." [PMID:14755292] +xref: MI:0314 +is_a: VariO:0262 ! interactor + +[Term] +id: VariO:0268 +name: ribonucleoprotein complex +def: "A macromolecular complex containing both protein and RNA molecules." [PMID:14755292] +synonym: "ribonucleoprot compl" EXACT [MI:0316] +xref: MI:0316 +is_a: VariO:0267 ! complex + +[Term] +id: VariO:0269 +name: protein complex +def: "A stable set of interacting proteins that can be copurified and operate as a functional unit." [PMID:14755292] +synonym: "protein-protein complex" EXACT [GO:0043234] +xref: GO:0043234 +xref: MI:0315 +is_a: VariO:0267 ! complex + +[Term] +id: VariO:0270 +name: protein dna complex +def: "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." [PMID:14755292] +xref: MI:0233 +is_a: VariO:0267 ! complex + +[Term] +id: VariO:0271 +name: unknown participant +def: "Any type of molecule, including complexes, that may be observed but not identified." [PMID:14755292] +xref: MI:0329 +is_a: VariO:0262 ! interactor + +[Term] +id: VariO:0272 +name: gene +def: "Interactor of genetic interaction." [MI:0000704] +xref: MI:0250 +is_a: VariO:0262 ! interactor + +[Term] +id: VariO:0273 +name: biopolymer +def: "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds." [PMID:14577292] +xref: MI:0383 +is_a: VariO:0262 ! interactor + +[Term] +id: VariO:0274 +name: nucleic acid +def: "Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages." [PMID:14755292] +xref: GO:0005561 +xref: MI:0318 +is_a: VariO:0273 ! biopolymer + +[Term] +id: VariO:0275 +name: peptide +def: "Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues." [PMID:14755292] +synonym: "oligopeptide" EXACT [MI:0327] +synonym: "polypeptide" EXACT [MI:0327] +xref: MI:0327 +is_a: VariO:0273 ! biopolymer + +[Term] +id: VariO:0276 +name: polysaccharide +def: "A polysaccharide is a complex polymer of carbohydrate monomers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules." [PMID:14755292] +xref: MI:0904 +is_a: VariO:0273 ! biopolymer + +[Term] +id: VariO:0277 +name: protein +def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence." [PMID:14755292] +xref: GO:0003675 +xref: MI:0326 +is_a: VariO:0273 ! biopolymer + +[Term] +id: VariO:0278 +name: association +def: "Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule." [PMID:14755292] +xref: MI:0914 +is_a: VariO:0236 ! interaction + +[Term] +id: VariO:0279 +name: interaction physical force +def: "Interaction physical force." [VariO:mv] +is_a: VariO:0236 ! interaction + +[Term] +id: VariO:0280 +name: covalent bond +def: "A chemical link between two atoms in which electrons are shared between them." [http://chemistry.about.com/od/chemistryglossary/a/covalentbonddef.htm] +is_a: VariO:0279 ! interaction physical force + +[Term] +id: VariO:0281 +name: disulphide bridge +def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain." [EBIBS:GAR, UniProt:curation_manual, VariO:mv] +xref: SO:0001088 +is_a: VariO:0280 ! covalent bond + +[Term] +id: VariO:0282 +name: non covalent bond +def: "Interaction between biochemical entities that results in the formation of a non-covalent bond." [VariO:mv] +xref: SBO:0000177 +is_a: VariO:0279 ! interaction physical force + +[Term] +id: VariO:0283 +name: hydrogen bond +def: "Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom." [VariO:mv] +synonym: "H-bond" RELATED [FIX:0000503] +xref: FIX:0000503 +xref: http://chemistry.about.com/od/chemistryglossary/g/hbond.htm +is_a: VariO:0282 ! non covalent bond + +[Term] +id: VariO:0284 +name: hydrogen bond network +def: "Network of interactions formed by several hydrogen bonds." [VariO:mv] +is_a: VariO:0283 ! hydrogen bond + +[Term] +id: VariO:0285 +name: hydrophobic interaction +def: "Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction." [http://medical-dictionary.thefreedictionary.com/Hydrophobic+Interaction] +is_a: VariO:0282 ! non covalent bond + +[Term] +id: VariO:0286 +name: salt bridge +def: "Interaction between charged groups." [VariO:mv] +is_a: VariO:0282 ! non covalent bond + +[Term] +id: VariO:0287 +name: van der Waals interaction +def: "Weak attractive electrical force between neutral groups or molecules." [VariO:mv] +xref: FIX:0000506 +is_a: VariO:0282 ! non covalent bond + +[Term] +id: VariO:0288 +name: electrostatic interaction +def: "Attraction between two electrically charged groups or molecules." [VariO:mv] +is_a: VariO:0282 ! non covalent bond + +[Term] +id: VariO:0289 +name: quantity change +def: "Quantity attribute." [VariO:mv] +is_a: VariO:0232 ! variation attribute + +[Term] +id: VariO:0290 +name: decreased +def: "The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.)." [SGD:curators] +xref: APO:0000003 +is_a: VariO:0289 ! quantity change + +[Term] +id: VariO:0291 +name: increased +def: "The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.)." [SGD:curators] +xref: APO:0000004 +is_a: VariO:0289 ! quantity change + +[Term] +id: VariO:0292 +name: missing +def: "The observed feature is missing compared to that in the wild type." [VariO:mv] +is_a: VariO:0289 ! quantity change + +[Term] +id: VariO:0293 +name: pathogenicity association +def: "Pathogenicity attribute." [VariO:mv] +is_a: VariO:0232 ! variation attribute + +[Term] +id: VariO:0294 +name: disease causing +def: "Variation is causative of disease." [VariO:mv] +is_a: VariO:0293 ! pathogenicity association + +[Term] +id: VariO:0295 +name: not related to clinical phenotype +def: "Variation is not related to clinical phenotype." [VariO:mv] +is_a: VariO:0293 ! pathogenicity association + +[Term] +id: VariO:0296 +name: disease associated +def: "Variation is disease related." [VariO:mv] +is_a: VariO:0293 ! pathogenicity association + +[Term] +id: VariO:0297 +name: variation affecting RNA +def: "Effects of a variation on RNA level." [VariO:mv] +is_a: VariO:0001 ! variation + +[Term] +id: VariO:0298 +name: variation affecting RNA property +def: "Variation affecting characteristic property of RNA." [VariO:mv] +is_a: VariO:0297 ! variation affecting RNA + +[Term] +id: VariO:0299 +name: effect on RNA degradation +def: "Variation affecting degradation of RNA." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property + +[Term] +id: VariO:0300 +name: effect on RNA folding +def: "Variation affecting folding of RNA." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property + +[Term] +id: VariO:0301 +name: effect on RNA stability +def: "Variation affecting stability of transcript." [VariO:mv] +xref: SO:0001546 +is_a: VariO:0298 ! variation affecting RNA property + +[Term] +id: VariO:0302 +name: conservation of RNA variation site +def: "Conservation of the variation site in related RNA sequences." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property + +[Term] +id: VariO:0303 +name: polysomy +def: "An excess of a particular chromosome in a cell or organism." [VariO:mv] +is_a: VariO:0206 ! chromosome number variation +created_by: gerard +creation_date: 2013-02-01T11:30:39Z + +[Term] +id: VariO:0304 +name: association of RNA variation to pathogenicity +def: "Implication of an RNA variant to pathogenicity." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property + +[Term] +id: VariO:0305 +name: effect on RNA interaction +def: "Variation affecting interaction of RNA with its partner." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property + +[Term] +id: VariO:0306 +name: RNA variation type +def: "Type of RNA variation. Describes origin and classification of a variant." [VariO:mv] +is_a: VariO:0297 ! variation affecting RNA + +[Term] +id: VariO:0307 +name: RNA variation of genetic origin +def: "RNA variation that has genetic origin." [VariO:mv] +is_a: VariO:0324 ! RNA variation origin + +[Term] +id: VariO:0308 +name: missense variation +def: "Nucleotide change in the mRNA triplet codon codes for another amino acid." [VariO:mv] +is_a: VariO:0312 ! RNA substitution + +[Term] +id: VariO:0309 +name: termination codon change +def: "RNA nucleotide change in termination codon." [VariO:mv] +xref: SO:0001590 +is_a: VariO:0328 ! RNA variation classification + +[Term] +id: VariO:0310 +name: nonsense variation +def: "Nucleotide change in the mRNA codon triplet creates a terminator codon." [VariO:mv] +is_a: VariO:0312 ! RNA substitution + +[Term] +id: VariO:0311 +name: RNA indel +def: "A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s)." [VariO:mv] +is_a: VariO:0328 ! RNA variation classification + +[Term] +id: VariO:0312 +name: RNA substitution +def: "Substitution of RNA nucleotide." [VariO:mv] +is_a: VariO:0328 ! RNA variation classification + +[Term] +id: VariO:0313 +name: transition +def: "Change of a pyrimidine nucleotide, C or T (or U), into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [VariO:mv] +is_a: VariO:0136 ! DNA substitution +is_a: VariO:0312 ! RNA substitution +relationship: owl:topObjectProperty VariO:0312 ! RNA substitution +relationship: part_of VariO:0136 ! DNA substitution + +[Term] +id: VariO:0314 +name: pyrimidine transition +def: "A substitution of a pyrimidine, C or T (or U), for another pyrimidine." [VariO:mv] +is_a: VariO:0313 ! transition + +[Term] +id: VariO:0315 +name: purine transition +def: "A substitution of a purine, A or G, for another purine." [VariO:mv] +is_a: VariO:0313 ! transition + +[Term] +id: VariO:0316 +name: transversion +def: "Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa." [VariO:mv] +xref: http://en.wikipedia.org/wiki/Transversion "wiki" +is_a: VariO:0136 ! DNA substitution +is_a: VariO:0312 ! RNA substitution +relationship: part_of VariO:0136 ! DNA substitution +relationship: part_of VariO:0312 ! RNA substitution + +[Term] +id: VariO:0317 +name: initiation codon change +def: "RNA nucleotide change in the initiation codon." [VariO:mv] +xref: SO:0001582 +is_a: VariO:0328 ! RNA variation classification + +[Term] +id: VariO:0318 +name: silent variation +def: "RNA variation that does not change the encoded amino acid." [VariO:mv] +is_a: VariO:0312 ! RNA substitution + +[Term] +id: VariO:0319 +name: RNA deletion +def: "One or more continuous nucleotides are missing from RNA sequence." [VariO:mv] +is_a: VariO:0328 ! RNA variation classification + +[Term] +id: VariO:0320 +name: in-frame deletion +def: "Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained." [VariO:mv] +is_a: VariO:0319 ! RNA deletion + +[Term] +id: VariO:0321 +name: out-of-frame deletion +def: "Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame." [VariO:mv] +is_a: VariO:0319 ! RNA deletion + +[Term] +id: VariO:0322 +name: DNA variation classification +def: "Classification of DNA variation." [VariO:mv] +is_a: VariO:0129 ! DNA variation type +created_by: Mauno Vihinen +creation_date: 2013-10-11T08:46:32Z + +[Term] +id: VariO:0323 +name: protein variation origin +def: "Origin of protein variation." [VariO:mv] +is_a: VariO:0012 ! protein variation type +created_by: Mauno Vihinen +creation_date: 2013-10-11T08:53:23Z + +[Term] +id: VariO:0324 +name: RNA variation origin +def: "Origin of RNA variation." [VariO:mv] +is_a: VariO:0306 ! RNA variation type +creation_date: 2013-10-11T09:04:23Z + +[Term] +id: VariO:0325 +name: protein variation classification +def: "Classification of protein variation." [VariO:mv] +is_a: VariO:0012 ! protein variation type +created_by: Mauno Vihinen +creation_date: 2013-10-11T08:59:04Z + +[Term] +id: VariO:0326 +name: RNA insertion +def: "Addition of one or more nucleotides between adjacent nucleotides in RNA sequence." [VariO:mv] +is_a: VariO:0328 ! RNA variation classification + +[Term] +id: VariO:0327 +name: out-of-frame insertion +def: "Insertion of nucleotide(s) causing alteration of mRNA reading frame." [VariO:mv] +is_a: VariO:0326 ! RNA insertion + +[Term] +id: VariO:0328 +name: RNA variation classification +def: "Classification of RNA variation." [VariO:mv] +is_a: VariO:0306 ! RNA variation type +created_by: Mauno Vihinen +creation_date: 2013-10-11T09:05:02Z + +[Term] +id: VariO:0329 +name: alternative RNA form +def: "RNA variation due to defective fidelity of transcription." [VariO:mv] +is_a: VariO:0333 ! RNA variation of non-genetic origin +creation_date: 2014-10-23T00:29:53Z + +[Term] +id: VariO:0330 +name: mistranslated protein +def: "Protein variation due to defective fidelity of translation." [VariO:mv] +is_a: VariO:0024 ! variation emerging at protein level +created_by: Mauno Vihinen +creation_date: 2014-10-23T00:31:56Z + +[Term] +id: VariO:0331 +name: alternative form of mRNA +def: "Alternative form of mRNA molecule." [VariO:mv] +is_a: VariO:0351 ! protein coding RNA +created_by: med-mnv +creation_date: 2018-04-26T14:47:12Z + +[Term] +id: VariO:0332 +name: in-frame insertion +def: "Insertion of nucleotides in multiples of three so that the reading frame is retained." [VariO:mv] +is_a: VariO:0326 ! RNA insertion + +[Term] +id: VariO:0333 +name: RNA variation of non-genetic origin +def: "RNA variation that does not have genetic origin being modified at RNA level." [VariO:mv] +is_a: VariO:0324 ! RNA variation origin + +[Term] +id: VariO:0334 +name: RNA splicing change +def: "Change to RNA splicing." [VariO:mv] +is_a: VariO:0328 ! RNA variation classification + +[Term] +id: VariO:0335 +name: decayed RNA +def: "RNA molecule destroyed due to appearance of a premature termination codon." [VariO:mv] +is_a: VariO:0333 ! RNA variation of non-genetic origin + +[Term] +id: VariO:0336 +name: modified RNA +def: "Post transcriptionally modified RNA." [VariO:mv] +is_a: VariO:0333 ! RNA variation of non-genetic origin + +[Term] +id: VariO:0337 +name: modified DNA +def: "DNA variation due to biological, chemical, physical or other modification." [VariO:mv] +is_a: VariO:0146 ! DNA variation of non-genetic origin +created_by: Mauno Vihinen +creation_date: 2014-10-23T00:42:47Z + +[Term] +id: VariO:0338 +name: variation affecting RNA structure +def: "Variation affecting structure of RNA." [VariO:mv] +is_a: VariO:0297 ! variation affecting RNA + +[Term] +id: VariO:0343 +name: synonymous variation +def: "mRNA variation not affecting the sequence of the translated protein." [VariO:mv] +is_a: VariO:0232 ! variation attribute +created_by: med-mnv +creation_date: 2015-06-04T13:23:24Z + +[Term] +id: VariO:0349 +name: affected RNA type +def: "Affected type of RNA." [VariO:mv] +is_a: VariO:0338 ! variation affecting RNA structure + +[Term] +id: VariO:0350 +name: non-protein coding RNA +def: "Variation affecting RNA not coding for protein." [VariO:mv] +synonym: "ncRNA" EXACT [] +synonym: "non-coding RNA\nncRNA" EXACT [] +is_a: VariO:0349 ! affected RNA type + +[Term] +id: VariO:0351 +name: protein coding RNA +def: "RNA coding for protein." [VariO:mv] +is_a: VariO:0349 ! affected RNA type + +[Term] +id: VariO:0352 +name: coding region of mRNA +def: "Variation affecting region coding for protein in protein coding RNA." [VariO:mv] +is_a: VariO:0351 ! protein coding RNA + +[Term] +id: VariO:0353 +name: non-coding region of mRNA +def: "Variation affecting region not coding for protein in protein coding mRNA." [VariO:mv] +is_a: VariO:0350 ! non-protein coding RNA + +[Term] +id: VariO:0354 +name: effect on post transcriptional RNA modification +def: "Variation affecting post transcriptional RNA modification." [VariO:mv] +is_a: VariO:0338 ! variation affecting RNA structure + +[Term] +id: VariO:0356 +name: alternatively polyadenylated mRNA +def: "Polyadenylation of mRNA molecule at alternative site." [VariO:mv] +is_a: VariO:0331 ! alternative form of mRNA + +[Term] +id: VariO:0361 +name: RNA sugar variation +def: "Post transcriptional modification of RNA nucleoside sugar." [VariO:mv] +is_a: VariO:0338 ! variation affecting RNA structure + +[Term] +id: VariO:0362 +name: effect on RNA splicing +def: "Effect to process where introns in mRNA are cut away from exons." [VariO:mv] +xref: SO:0001568 +is_a: VariO:0354 ! effect on post transcriptional RNA modification + +[Term] +id: VariO:0363 +name: effect on RNA localization +def: "Variation affecting cellular localization of RNA." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property +created_by: med-mnv +creation_date: 2018-05-07T11:20:14Z + +[Term] +id: VariO:0364 +name: effect on RNA aggregation +def: "Variation affecting aggregation tendency of RNA." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property +created_by: med-mnv +creation_date: 2018-05-07T11:20:14Z + +[Term] +id: VariO:0365 +name: effect on cis splicing +def: "Intronic splicing within an RNA molecule." [VariO:mv] +is_a: VariO:0362 ! effect on RNA splicing + +[Term] +id: VariO:0366 +name: variation at recursive splice site +def: "Variation affecting splicing at recursive splice site which subdivides a large intron." [VariO:mv] +is_a: VariO:0508 ! affected splice site + +[Term] +id: VariO:0367 +name: variation at five prime splice site +def: "Variation affecting intronic region bordering exon or retained RNA region, at the five prime end of the intron." [VariO:mv] +is_a: VariO:0508 ! affected splice site + +[Term] +id: VariO:0368 +name: variation at canonical five prime splice site +def: "Variation affecting canonical prime splice site at five prime end." [VariO:mv] +is_a: VariO:0367 ! variation at five prime splice site + +[Term] +id: VariO:0369 +name: variation at non canonical five prime splice site +def: "Variation affecting non canonical splice site at five prime end." [VariO:mv] +is_a: VariO:0367 ! variation at five prime splice site + +[Term] +id: VariO:0370 +name: variation at three prime splice site +def: "Variation affecting intronic region bordering the exon or retained RNA region, at the 3' edge of the intron." [VariO:mv] +is_a: VariO:0508 ! affected splice site + +[Term] +id: VariO:0371 +name: variation at non canonical three prime splice site +def: "Variation affecting non canonical splice site at three prime end." [VariO:mv] +is_a: VariO:0370 ! variation at three prime splice site + +[Term] +id: VariO:0372 +name: variation at canonical three prime splice site +def: "Variation affecting canonical splice site at three prime end." [VariO:mv] +is_a: VariO:0370 ! variation at three prime splice site + +[Term] +id: VariO:0373 +name: cryptic splice site activation +def: "Activation of new splice site." [VariO:mv] +xref: SO:0001569 +is_a: VariO:0504 ! inclusion of cryptic exon + +[Term] +id: VariO:0374 +name: cryptic splice donor activation +def: "Activation of new splice donor site." [VariO:mv] +xref: SO:0001571 +is_a: VariO:0373 ! cryptic splice site activation + +[Term] +id: VariO:0375 +name: cryptic splice acceptor activation +def: "Activation of new splice acceptor site." [VariO:mv] +xref: SO:0001570 +is_a: VariO:0373 ! cryptic splice site activation + +[Term] +id: VariO:0376 +name: effect on trans splicing +def: "Variation affecting splicing and ligation different RNA molecules." [VariO:mv] +is_a: VariO:0362 ! effect on RNA splicing + +[Term] +id: VariO:0377 +name: retrotransposon insertion +def: "Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA." [VariO:mv] +is_a: VariO:0192 ! DNA mobile genetic element insertion +created_by: med-mnv +creation_date: 2015-08-26T12:50:29Z + +[Term] +id: VariO:0378 +name: DNA transposon +def: "Insertion of a DNA transposable element into chromosome." [VariO:mv] +is_a: VariO:0192 ! DNA mobile genetic element insertion +created_by: med-mnv +creation_date: 2015-08-26T12:50:29Z + +[Term] +id: VariO:0379 +name: LINE +def: "Long interspersed nuclear element generated by retrotransposition." [VariO:mv] +is_a: VariO:0377 ! retrotransposon insertion +created_by: med-mnv +creation_date: 2015-08-26T12:51:03Z + +[Term] +id: VariO:0380 +name: SINE +def: "Short interspersed nuclear element generated by retrotransposition. Length below 500 bp." [VariO:mv] +is_a: VariO:0377 ! retrotransposon insertion +created_by: med-mnv +creation_date: 2015-08-26T12:51:03Z + +[Term] +id: VariO:0381 +name: effect on RNA double helix +def: "Variation affecting RNA double helix." [VariO:mv] +is_a: VariO:0137 ! effect on RNA tertiary structure +created_by: med-mnv +creation_date: 2018-05-07T11:22:31Z + +[Term] +id: VariO:0382 +name: effect on RNA secondary structure +def: "Variation affecting RNA secondary structure." [VariO:mv] +is_a: VariO:0338 ! variation affecting RNA structure + +[Term] +id: VariO:0383 +name: effect on RNA multiloop +def: "Variation affecting closed RNA structure in which at least two double stranded regions meet." [VariO:mv] +is_a: VariO:0382 ! effect on RNA secondary structure + +[Term] +id: VariO:0384 +name: effect on RNA bulge +def: "Variation affecting RNA structure in which nucleotides in one strand do not form base pairs." [VariO:mv] +is_a: VariO:0382 ! effect on RNA secondary structure + +[Term] +id: VariO:0385 +name: effect on RNA interior loop +def: "Variation affecting RNA structure in which both the strands do not form base pairs." [VariO:mv] +is_a: VariO:0382 ! effect on RNA secondary structure + +[Term] +id: VariO:0386 +name: effect on RNA stem +def: "Variation effecting hydrogen bonding in contiguous nested base pairs in RNA." [VariO:mv] +is_a: VariO:0382 ! effect on RNA secondary structure + +[Term] +id: VariO:0387 +name: effect on RNA hairpin loop +def: "Variation affecting loop connecting adjacent regions forming helix in RNA." [VariO:mv] +is_a: VariO:0382 ! effect on RNA secondary structure + +[Term] +id: VariO:0388 +name: LTR +def: "Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb." [VariO:mv] +is_a: VariO:0377 ! retrotransposon insertion +created_by: med-mnv +creation_date: 2015-08-26T12:51:03Z + +[Term] +id: VariO:0389 +name: pentanucleotide expansion +def: "Tandem repetitive sequence consisting of five nucleotide units." [VariO:mv] +is_a: VariO:0188 ! microsatellite +created_by: med-mnv +creation_date: 2015-09-17T10:55:04Z + +[Term] +id: VariO:0390 +name: effect on DNA double helix +def: "Variation affecting DNA double helical structure." [VariO:mv] +is_a: VariO:0167 ! effect on DNA form +created_by: med-mnv +creation_date: 2017-01-16T12:53:57Z + +[Term] +id: VariO:0391 +name: plasmid affected +def: "Variation effect on independently replicating small DNA molecule." [VariO:mv] +is_a: VariO:0072 ! extrachromosomal DNA affected +created_by: med-mnv +creation_date: 2015-09-18T20:15:22Z + +[Term] +id: VariO:0392 +name: insertion sequence +def: "Simple, relatively short transposable element. IS elements contain only transposition related genes." [VariO:mv] +is_a: VariO:0192 ! DNA mobile genetic element insertion +created_by: med-mnv +creation_date: 2015-09-18T20:28:19Z + +[Term] +id: VariO:0393 +name: epigenetic RNA variation +def: "RNA variation of epigenetic origin." [VariO:mv] +is_a: VariO:0333 ! RNA variation of non-genetic origin +created_by: med-mnv +creation_date: 2018-05-07T11:43:50Z + +[Term] +id: VariO:0394 +name: effect on DNA cruciform +def: "Variation affecting double stranded DNA structure that contains in both strands at corresponding positions a single stranded base pairing forming stem and a connecting loop." [VariO:mv] +is_a: VariO:0420 ! effect on four-stranded DNA +created_by: med-mnv +creation_date: 2015-09-18T20:44:08Z + +[Term] +id: VariO:0396 +name: variation affecting RNA function +def: "Variation having effect on RNA function and usage." [VariO:mv] +is_a: VariO:0297 ! variation affecting RNA + +[Term] +id: VariO:0397 +name: effect on RNA splicing function +def: "Variation affecting splicing function of RNA." [VariO:mv] +is_a: VariO:0396 ! variation affecting RNA function + +[Term] +id: VariO:0398 +name: effect on catalytic RNA activity +def: "Variation affecting catalytic function of RNA." [VariO:mv] +is_a: VariO:0396 ! variation affecting RNA function + +[Term] +id: VariO:0399 +name: effect on translation +def: "Variation affecting translation of protein." [VariO:mv] +is_a: VariO:0396 ! variation affecting RNA function + +[Term] +id: VariO:0400 +name: effect on regulatory function of RNA +def: "Variation affecting regulatory function of RNA." [VariO:mv] +is_a: VariO:0396 ! variation affecting RNA function + +[Term] +id: VariO:0401 +name: effect on amino acid transfer of RNA +def: "Variation affecting RNA function in amino acid transfer." [VariO:mv] +is_a: VariO:0396 ! variation affecting RNA function + +[Term] +id: VariO:0402 +name: effect on RNA information transfer +def: "Variation affecting information transfer by RNA." [VariO:mv] +is_a: VariO:0396 ! variation affecting RNA function + +[Term] +id: VariO:0403 +name: group I intron +def: "Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine." [VariO:mv] +is_a: VariO:0472 ! self-splicing intron +created_by: med-mnv +creation_date: 2015-09-21T10:06:37Z + +[Term] +id: VariO:0404 +name: group II intron +def: "Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP." [VariO:mv] +is_a: VariO:0472 ! self-splicing intron +created_by: med-mnv +creation_date: 2015-09-21T10:06:37Z + +[Term] +id: VariO:0405 +name: dicentric translocation +def: "Fusion of two chromosome segments both containing a centromere." [VariO:mv] +is_a: VariO:0202 ! interchromosomal translocation +created_by: med-mnv +creation_date: 2015-09-22T19:15:03Z + +[Term] +id: VariO:0407 +name: edited DNA +def: "Variation generated by chromosome editing." [VariO:mv] +is_a: VariO:0146 ! DNA variation of non-genetic origin +created_by: med-mnv +creation_date: 2015-09-22T19:20:45Z + +[Term] +id: VariO:0408 +name: RNA chimera +def: "Fusion transcript of exons from two or more genes." [VariO:mv] +is_a: VariO:0333 ! RNA variation of non-genetic origin +created_by: med-mnv +creation_date: 2015-09-24T13:21:02Z + +[Term] +id: VariO:0409 +name: frameshifted RNA +def: "Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome." [VariO:mv] +is_a: VariO:0333 ! RNA variation of non-genetic origin +created_by: med-mnv +creation_date: 2015-09-24T13:21:02Z + +[Term] +id: VariO:0410 +name: effect on single stranded DNA structure +def: "Variation affecting single stranded DNA structure." [VariO:mv] +is_a: VariO:0167 ! effect on DNA form +created_by: med-mnv +creation_date: 2018-11-08T10:04:23Z + +[Term] +id: VariO:0411 +name: alternatively spliced RNA +def: "mRNA molecule matured by splicing at an alternative site." [VariO:mv] +is_a: VariO:0331 ! alternative form of mRNA +created_by: med-mnv +creation_date: 2015-10-13T19:36:23Z + +[Term] +id: VariO:0412 +name: effect on catalytic DNA activity +def: "Variation affecting catalytic function of DNA." [VariO:mv] +is_a: VariO:0148 ! variation affecting DNA function +created_by: med-mnv +creation_date: 2016-11-29T11:11:11Z + +[Term] +id: VariO:0413 +name: effect on A DNA +def: "Variation affecting A form of right-handed DNA." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-16T12:55:40Z + +[Term] +id: VariO:0414 +name: effect on B DNA +def: "Variation affecting B form of right-handed DNA." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-16T12:55:40Z + +[Term] +id: VariO:0415 +name: effect on C DNA +def: "Variation affecting C form of right-handed DNA." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-16T12:55:40Z + +[Term] +id: VariO:0416 +name: effect on L DNA +def: "Variation affecting L form of right-handed DNA." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-16T12:55:40Z + +[Term] +id: VariO:0417 +name: effect on S DNA +def: "Variation affecting S form of right-handed DNA." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-16T12:55:40Z + +[Term] +id: VariO:0418 +name: effect on D DNA +def: "Variation affecting D form of right-handed DNA." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-16T13:10:01Z + +[Term] +id: VariO:0419 +name: effect on H DNA +def: "Variation affecting H form of intramolecular triple helical DNA." [VariO:mv] +is_a: VariO:0422 ! effect on intramolecular DNA triple helix +created_by: med-mnv +creation_date: 2017-01-16T13:14:56Z + +[Term] +id: VariO:0420 +name: effect on four-stranded DNA +def: "Variation affecting four-stranded DNA." [VariO:mv] +is_a: VariO:0167 ! effect on DNA form +created_by: med-mnv +creation_date: 2017-01-16T13:17:51Z + +[Term] +id: VariO:0421 +name: effect on Z DNA +def: "Variation affecting Z form of left-handed DNA." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-16T13:20:36Z + +[Term] +id: VariO:0422 +name: effect on intramolecular DNA triple helix +def: "Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex." [VariO:mv] +is_a: VariO:0175 ! effect on DNA triple helix +created_by: med-mnv +creation_date: 2017-01-16T13:22:35Z + +[Term] +id: VariO:0423 +name: effect on intermolecular DNA triple helix +def: "Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule." [VariO:mv] +is_a: VariO:0175 ! effect on DNA triple helix +created_by: med-mnv +creation_date: 2017-01-16T13:24:18Z + +[Term] +id: VariO:0424 +name: effect on DNA-RNA hybrid +def: "Variation affecting DNA-RNA hybrid." [VariO:mv] +is_a: VariO:0137 ! effect on RNA tertiary structure +is_a: VariO:0167 ! effect on DNA form +created_by: med-mnv +creation_date: 2017-01-16T13:29:46Z + +[Term] +id: VariO:0425 +name: effect on RNA triple helix +def: "Variation affecting RNA helix formed of three strands." [VariO:mv] +is_a: VariO:0137 ! effect on RNA tertiary structure +created_by: med-mnv +creation_date: 2017-01-16T13:48:49Z + +[Term] +id: VariO:0426 +name: effect on four-stranded RNA +def: "Variation affecting four-stranded RNA." [VariO:mv] +is_a: VariO:0137 ! effect on RNA tertiary structure +created_by: med-mnv +creation_date: 2017-01-16T13:48:49Z + +[Term] +id: VariO:0427 +name: type of chromosomal amplification +def: "Classification of chromosomal amplification type." [VariO:mv] +is_a: VariO:0183 ! chromosomal amplification +created_by: med-mnv +creation_date: 2017-01-17T09:34:30Z + +[Term] +id: VariO:0428 +name: genome variation +def: "Variation affecting genome." [VariO:mv] +is_a: VariO:0155 ! variation affecting DNA structure +created_by: med-mnv +creation_date: 2017-01-23T09:01:36Z + +[Term] +id: VariO:0429 +name: complex genomic variation +def: "Chromosome structure variation due to several breakpoints." [VariO:mv] +is_a: VariO:0428 ! genome variation +created_by: med-mnv +creation_date: 2017-01-23T09:03:57Z + +[Term] +id: VariO:0430 +name: nucleotide expansion +def: "Repetitive sequence consisting of one more nucleotide units." [VariO:mv] +is_a: VariO:0183 ! chromosomal amplification +created_by: med-mnv +creation_date: 2017-01-23T09:09:22Z + +[Term] +id: VariO:0431 +name: effect on R loop +def: "Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA." [VariO:mv] +is_a: VariO:0424 ! effect on DNA-RNA hybrid +created_by: med-mnv +creation_date: 2017-01-23T09:32:22Z + +[Term] +id: VariO:0432 +name: effect on T loop +def: "Effect on DNA-RNA T loop structure formed by single-stranded 3' strand looping back to anneal with double-stranded repeats. Appears in telomere end-replication." [VariO:mv] +is_a: VariO:0390 ! effect on DNA double helix +created_by: med-mnv +creation_date: 2017-01-23T09:34:30Z + +[Term] +id: VariO:0433 +name: effect on D loop +def: "Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA." [VariO:mv] +is_a: VariO:0423 ! effect on intermolecular DNA triple helix +relationship: part_of VariO:0423 ! effect on intermolecular DNA triple helix +relationship: part_of VariO:0424 ! effect on DNA-RNA hybrid +created_by: med-mnv +creation_date: 2017-01-23T09:45:49Z + +[Term] +id: VariO:0434 +name: DNA sugar variation +def: "Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone." [VariO:mv] +is_a: VariO:0155 ! variation affecting DNA structure +created_by: med-mnv +creation_date: 2017-03-23T10:54:09Z + +[Term] +id: VariO:0435 +name: effect on protein reaction kinetics +def: "Effect of variation to protein reaction kinetics." [VariO:mv] +is_a: VariO:0053 ! effect on protein activity +created_by: med-mnv +creation_date: 2017-04-28T14:52:51Z + +[Term] +id: VariO:0436 +name: mature RNA +def: "Completely processed RNA molecule." [VariO:mv] +is_a: VariO:0336 ! modified RNA +created_by: med-mnv +creation_date: 2017-04-28T14:58:30Z + +[Term] +id: VariO:0437 +name: alternatively initiated mRNA +def: "RNA variation causing alternative translation initiation." [VariO:mv] +is_a: VariO:0331 ! alternative form of mRNA +created_by: med-mnv +creation_date: 2017-04-28T16:01:26Z + +[Term] +id: VariO:0438 +name: epigenetic RNA modification +def: "Epigenetic modification of RNA." [VariO:mv] +is_a: VariO:0338 ! variation affecting RNA structure +created_by: med-mnv +creation_date: 2018-05-07T14:40:53Z + +[Term] +id: VariO:0439 +name: effect on RNA activity +def: "Effect of variation on RNA activity." [VariO:mv] +is_a: VariO:0298 ! variation affecting RNA property +created_by: med-mnv +creation_date: 2017-04-28T16:23:47Z + +[Term] +id: VariO:0440 +name: effect on RNA reaction kinetics +def: "Effect of variation on RNA reaction kinetics." [VariO:mv] +is_a: VariO:0439 ! effect on RNA activity +created_by: med-mnv +creation_date: 2017-04-28T16:26:01Z + +[Term] +id: VariO:0441 +name: effect on RNA affinity +def: "Effect of variation on RNA affinity to binding molecule(s)." [VariO:mv] +is_a: VariO:0439 ! effect on RNA activity +created_by: med-mnv +creation_date: 2017-04-28T16:26:01Z + +[Term] +id: VariO:0442 +name: effect on RNA specificity +def: "Effect of variation on substrate binding specificity of RNA." [VariO:mv] +is_a: VariO:0439 ! effect on RNA activity +created_by: med-mnv +creation_date: 2017-04-28T16:26:01Z + +[Term] +id: VariO:0443 +name: alternatively initiated protein +def: "Protein variant originating from alternative translation initiation." [VariO:mv] +is_a: VariO:0024 ! variation emerging at protein level +created_by: med-mnv +creation_date: 2017-05-03T09:09:05Z + +[Term] +id: VariO:0444 +name: de novo variation +def: "Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis." [VariO:mv] +is_a: VariO:0130 ! DNA variation of genetic origin +created_by: med-mnv +creation_date: 2018-01-08T11:31:50Z + +[Term] +id: VariO:0445 +name: germinal variation +def: "Variation that has been inherited from a germline cell." [VariO:mv] +synonym: "germline variation" RELATED [] +is_a: VariO:0130 ! DNA variation of genetic origin +created_by: med-mnv +creation_date: 2017-12-15T09:58:57Z + +[Term] +id: VariO:0446 +name: somatic variation +def: "Variation that has its origin in a cell in soma." [VariO:mv] +is_a: VariO:0130 ! DNA variation of genetic origin +created_by: med-mnv +creation_date: 2017-12-15T09:58:57Z + +[Term] +id: VariO:0447 +name: immunological recognition molecule diversification +def: "Processes that recombine and modify genes coding for immunological recognition molecules (antigens, B- and T-cell receptors, MCH type I and II molecules)." [VariO:mv] +is_a: VariO:0180 ! chromosome structure variation +created_by: med-mnv +creation_date: 2017-12-15T10:47:27Z + +[Term] +id: VariO:0448 +name: organellar DNA affected +def: "Variation effect on DNA within cellular compartment." [VariO:mv] +is_a: VariO:0072 ! extrachromosomal DNA affected +created_by: med-mnv +creation_date: 2018-02-01T12:42:12Z + +[Term] +id: VariO:0449 +name: extrachromosomal circular DNA +def: "Circular DNA molecule not part of the chromosomes." [VariO:mv] +is_a: VariO:0072 ! extrachromosomal DNA affected +created_by: med-mnv +creation_date: 2018-02-01T12:47:35Z + +[Term] +id: VariO:0450 +name: mitochondrial DNA affected +def: "Variation affecting DNA within mitochondria." [VariO:mv] +is_a: VariO:0448 ! organellar DNA affected +created_by: med-mnv +creation_date: 2018-02-01T12:52:27Z + +[Term] +id: VariO:0451 +name: plastid DNA affected +def: "Variation affecting DNA within plastids e.g. chloroplasts." [VariO:mv] +is_a: VariO:0448 ! organellar DNA affected +created_by: med-mnv +creation_date: 2018-02-01T12:53:15Z + +[Term] +id: VariO:0452 +name: heptanucleotide expansion +def: "Tandem repetitive sequence consisting of six nucleotide units." [VariO:mv] +is_a: VariO:0188 ! microsatellite +created_by: med-mnv +creation_date: 2018-02-01T14:49:25Z + +[Term] +id: VariO:0453 +name: histone modification +def: "Epigenetic modification of histone." [VariO:mv] +is_a: VariO:0156 ! epigenetic DNA modification +created_by: med-mnv +creation_date: 2018-02-06T09:08:59Z + +[Term] +id: VariO:0454 +name: variation at topology associating domain +def: "Variation affecting topology associating domain (TAD)." [VariO:mv] +is_a: VariO:0226 ! chromatin structure variation +created_by: med-mnv +creation_date: 2018-03-05T16:55:07Z + +[Term] +id: VariO:0455 +name: effect on A motif +is_a: VariO:0410 ! effect on single stranded DNA structure +created_by: med-mnv +creation_date: 2018-11-08T10:05:56Z + +[Term] +id: VariO:0456 +name: RNA genome +def: "Genome composed of RNA molecule." [] +is_a: VariO:0351 ! protein coding RNA + +[Term] +id: VariO:0457 +name: RNA virus genome +def: "Genome for a RNA virus." [] +is_a: VariO:0456 ! RNA genome + +[Term] +id: VariO:0458 +name: viroid genome +def: "Genome for an infectious particle." [] +is_a: VariO:0456 ! RNA genome + +[Term] +id: VariO:0459 +name: satelletite genome +def: "Genome for a subviral agent." [] +is_a: VariO:0456 ! RNA genome + +[Term] +id: VariO:0460 +name: pre-mRNA +def: "Unprocessed mRNA." [] +is_a: VariO:0351 ! protein coding RNA + +[Term] +id: VariO:0461 +name: mRNA +def: "Mature mRNA." [] +is_a: VariO:0460 ! pre-mRNA + +[Term] +id: VariO:0462 +name: circular RNA +def: "Covalently closed single-stranded RNA chain." [] +synonym: "circRNA" EXACT [] +is_a: VariO:0351 ! protein coding RNA + +[Term] +id: VariO:0463 +name: antisense RNA +def: "Single-stranded non-coding RNA compelementary to a mRNA or part of it." [] +is_a: VariO:0477 ! regulatory RNA + +[Term] +id: VariO:0464 +name: non-coding sense RNA +def: "Single-stranded noncoding RNA overlapping with mRNA but not coding for a protein." [] +is_a: VariO:0477 ! regulatory RNA + +[Term] +id: VariO:0465 +name: functional non-coding RNA +def: "Non-coding RNA with a function." [] +is_a: VariO:0350 ! non-protein coding RNA + +[Term] +id: VariO:0466 +name: retrotransposon RNA intermediate +def: "RNA intermediate of a retrotransposon." [] +synonym: "class I transposable element\ntransposon via RNA intermediate" EXACT [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0467 +name: translation related non-coding RNA +def: "RNA involved in protein synthesis." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0468 +name: transfer RNA +def: "Transfer RNA involved in protein synthesis. Modiefied tRNA contains amino acid and carries it to ribosome." [] +synonym: "tRNA" EXACT [] +is_a: VariO:0467 ! translation related non-coding RNA + +[Term] +id: VariO:0469 +name: large subunit ribosomal RNA +def: "Non-coding RNA that is a constituent of the large ribosomal subunit." [] +synonym: "LSU RNA" EXACT [] +is_a: VariO:0493 ! ribosomal RNA + +[Term] +id: VariO:0470 +name: small subunit ribosomal RNA +def: "Non-coding RNA that is a constituent of the small ribosomal unit." [] +synonym: "SSU RNA" EXACT [] +is_a: VariO:0493 ! ribosomal RNA + +[Term] +id: VariO:0471 +name: intron +synonym: "Intervening region ithat is spliced off during RNA maturation." EXACT [] +is_a: VariO:0467 ! translation related non-coding RNA + +[Term] +id: VariO:0472 +name: self-splicing intron +def: "Intron with an intrinsic splicing activity." [] +is_a: VariO:0471 ! intron + +[Term] +id: VariO:0473 +name: spliceosomal intron +def: "Intron removed by spliceosome." [] +is_a: VariO:0471 ! intron + +[Term] +id: VariO:0474 +name: intron retention +def: "Inclusion intron sequence to mRNA." [] +is_a: VariO:0365 ! effect on cis splicing +property_value: owl:backwardCompatibleWith "targeting RNA" xsd:string + +[Term] +id: VariO:0475 +name: telomerase RNA +def: "Non-coding RNA component of telomerase." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0476 +name: catalytic RNA +def: "RNA with catalytic activity." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0477 +name: regulatory RNA +def: "RNA with regulatory activity." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0478 +name: microRNA +def: "Short non-coding RNA that binds to complementary region in mRNA and silences and regulates gene expression." [] +synonym: "miRNA" EXACT [] +is_a: VariO:0477 ! regulatory RNA + +[Term] +id: VariO:0479 +name: small intervening RNA +def: "Short double-stranded non-coding RNA regulating gene expresion by causing degration of mRNA with complementary sequence." [] +synonym: "siRNA" EXACT [] +is_a: VariO:0477 ! regulatory RNA + +[Term] +id: VariO:0480 +name: piwi-interacting RNA +def: "Non-coding RNA binding to piwi-superfamily Argonaute proteins to silence transposons, repeat-derived transcripts and genetic elements." [] +synonym: "piRNA" EXACT [] +is_a: VariO:0477 ! regulatory RNA + +[Term] +id: VariO:0481 +name: signal recognition particle RNA +def: "Non-coding RNA component of signal recognition particle." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0482 +name: X-chromosome inactivation center RNA +def: "Non-coding RNA component of X-inactivation center." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0483 +name: RNA editing related RNA +def: "Non-coding RNA component of editosome complex." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0484 +name: DNA editing related RNA +def: "Non-coding RNA component of DNA editing complex." [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0485 +name: spliceosomal RNA +synonym: "Non-coding RNA component of spliceosome." EXACT [] +is_a: VariO:0465 ! functional non-coding RNA + +[Term] +id: VariO:0486 +name: location or origin of non-coding RNA +is_a: VariO:0350 ! non-protein coding RNA + +[Term] +id: VariO:0487 +name: nuclear non-coding RNA +def: "Non-coding RNA in nucleus." [] +is_a: VariO:0486 ! location or origin of non-coding RNA + +[Term] +id: VariO:0488 +name: mitochondrial non-coding RNA +def: "Non-coding RNA in mitochondrion." [] +is_a: VariO:0486 ! location or origin of non-coding RNA + +[Term] +id: VariO:0489 +name: chromatin related non-coding RNA +def: "Non-coding RNA related to chromatin." [] +is_a: VariO:0486 ! location or origin of non-coding RNA + +[Term] +id: VariO:0490 +name: centromeric non-coding RNA +def: "Non-coding RNA related to centromere." [] +is_a: VariO:0486 ! location or origin of non-coding RNA + +[Term] +id: VariO:0491 +name: size of non-coding RNA +def: "Classification of non-coding RNA based on the length." [] +is_a: VariO:0350 ! non-protein coding RNA + +[Term] +id: VariO:0492 +name: short non-coding RNA +def: "Non-coding RNA shorter than 200 nucleotides or base pairs." [] +synonym: "small non-coding RNA\nsRNA" EXACT [] +is_a: VariO:0491 ! size of non-coding RNA + +[Term] +id: VariO:0493 +name: ribosomal RNA +def: "Non-coding RNA constituent of ribosome." [] +synonym: "rRNA" EXACT [] +is_a: VariO:0467 ! translation related non-coding RNA + +[Term] +id: VariO:0494 +name: long non-coding RNA +def: "Non-coding RNA longer than 200 nucleotides or base pairs." [] +synonym: "large non-coding RNA\nlncRNA" EXACT [] +is_a: VariO:0491 ! size of non-coding RNA + +[Term] +id: VariO:0495 +name: very long non-coding RNA +def: "Non-coding RNA longer than 10 kb." [] +synonym: "vlnicRNA" EXACT [] +is_a: VariO:0491 ! size of non-coding RNA + +[Term] +id: VariO:0496 +name: exon +def: "Transcript region that is part in mature mRNA." [] +is_a: VariO:0461 ! mRNA + +[Term] +id: VariO:0497 +name: alternatively terminated mRNA +def: "Variation causing alternative mRNA termination." [] +is_a: VariO:0331 ! alternative form of mRNA + +[Term] +id: VariO:0498 +name: effect on RNA modification +def: "Variation affecting post transcriptional RNA modification." [] +is_a: VariO:0354 ! effect on post transcriptional RNA modification + +[Term] +id: VariO:0499 +name: modified mRNA nucleotide +def: "Post transcriptionally modified nucleotide in mRNA." [] +is_a: VariO:0331 ! alternative form of mRNA + +[Term] +id: VariO:0500 +name: effect on RNA pseudoknot +def: "Variation affecting RNA stucture containing at teast two stem loops where part of one stem is intercalated to the other stem." [] +is_a: VariO:0382 ! effect on RNA secondary structure + +[Term] +id: VariO:0501 +name: RNA fragment +def: "RNA produced by degradation of processing of an RNA molecule." [] +is_a: VariO:0486 ! location or origin of non-coding RNA + +[Term] +id: VariO:0502 +name: exon skipping +def: "Variation where an exon is completele cleaved out from a mature transcript." [] +is_a: VariO:0365 ! effect on cis splicing + +[Term] +id: VariO:0503 +name: loss of exon fragment +def: "Transcript from which part of an exon is missing." [] +is_a: VariO:0365 ! effect on cis splicing + +[Term] +id: VariO:0504 +name: inclusion of cryptic exon +def: "Transcript that includes a cryptic exon from the middle of intron." [] +is_a: VariO:0365 ! effect on cis splicing + +[Term] +id: VariO:0505 +name: inclusion of intron fragment +def: "Transcript that contains and additional stretch from intron." [] +is_a: VariO:0365 ! effect on cis splicing + +[Term] +id: VariO:0508 +name: affected splice site +def: "Type of variation affecting splice site." [] +is_a: VariO:0365 ! effect on cis splicing + +[Term] +id: VariO:0509 +name: effect on mode of splicing +def: "Variation affecting the type of RNA splicing." [] +is_a: VariO:0362 ! effect on RNA splicing + +[Term] +id: VariO:0510 +name: effect on co-transcriptional splicing +def: "Variation affecting splicing occurring simultnaeously with transcription." [] +is_a: VariO:0509 ! effect on mode of splicing + +[Term] +id: VariO:0511 +name: effect on non-sequential splicing +def: "Variation affecting splicing that does not occur in sequential order." [] +is_a: VariO:0509 ! effect on mode of splicing + +[Term] +id: VariO:0512 +name: effect on recursive splicing +def: "Variation affecting intron splicing that occurs in several splicing events." [] +is_a: VariO:0509 ! effect on mode of splicing + +[Term] +id: VariO:0513 +name: mutually exclusive exon +def: "Only one of two exons is incluided into mRNA." [] +synonym: "snoRNA" EXACT [] +is_a: VariO:0365 ! effect on cis splicing + +[Typedef] +id: adjacent_to +name: adjacent_to +def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke] + +[Typedef] +id: associated_with +name: associated_with +comment: This relationship is vague and up for discussion. + +[Typedef] +id: complete_evidence_for_feature +name: complete_evidence_for_feature +def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke] +comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. +is_transitive: true + +[Typedef] +id: contains +name: contains +def: "'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'." [PSI-MOD:ref] +comment: The inverse relationship to "part of". +is_transitive: true + +[Typedef] +id: derives_from +name: derives_from +is_transitive: true + +[Typedef] +id: evidence_for_feature +name: evidence_for_feature +def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke] +comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. +is_transitive: true + +[Typedef] +id: genome_of +name: genome_of + +[Typedef] +id: has_functional_parent +name: has functional parent +def: "'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification." [PSI-MOD:ref] +comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent. +is_transitive: true + +[Typedef] +id: has_origin +name: has_origin + +[Typedef] +id: has_part +name: has_part + +[Typedef] +id: has_quality +name: has_quality +comment: The relationship between a feature and an attribute. + +[Typedef] +id: member_of +name: member_of +comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. +is_transitive: true + +[Typedef] +id: negatively_regulates +name: negatively_regulates + +[Typedef] +id: non_functional_homolog_of +name: non_functional_homolog_of +def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] + +[Typedef] +id: part_of +name: part_of +is_transitive: true + +[Typedef] +id: partial_evidence_for_feature +name: partial_evidence_for_feature +def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke] + +[Typedef] +id: position_of +name: position_of + +[Typedef] +id: positively_regulates +name: positively_regulates + +[Typedef] +id: regulates +name: regulates +transitive_over: part_of ! part_of + +[Typedef] +id: sequence_of +name: sequence_of + +[Typedef] +id: variant_of +name: variant_of +def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop] +comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith. + diff --git a/test/helpers/test_access_control_helper.rb b/test/helpers/test_access_control_helper.rb index 1e3807d5..19b0ae0f 100644 --- a/test/helpers/test_access_control_helper.rb +++ b/test/helpers/test_access_control_helper.rb @@ -2,8 +2,8 @@ class TestAccessControlHelper < TestCaseHelpers - def self.before_suite - self.new("before_suite").delete_ontologies_and_submissions + def before_suite + self.backend_4s_delete @@usernames = ["user1", "user2", "user3", "admin"] @@usernames.each do |username| @@ -14,7 +14,7 @@ def self.before_suite ) user.save user.bring_remaining - self.class_variable_set(:"@@#{username}", user) + self.class.class_variable_set(:"@@#{username}", user) end @@admin.role = [LinkedData::Models::Users::Role.find(LinkedData::Models::Users::Role::ADMIN).first] @@ -42,8 +42,9 @@ def self.before_suite LinkedData.settings.enable_security = true end - def self.after_suite - LinkedData.settings.enable_security = @@old_security_setting if class_variable_defined?("@@old_security_setting") + def after_suite + self.backend_4s_delete + LinkedData.settings.enable_security = @@old_security_setting unless @@old_security_setting.nil? end def test_filtered_list diff --git a/test/helpers/test_application_helper.rb b/test/helpers/test_application_helper.rb index b90aa30f..2315a677 100644 --- a/test/helpers/test_application_helper.rb +++ b/test/helpers/test_application_helper.rb @@ -3,7 +3,7 @@ class TestApplicationHelper < TestCaseHelpers - def self.before_suite + def before_suite @@ontologies = LinkedData::SampleData::Ontology.create_ontologies_and_submissions[2] end diff --git a/test/helpers/test_http_cache_helper.rb b/test/helpers/test_http_cache_helper.rb index 5268066a..8a88cc55 100644 --- a/test/helpers/test_http_cache_helper.rb +++ b/test/helpers/test_http_cache_helper.rb @@ -2,9 +2,10 @@ class TestHTTPCacheHelper < TestCaseHelpers - def self.before_suite + def before_suite raise Exception, "Redis is unavailable, caching will not function" if LinkedData::HTTPCache.redis.ping.nil? - ontologies = self.new("before_suite")._ontologies + self.delete_ontologies_and_submissions + ontologies = self._ontologies @@ontology = ontologies.shift @@ontology_alt = ontologies.shift @@ontology.bring_remaining @@ -38,7 +39,7 @@ def self.before_suite LinkedData.settings.enable_http_cache = true end - def self.after_suite + def after_suite LinkedData.settings.enable_http_cache = @orig_enable_cache LinkedData::HTTPCache.invalidate_all end diff --git a/test/helpers/test_slices_helper.rb b/test/helpers/test_slices_helper.rb index bddd5c2d..ae01aae7 100644 --- a/test/helpers/test_slices_helper.rb +++ b/test/helpers/test_slices_helper.rb @@ -2,13 +2,15 @@ class TestSlicesHelper < TestCaseHelpers - def self.before_suite - self.new("before_suite").delete_ontologies_and_submissions + def before_suite + self.backend_4s_delete + LinkedData::Models::Class.indexClear + @@orig_slices_setting = LinkedData.settings.enable_slices LinkedData.settings.enable_slices = true @@onts = LinkedData::SampleData::Ontology.create_ontologies_and_submissions(ont_count: 5, submission_count: 0)[2] @@group_acronym = "test-group" - @@group = _create_group + @@group = self.class._create_group @@onts[0..2].each do |o| o.bring_remaining o.group = [@@group] @@ -30,6 +32,10 @@ def self.before_suite LinkedData::Models::Slice.synchronize_groups_to_slices end + def after_suite + self.backend_4s_delete + end + def test_filtered_list get "http://#{@@group_acronym}.dev/ontologies" assert last_response.ok? diff --git a/test/helpers/test_users_helper.rb b/test/helpers/test_users_helper.rb index 6cd5bd50..9f1614f1 100644 --- a/test/helpers/test_users_helper.rb +++ b/test/helpers/test_users_helper.rb @@ -2,9 +2,10 @@ class TestUsersHelper < TestCaseHelpers - def self.before_suite - @@user = _create_user - @@non_custom_user = _create_user("notcustom") + def before_suite + self.backend_4s_delete + @@user = self.class._create_user + @@non_custom_user = self.class._create_user("notcustom") @@onts = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({ ont_count: 5, @@ -29,7 +30,7 @@ def self.before_suite LinkedData.settings.enable_security = true end - def self.after_suite + def after_suite LinkedData.settings.enable_security = @@old_security_setting end diff --git a/test/middleware/test_rack_attack.rb b/test/middleware/test_rack_attack.rb index 53f5fe3b..92b4d636 100644 --- a/test/middleware/test_rack_attack.rb +++ b/test/middleware/test_rack_attack.rb @@ -6,13 +6,13 @@ class TestRackAttack < TestCase - def self.before_suite + def before_suite # Store app settings @@auth_setting = LinkedData.settings.enable_security @@throttling_setting = LinkedData.settings.enable_throttling @@req_per_sec_limit = LinkedData::OntologiesAPI.settings.req_per_second_per_ip @@safe_ips = LinkedData::OntologiesAPI.settings.safe_ips - + LinkedData.settings.enable_security = true LinkedData::OntologiesAPI.settings.enable_throttling = true LinkedData::OntologiesAPI.settings.req_per_second_per_ip = 1 @@ -29,11 +29,13 @@ def self.before_suite @@admin.save # Redirect output or we get a bunch of noise from Rack (gets reset in the after_suite method). + # Disable output redirect when debugging + $stdout = File.open("/dev/null", "w") $stderr = File.open("/dev/null", "w") - @@port1 = self.new('').unused_port + @@port1 = unused_port # Fork the process to create two servers. This isolates the Rack::Attack configuration, which makes other tests fail if included. @@pid1 = fork do @@ -45,7 +47,7 @@ def self.before_suite Signal.trap("HUP") { Process.exit! } end - @@port2 = self.new('').unused_port + @@port2 = unused_port @@pid2 = fork do require_relative '../../config/rack_attack' Rack::Server.start( @@ -59,21 +61,21 @@ def self.before_suite sleep(5) end - def self.after_suite + def after_suite # Restore app settings LinkedData.settings.enable_security = @@auth_setting LinkedData::OntologiesAPI.settings.enable_throttling = @@throttling_setting LinkedData::OntologiesAPI.settings.req_per_second_per_ip = @@req_per_sec_limit LinkedData::OntologiesAPI.settings.safe_ips = @@safe_ips - - Process.kill("HUP", @@pid1) + + Process.kill("TERM", @@pid1) Process.wait(@@pid1) - Process.kill("HUP", @@pid2) + Process.kill("TERM", @@pid2) Process.wait(@@pid2) - + $stdout = STDOUT $stderr = STDERR - + @@admin.delete @@user.delete @@bp_user.delete @@ -81,7 +83,7 @@ def self.after_suite def test_throttling_limit request_in_threads do - assert_raises(OpenURI::HTTPError) { request() } + assert_raises(OpenURI::HTTPError) { request } end end @@ -90,10 +92,10 @@ def test_throttling_limit def test_throttling_limit_with_forwarding limit = LinkedData::OntologiesAPI.settings.req_per_second_per_ip headers = {"Authorization" => "apikey token=#{@@user.apikey}", "X-Forwarded-For" => "1.2.3.6"} - + exception = assert_raises(OpenURI::HTTPError) do (limit * 5).times do - open("http://127.0.0.1:#{@@port1}/ontologies", headers) + URI.open("http://127.0.0.1:#{@@port1}/ontologies", headers) end end assert_match /429 Too Many Requests/, exception.message @@ -101,7 +103,7 @@ def test_throttling_limit_with_forwarding def test_throttling_admin_override request_in_threads do - assert_raises(OpenURI::HTTPError) { request() } + assert_raises(OpenURI::HTTPError) { request } request(user: @@admin) do |r| assert r.status[0].to_i == 200 @@ -111,14 +113,14 @@ def test_throttling_admin_override def test_two_servers_one_ip request_in_threads do - assert_raises(OpenURI::HTTPError) { request() } + assert_raises(OpenURI::HTTPError) { request } assert_raises(OpenURI::HTTPError) { request(port: @@port2) } end end def test_throttling_ui_override request_in_threads do - assert_raises(OpenURI::HTTPError) { request() } + assert_raises(OpenURI::HTTPError) { request } request(user: @@bp_user) do |r| assert r.status[0].to_i == 200 @@ -133,8 +135,8 @@ def test_throttling_safe_ips_override safe_ips.each do |safe_ip| headers = {"Authorization" => "apikey token=#{@@user.apikey}", "X-Forwarded-For" => "#{safe_ip}"} (limit * 5).times do - response = open("http://127.0.0.1:#{@@port1}/ontologies", headers) - refute_match /429/, response.status.first, "Requests from a safelisted IP address were throttled" + response = URI.open("http://127.0.0.1:#{@@port1}/ontologies", headers) + refute_match /429/, response.status.first, "Requests from a safelisted IP address were throttled" end end end @@ -150,7 +152,7 @@ def request(user: nil, port: nil) # Sometimes a single request can get through without failing depending # on the order of the request as it coincides with the threaded requests. (LinkedData::OntologiesAPI.settings.req_per_second_per_ip * 2).times do - open("http://localhost:#{port}/ontologies", headers) + URI.open("http://127.0.0.1:#{port}/ontologies", headers) end end @@ -162,7 +164,7 @@ def request_in_threads(&block) threads << Thread.new do while true sleep(0.2) - request() rescue next + request rescue next end end end diff --git a/test/solr/configsets/term_search/conf/schema.xml b/test/solr/configsets/term_search/conf/schema.xml index fa95e127..a1a080fd 100644 --- a/test/solr/configsets/term_search/conf/schema.xml +++ b/test/solr/configsets/term_search/conf/schema.xml @@ -169,8 +169,8 @@ - - + + @@ -281,7 +281,7 @@ - + - - - + + + - - - - + + + + - - - - - - - - - - - - + + + + + + + + + + + + - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - + + + + - - - - + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - + + + + - - - - + + + + - - - - + + + + @@ -798,255 +798,255 @@ - - - - - - - - - + + + + + + + + + - - - - - - + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - + + + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - - - - + + + + + + + + + - - - - - - - + + + + + + + - - - - - - - + + + + + + + - - - - - - + + + + + + - - - - - - - - - + + + + + + + + + - - - - - - - + + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - - - - + + + + + + + - - - - - - - - - - + + + + + + + + + + - - - - - - - + + + + + + + - - - - - - + + + + + + - - - - - - - + + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - + + + + + + - - - - - - - + + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - - - - + + + + + + + + + + + - - - - - - + + + + + + - - - - - - - + + + + + + + - - - - - - - + + + + + + + - - - - - + + + + + - - - - - - + + + + + + - + \ No newline at end of file diff --git a/test/solr/generate_ncbo_configsets.sh b/test/solr/generate_ncbo_configsets.sh index 7b4281f7..29134dad 100755 --- a/test/solr/generate_ncbo_configsets.sh +++ b/test/solr/generate_ncbo_configsets.sh @@ -12,7 +12,7 @@ if [[ ! -d ${ld_config}/property_search ]]; then exit 1 fi if [[ ! -d ${configsets}/_default/conf ]]; then - echo 'cant find default solr configset' + echo 'cant find default solr configset' exit 1 fi mkdir -p ${configsets}/property_search/conf diff --git a/test/test_case.rb b/test/test_case.rb index 06bbc99f..e9b8956d 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -20,9 +20,9 @@ require_relative 'test_log_file' require_relative '../app' -require 'minitest/unit' +require 'minitest/autorun' +require 'minitest/hooks/test' require 'webmock/minitest' -MiniTest::Unit.autorun WebMock.allow_net_connect! require 'rack/test' require 'multi_json' @@ -62,7 +62,9 @@ def safe_redis_hosts?(sh) $stdout.flush end -class AppUnit < MiniTest::Unit +class AppUnit < Minitest::Test + include Minitest::Hooks + def count_pattern(pattern) q = "SELECT (count(DISTINCT ?s) as ?c) WHERE { #{pattern} }" rs = Goo.sparql_query_client.query(q) @@ -93,26 +95,34 @@ def backend_4s_delete end end - def before_suites + def before_suite # code to run before the first test (gets inherited in sub-tests) end - def after_suites + def after_suite # code to run after the last test (gets inherited in sub-tests) end - def _run_suites(suites, type) - begin - before_suites - super(suites, type) - ensure - after_suites - end + def before_all + super + backend_4s_delete + before_suite + end + + def after_all + after_suite + super end + + def _run_suite(suite, type) begin backend_4s_delete + LinkedData::Models::Ontology.indexClear + LinkedData::Models::Agent.indexClear + LinkedData::Models::Class.indexClear + LinkedData::Models::OntologyProperty.indexClear suite.before_suite if suite.respond_to?(:before_suite) super(suite, type) rescue Exception => e @@ -127,12 +137,12 @@ def _run_suite(suite, type) end end -AppUnit.runner = AppUnit.new + # All tests should inherit from this class. # Use 'rake test' from the command line to run tests. # See http://www.sinatrarb.com/testing.html for testing information -class TestCase < MiniTest::Unit::TestCase +class TestCase < AppUnit include Rack::Test::Methods @@ -222,6 +232,7 @@ def get_errors(response) end def self.enable_security + @@old_security_setting = LinkedData.settings.enable_security LinkedData.settings.enable_security = true end @@ -243,16 +254,12 @@ def self.reset_to_not_admin(user) end def unused_port - max_retries = 5 - retries = 0 - server_port = Random.rand(55000..65535) - while port_in_use?(server_port) - retries += 1 - break if retries >= max_retries - server_port = Random.rand(55000..65535) - end - server_port + server = TCPServer.new('127.0.0.1', 0) + port = server.addr[1] + server.close + port end + private def port_in_use?(port) server = TCPServer.new(port)