diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..6cc718d --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,27 @@ +# Basic ODK workflow +name: Docs + +# Controls when the action will run. +on: + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + push: + branches: + - master + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + build: + name: Deploy docs + runs-on: ubuntu-latest + steps: + - name: Checkout main + uses: actions/checkout@v2 + + - name: Deploy docs + uses: mhausenblas/mkdocs-deploy-gh-pages@master + # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + CONFIG_FILE: mkdocs.yaml + diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml new file mode 100644 index 0000000..21966a7 --- /dev/null +++ b/.github/workflows/qc.yml @@ -0,0 +1,33 @@ +# Basic ODK workflow + +name: CI + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events but only for the master branch + push: + branches: [ master ] + pull_request: + branches: [ master ] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "ontology_qc" + ontology_qc: + # The type of runner that the job will run on + runs-on: ubuntu-latest + container: obolibrary/odkfull:v1.3.0 + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - uses: actions/checkout@v2 + + - name: Run ontology QC checks + env: + DEFAULT_BRANCH: master + run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false + diff --git a/.gitignore b/.gitignore index 9bea433..0fcf6a5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,39 @@ - .DS_Store +semantic.cache +bin/ + +*.tmp +*.tmp.obo +*.tmp.owl +*.tmp.json + +src/ontology/mirror +src/ontology/mirror/* +src/ontology/reports/* +src/ontology/omo.owl +src/ontology/omo.obo +src/ontology/omo.json +src/ontology/omo-base.* +src/ontology/omo-basic.* +src/ontology/omo-full.* +src/ontology/omo-simple.* +src/ontology/omo-simple-non-classified.* + +src/ontology/seed.txt +src/ontology/dosdp-tools.log +src/ontology/ed_definitions_merged.owl +src/ontology/ontologyterms.txt +src/ontology/simple_seed.txt +src/ontology/patterns +src/ontology/merged-omo-edit.owl + +src/ontology/target/ +src/ontology/tmp/* +!src/ontology/tmp/README.md + +src/ontology/imports/*_terms_combined.txt + +src/patterns/data/**/*.ofn +src/patterns/data/**/*.txt +src/patterns/pattern_owl_seed.txt +src/patterns/all_pattern_terms.txt \ No newline at end of file diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..c8d8a85 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,15 @@ +## Before you write a new request, please consider the following: + +- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, either as a primary term or a synonym term. You can search using [OLS](http://www.ebi.ac.uk/ols/ontologies/omo) + +## Guidelines for creating GitHub tickets with contributions to the ontology: + +1. **Write a detailed request:** Please be specific and include as many details as necessary, providing background information, and if possible, suggesting a solution. GOC editors will be better equipped to address your suggestions if you offer details regarding *'what is wrong'*, *'why'*, and *'how to fix it'*. + +2. **Provide examples and references:** Please include PMIDs for new term requests, and include also screenshots, or URLs illustrating the current ontology structure for other types of requests. + +3. **For new term request:** Be sure to provide suggestions for label (name), definition, references, position in hierarchy, etc. + +4. **For updates to relationships:** Provide details of the current axioms, why you think they are wrong or not sufficient, and what exactly should be added or removed. + +On behalf of the OBO Metadata Ontology editorial team, Thanks! \ No newline at end of file diff --git a/docs/cite.md b/docs/cite.md new file mode 100644 index 0000000..218e877 --- /dev/null +++ b/docs/cite.md @@ -0,0 +1 @@ +# How to cite OMO diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 0000000..af02618 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1 @@ +# How to contribute to OMO diff --git a/docs/history.md b/docs/history.md new file mode 100644 index 0000000..4669e26 --- /dev/null +++ b/docs/history.md @@ -0,0 +1,3 @@ +# A brief history of OMO + +The following page gives an overview of the history of OMO. diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..006069e --- /dev/null +++ b/docs/index.md @@ -0,0 +1,7 @@ +# OMO Ontology Documentation + +[//]: # "This file is meant to be edited by the ontology maintainer." + +Welcome to the OMO documentation! + +You can find descriptions of the standard ontology engineering workflows [here](odk-workflows/index.md). diff --git a/docs/odk-workflows/ContinuousIntegration.md b/docs/odk-workflows/ContinuousIntegration.md new file mode 100644 index 0000000..ef5aadd --- /dev/null +++ b/docs/odk-workflows/ContinuousIntegration.md @@ -0,0 +1,15 @@ +# Introduction to Continuous Integration Workflows with ODK + +Historically, most repos have been using Travis CI for continuous integration testing and building, but due to +runtime restrictions, we recently switched a lot of our repos to GitHub actions. You can set up your repo with CI by adding +this to your configuration file (src/ontology/omo-odk.yaml): + +``` +ci: + - github_actions +``` + +When [updateing your repo](RepoManagement.md), you will notice a new file being added: `.github/workflows/qc.yml`. + +This file contains your CI logic, so if you need to change, or add anything, this is the place! + diff --git a/docs/odk-workflows/EditorsWorkflow.md b/docs/odk-workflows/EditorsWorkflow.md new file mode 100644 index 0000000..968a993 --- /dev/null +++ b/docs/odk-workflows/EditorsWorkflow.md @@ -0,0 +1,124 @@ +# Editors Workflow + +The editors workflow is one of the formal [workflows](index.md) to ensure that the ontology is developed correctly according to ontology engineering principles. There are a few different editors workflows: + +1. Local editing workflow: Editing the ontology in your local environment by hand, using tools such as Protégé, ROBOT templates or DOSDP patterns. +2. Completely automated data pipeline (GitHub Actions) +3. DROID workflow + +This document only covers the first editing workflow, but more will be added in the future + +### Local editing workflow + +Workflow requirements: +- git +- github +- docker +- editing tool of choice, e.g. Protégé, your favourite text editor, etc + +#### 1. _Create issue_ +Ensure that there is a ticket on your issue tracker that describes the change you are about to make. While this seems optional, this is a very important part of the social contract of building an ontology - no change to the ontology should be performed without a good ticket, describing the motivation and nature of the intended change. + +#### 2. _Update main branch_ +In your local environment (e.g. your laptop), make sure you are on the `main` (prev. `master`) branch and ensure that you have all the upstream changes, for example: + +``` +git checkout master +git pull +``` + +#### 3. _Create feature branch_ +Create a new branch. Per convention, we try to use meaningful branch names such as: +- issue23removeprocess (where issue 23 is the related issue on GitHub) +- issue26addcontributor +- release20210101 (for releases) + +On your command line, this looks like this: + +``` +git checkout -b issue23removeprocess +``` + +#### 4. _Perform edit_ +Using your editor of choice, perform the intended edit. For example: + +_Protege_ + +1. Open `src/ontology/omo-edit.owl` in Protege +2. Make the change +3. Save the file + +_TextEdit_ + +1. Open `src/ontology/omo-edit.owl` in TextEdit (or Sublime, Atom, Vim, Nano) +2. Make the change +3. Save the file + +Consider the following when making the edit. + +1. According to our development philosophy, the only places that should be manually edited are: + - `src/ontology/omo-edit.owl` + - Any ROBOT templates you chose to use (the TSV files only) + - Any DOSDP data tables you chose to use (the TSV files, and potentially the associated patterns) + - components (anything in `src/ontology/components`), see [here](RepositoryFileStructure.md). +2. Imports should not be edited (any edits will be flushed out with the next update). However, refreshing imports is a potentially breaking change - and is discussed [elsewhere](UpdateImports.md). +3. Changes should usually be small. Adding or changing 1 term is great. Adding or changing 10 related terms is ok. Adding or changing 100 or more terms at once should be considered very carefully. + +#### 4. _Check the Git diff_ +This step is very important. Rather than simply trusting your change had the intended effect, we should always use a git diff as a first pass for sanity checking. + +In our experience, having a visual git client like [GitHub Desktop](https://desktop.github.com/) or [sourcetree](https://www.sourcetreeapp.com/) is really helpful for this part. In case you prefer the command line: + +``` +git status +git diff +``` +#### 5. Quality control +Now its time to run your quality control checks. This can either happen locally ([5a](#Local-testing)) or through your continuous integration system ([7/5b](#continuous-integration-testing)). + +#### 5a. Local testing +If you chose to run your test locally: + +``` +sh run.sh make IMP=false test +``` +This will run the whole set of configured ODK tests on including your change. If you have a complex DOSDP pattern pipeline you may want to add `PAT=false` to skip the potentially lengthy process of rebuilding the patterns. + +``` +sh run.sh make IMP=false PAT=false test +``` + +#### 6. Pull request + +When you are happy with the changes, you commit your changes to your feature branch, push them upstream (to GitHub) and create a pull request. For example: + +``` +git add NAMEOFCHANGEDFILES +git commit -m "Added biological process term #12" +git push -u origin issue23removeprocess +``` + +Then you go to your project on GitHub, and create a new pull request from the branch, for example: https://github.com/INCATools/ontology-development-kit/pulls + +There is a lot of great advise on how to write pull requests, but at the very least you should: +- mention the tickets affected: `see #23` to link to a related ticket, or `fixes #23` if, by merging this pull request, the ticket is fixed. Tickets in the latter case will be closed automatically by Github when the pull request is merged. +- summarise the changes in a few sentences. Consider the reviewer: what would they want to know right away. +- If the diff is large, provide instructions on how to review the pull request best (sometimes, there are many changed files, but only one important change). + +#### 7/5b. Continuous Integration Testing +If you didn't run and local quality control checks (see [5a](#Local-testing)), you should have Continuous Integration (CI) set up, for example: +- Travis +- GitHub Actions + +More on how to set this up [here](ContinuousIntegration.md). Once the pull request is created, the CI will automatically trigger. If all is fine, it will show up green, otherwise red. + +#### 8. Community review +Once all the automatic tests have passed, it is important to put a second set of eyes on the pull request. Ontologies are inherently social - as in that they represent some kind of community consensus on how a domain is organised conceptually. This seems high brow talk, but it is very important that as an ontology editor, you have your work validated by the community you are trying to serve (e.g. your colleagues, other contributors etc). In our experience, it is hard to get more than one review on a pull request - two is great. You can set up GitHub branch protection to actually require a review before a pull request can be merged! We recommend this. + +This step seems daunting to some hopefully under-resourced ontologies, but we recommend to put this high up on your list of priorities - train a colleague, reach out! + +#### 9. Merge and cleanup +When the QC is green and the reviews are in (approvals), it is time to merge the pull request. After the pull request is merged, remember to delete the branch as well (this option will show up as a big button right after you have merged the pull request). If you have not done so, close all the associated tickets fixed by the pull request. + +#### 10. Changelog (Optional) +It is sometimes difficult to keep track of changes made to an ontology. Some ontology teams opt to document changes in a changelog (simply a text file in your repository) so that when release day comes, you know everything you have changed. This is advisable at least for major changes (such as a new release system, a new pattern or template etc). diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md new file mode 100644 index 0000000..9bae85d --- /dev/null +++ b/docs/odk-workflows/ManageDocumentation.md @@ -0,0 +1,45 @@ +# Updating the Documentation + +The documentation for OMO is managed in two places (relative to the repository root): + +1. The `docs` directory contains all the files that pertain to the content of the documentation (more below) +2. the `mkdocs.yaml` file cotains the documentation config, in particular its navigation bar and theme. + +The documentation is hosted using github pages, on a special branch of the repository (called `gh-pages`). It is important that this branch is never deleted - it contains all the files GitHub pages needs to render and deploy the site. It is also important to note that _the gh-pages branch should never be edited manually_. All changes to the docs happen inside the `docs` directory on the `main` branch. + +## Editing the docs + +### Changing content +All the documentation is contained in the `docs` directory, and is managed in _Markdown_. Markdown is a very simple and convenient way to produce text documents with formatting instructions, and is very easy to learn - it is also used, for example, in GitHub issues. This is a normal editing workflow: + +1. Open the `.md` file you want to change in an editor of choice (a simple text editor is often best). _IMPORTANT_: Do not edit any files in the `docs/odk-workflows/` directory. These files are managed by the ODK system and will be overwritten when the repository is upgraded! If you wish to change these files, make an issue on the [ODK issue tracker](https://github.com/INCATools/ontology-development-kit/issues). +2. Perform the edit and save the file +3. Commit the file to a branch, and create a pull request as usual. +4. If your development team likes your changes, merge the docs into master branch. +5. Deploy the documentation (see below) + +## Deploy the documentation + +The documentation is _not_ automatically updated from the Markdown, and needs to be deployed deliberately. To do this, perform the following steps: + +1. In your terminal, navigate to the edit directory of your ontology, e.g.: + ``` + cd omo/src/ontology + ``` +2. Now you are ready to build the docs as follows: + ``` + sh run.sh make update_docs + ``` + [Mkdocs](https://www.mkdocs.org/) now sets off to build the site from the markdown pages. You will be asked to + - Enter your username + - Enter your password (see [here](https://docs.github.com/en/github/authenticating-to-github/creating-a-personal-access-token) for using GitHub access tokens instead) + _IMPORTANT_: Using password based authentication will be deprecated this year (2021). Make sure you read up on [personal access tokens](https://docs.github.com/en/github/authenticating-to-github/creating-a-personal-access-token) if that happens! + + If everything was successful, you will see a message similar to this one: + + ``` + INFO - Your documentation should shortly be available at: https://information-artifact-ontology.github.io/ontology-metadata/ + ``` +3. Just to double check, you can now navigate to your documentation pages (usually https://information-artifact-ontology.github.io/ontology-metadata/). + Just make sure you give GitHub 2-5 minutes to build the pages! + diff --git a/docs/odk-workflows/ReleaseWorkflow.md b/docs/odk-workflows/ReleaseWorkflow.md new file mode 100644 index 0000000..3fb24a5 --- /dev/null +++ b/docs/odk-workflows/ReleaseWorkflow.md @@ -0,0 +1,69 @@ +# The release workflow +The release workflow recommended by the ODK is based on GitHub releases and works as follows: + +1. Run a release with the ODK +2. Review the release +3. Merge to main branch +4. Create a GitHub release + +These steps are outlined in detail in the following. + +## Run a release with the ODK + +Preparation: + +1. Ensure that all your pull requests are merged into your main (master) branch +2. Make sure that all changes to master are committed to Github (`git status` should say that there are no modified files) +3. Locally make sure you have the latest changes from master (`git pull`) +4. Checkout a new branch (e.g. `git checkout -b release-2021-01-01`) +5. You may or may not want to refresh your imports as part of your release strategy (see [here](UpdateImports.md)) +6. Make sure you have the latest ODK installed by running `docker pull obolibrary/odkfull` + +To actually run the release, you: + +1. Open a command line terminal window and navigate to the src/ontology directory (`cd omo/src/ontology`) +2. Run release pipeline:`sh run.sh make prepare_release -B`. Note that for some ontologies, this process can take up to 90 minutes - especially if there are large ontologies you depend on, like PRO or CHEBI. +3. If everything went well, you should see the following output on your machine: `Release files are now in ../.. - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab`. + +This will create all the specified release targets (OBO, OWL, JSON, and the variants, ont-full and ont-base) and copy them into your release directory (the top level of your repo). + +## Review the release + +1. (Optional) Rough check. This step is frequently skipped, but for the more paranoid among us (like the author of this doc), this is a 3 minute additional effort for some peace of mind. Open the main release (omo.owl) in you favourite development environment (i.e. Protege) and eyeball the hierarchy. We recommend two simple checks: + 1. Does the very top level of the hierarchy look ok? This means that all new terms have been imported/updated correctly. + 2. Does at least one change that you know should be in this release appear? For example, a new class. This means that the release was actually based on the recent edit file. +2. Commit your changes to the branch and make a pull request +3. In your GitHub pull request, review the following three files in detail (based on our experience): + 1. `omo.obo` - this reflects a useful subset of the whole ontology (everything that can be covered by OBO format). OBO format has that speaking for it: it is very easy to review! + 2. `omo-base.owl` - this reflects the asserted axioms in your ontology that you have actually edited. + 3. Ideally also take a look at `omo-full.owl`, which may reveal interesting new inferences you did not know about. Note that the diff of this file is sometimes quite large. +4. Like with every pull request, we recommend to always employ a second set of eyes when reviewing a PR! + +## Merge the main branch +Once your [CI checks](ContinuousIntegration.md) have passed, and your reviews are completed, you can now merge the branch into your main branch (don't forget to delete the branch afterwards - a big button will appear after the merge is finished). + +## Create a GitHub release + +1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/information-artifact-ontology/ontology-metadata/releases. Then click "Draft new release" +1. As the tag version you **need to choose the date on which your ontologies were build.** You can find this, for example, by looking at the `omo.obo` file and check the `data-version:` property. The date needs to be prefixed with a `v`, so, for example `v2020-02-06`. +1. You can write whatever you want in the release title, but we typically write the date again. The description underneath should contain a concise list of changes or term additions. +1. Click "Publish release". Done. + +## Debugging typical ontology release problems + +### Problems with memory + +When you are dealing with large ontologies, you need a lot of memory. When you see error messages relating to large ontologies such as CHEBI, PRO, NCBITAXON, or Uberon, you should think of memory first, see [here](https://github.com/INCATools/ontology-development-kit/blob/master/docs/DealWithLargeOntologies.md). + +### Problems when using OBO format based tools + +Sometimes you will get cryptic error messages when using legacy tools using OBO format, such as the ontology release tool (OORT), which is also available as part of the ODK docker container. In these cases, you need to track down what axiom or annotation actually caused the breakdown. In our experience (in about 60% of the cases) the problem lies with duplicate annotations (`def`, `comment`) which are illegal in OBO. Here is an example recipe of how to deal with such a problem: + +1. If you get a message like `make: *** [cl.Makefile:84: oort] Error 255` you might have a OORT error. +2. To debug this, in your terminal enter `sh run.sh make IMP=false PAT=false oort -B` (assuming you are already in the ontology folder in your directory) +3. This should show you where the error is in the log (eg multiple different definitions) +WARNING: THE FIX BELOW IS NOT IDEAL, YOU SHOULD ALWAYS TRY TO FIX UPSTREAM IF POSSIBLE +4. Open `omo-edit.owl` in Protege and find the offending term and delete all offending issue (e.g. delete ALL definition, if the problem was "multiple def tags not allowed") and save. +*While this is not idea, as it will remove all definitions from that term, it will be added back again when the term is fixed in the ontology it was imported from and added back in. +5. Rerun `sh run.sh make IMP=false PAT=false oort -B` and if it all passes, commit your changes to a branch and make a pull request as usual. + diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md new file mode 100644 index 0000000..d9f74a5 --- /dev/null +++ b/docs/odk-workflows/RepoManagement.md @@ -0,0 +1,134 @@ +# Managing your ODK repository + +## Updating your ODK repository + +Your ODK repositories configuration is managed in `src/ontology/omo-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository: + + +``` +sh run.sh make update_repo +``` + +There are a large number of options that can be set to configure your ODK, but we will only discuss a few of them here. + +## Managing imports + +You can use the update repository worflow described on this page to perform the following operations to your imports: + +1. Add a new import +2. Modify an existing import +3. Remove an import you no longer want +4. Customise an import + +We will discuss all these workflows in the following. + + +### Add new import + +To add a new import, you first edit your odk config as described [above](#Updating-your-ODK-repository), adding an `id` to the `product` list in the `import_group` section (for the sake of this example, we assume you already import RO, and your goal is to also import GO): + +``` +import_group: + products: + - id: ro + - id: go +``` + +Note: our ODK file should only have one `import_group` which can contain multiple imports (in the `products` section). Next, you run the [update repo workflow](#Updating-your-ODK-repository) to apply these changes. Note that by default, this module is going to be a SLME Bottom module, see [here](http://robot.obolibrary.org/extract). To change that or customise your module, see section "Customise an import". To finalise the addition of your import, perform the following steps: + +1. Add an imports statement to your `src/ontology/omo-edit.owl` file. We suggest to do this using a text editor, by simply copying an existing imports declaration and renaming it to the new ontology import, for example as follows: + +``` +... +Ontology( +Import() +Import() +... +``` + +2. Add your imports redirect to your catalog file `src/ontology/catalog-v001.xml`, for example: + +``` + +``` + +3. Test whether everything is in order: + 1. [Refresh your import](UpdateImports.md) + 2. Open in your Ontology Editor of choice (Protege) and ensure that the expected terms are imported. + +### Modify an existing import + +If you simply wish to refresh your import in light of new terms, see [here](UpdateImports.md). If you wish to change the type of your module see section "Customise an import". + +### Remove an existing import + +To remove an existing import, perform the following steps: + +1. remove the import declaration from your `src/ontology/omo-edit.owl`. +2. remove the id from your `src/ontology/omo-odk.yaml`, eg. `- id: go` from the list of `products` in the `import_group`. +3. run [update repo workflow](#Updating-your-ODK-repository) +4. delete the associated files manually: + - `src/imports/go_import.owl` + - `src/imports/go_terms.txt` +5. Remove the respective entry from the `src/ontology/catalog-v001.xml` file. + +### Customise an import + +By default, an import module extracted from a source ontology will be a SLME module, see [here](http://robot.obolibrary.org/extract). There are various options to change the default. + +The following change to your repo config (`src/ontology/omo-odk.yaml`) will switch the go import from an SLME module to a simple ROBOT filter module: + +``` +import_group: + products: + - id: ro + - id: go + module_type: filter +``` + +A ROBOT filter module is, essentially, importing all external terms declared by the your ontology (see [here](UpdateImports.md)] on how to declare external terms to be imported). Note that the `filter` module does +not consider terms/annotations from namespaces other than the base-namespace of the ontology itself. For example, in the +example of GO above, only annotations / axioms related to the GO base IRI (http://purl.obolibrary.org/obo/GO_) would be considered. This +behaviour can be changed by adding additional base IRIs as follows: + + +``` +import_group: + products: + - id: go + module_type: filter + base_iris: + - http://purl.obolibrary.org/obo/GO_ + - http://purl.obolibrary.org/obo/CL_ + - http://purl.obolibrary.org/obo/BFO +``` + +If you wish to customise your import entirely, you can specify your own ROBOT command to do so. To do that, add the following to your repo config (`src/ontology/omo-odk.yaml`): + +``` +import_group: + products: + - id: ro + - id: go + module_type: custom +``` + +Now add a new goal in your custom Makefile (`src/ontology/omo.Makefile`, _not_ `src/ontology/Makefile`). + +``` +imports/go_import.owl: mirror/ro.owl imports/ro_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T imports/ro_terms_combined.txt --force true --individuals exclude --method BOT \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \ + annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi +``` + +Now feel free to change this goal to do whatever you wish it to do! It probably makes some sense (albeit not being a strict necessity), to leave most of the goal instead and replace only: + +``` +extract -T imports/ro_terms_combined.txt --force true --individuals exclude --method BOT \ +``` + +to another ROBOT pipeline. + +_Note_: if your mirror is particularly large and complex, read [this ODK recommendation](https://github.com/INCATools/ontology-development-kit/blob/master/docs/DealWithLargeOntologies.md). diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md new file mode 100644 index 0000000..dd06bcc --- /dev/null +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -0,0 +1,27 @@ +# Repository structure + +The main kinds of files in the repository: + +1. Release files +2. Imports +3. [Components](#Components) + +## Release files +Release file are the file that are considered part of the official ontology release and to be used by the community. A detailed descripts of the release artefacts can be found [here](https://github.com/INCATools/ontology-development-kit/blob/master/docs/ReleaseArtefacts.md). + +## Imports +Imports are subsets of external ontologies that contain terms and axioms you would like to re-use in your ontology. These are considered "external", like dependencies in software development, and are not included in your "base" product, which is the [release artefact](https://github.com/INCATools/ontology-development-kit/blob/master/docs/ReleaseArtefacts.md) which contains only those axioms that you personally maintain. + +These are the current imports in OMO + +| Import | URL | Type | +| ------ | --- | ---- | + +## Components +Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: + +1. There is an automated process that generates and re-generates a part of the ontology +2. A part of the ontology is managed in ROBOT templates +3. The expressivity of the component is higher than the format of the edit file. For example, people still choose to manage their ontology in OBO format (they should not) missing out on a lot of owl features. They may chose to manage logic that is beyond OBO in a specific OWL component. + + diff --git a/docs/odk-workflows/SettingUpDockerForODK.md b/docs/odk-workflows/SettingUpDockerForODK.md new file mode 100644 index 0000000..4424354 --- /dev/null +++ b/docs/odk-workflows/SettingUpDockerForODK.md @@ -0,0 +1,13 @@ +# Setting up your Docker environment for ODK use + +One of the most frequent problems with running the ODK for the first time is failure because of lack of memory. This can look like a Java OutOfMemory exception, +but more often than not it will appear as something like an `Error 137`. There are two places you need to consider to set your memory: + +1. Your src/ontology/run.sh (or run.bat) file. You can set the memory in there by adding +`robot_java_args: '-Xmx8G'` to your src/ontology/omo-odk.yaml file, see for example [here](https://github.com/INCATools/ontology-development-kit/blob/0e0aef2b26b8db05f5e78b7c38f807d04312d06a/configs/uberon-odk.yaml#L36). +2. Set your docker memory. By default, it should be about 10-20% more than your `robot_java_args` variable. You can manage your memory settings +by right-clicking on the docker whale in your system bar-->Preferences-->Resources-->Advanced, see picture below. + +![dockermemory](https://github.com/INCATools/ontology-development-kit/raw/master/docs/img/docker_memory.png) + + diff --git a/docs/odk-workflows/UpdateImports.md b/docs/odk-workflows/UpdateImports.md new file mode 100644 index 0000000..12f13ab --- /dev/null +++ b/docs/odk-workflows/UpdateImports.md @@ -0,0 +1,176 @@ +# Update Imports Workflow + +This page discusses how to update the contents of your imports, like adding or removing terms. If you are looking to customise imports, like changing the module type, see [here](RepoManagement.md). + +## Importing a new term + +Note: some ontologies now use a merged-import system to manage dynamic imports, for these please follow instructions in the section title "Using the Base Module approach". + +Importing a new term is split into two sub-phases: + +1. Declaring the terms to be imported +2. Refreshing imports dynamically + +### Declaring terms to be imported +There are three ways to declare terms that are to be imported from an external ontology. Choose the appropriate one for your particular scenario (all three can be used in parallel if need be): + +1. Protege-based declaration +2. Using term files +3. Using the custom import template + +#### Protege-based declaration + +This workflow is to be avoided, but may be appropriate if the editor _does not have access to the ODK docker container_. +This approach also applies to ontologies that use base module import approach. + +1. Open your ontology (edit file) in Protege (5.5+). +1. Select 'owl:Thing' +1. Add a new class as usual. +1. Paste the _full iri_ in the 'Name:' field, for example, http://purl.obolibrary.org/obo/CHEBI_50906. +1. Click 'OK' + +Adding Classes + +Now you can use this term for example to construct logical definitions. The next time the imports are refreshed (see how to refresh [here](#Refresh-imports)), the metadata (labels, definitions, etc) for this term are imported from the respective external source ontology and becomes visible in your ontology. + + +#### Using term files + +Every import has, by default a term file associated with it, which can be found in the imports directory. For example, if you have a GO import in `src/ontology/go_import.owl`, you will also have an associated term file `src/ontology/go_terms.txt`. You can add terms in there simply as a list: + +``` +GO:0008150 +GO:0008151 +``` + +Now you can run the [refresh imports workflow](#Refresh-imports)) and the two terms will be imported. + +#### Using the custom import template + +This workflow is appropriate if: + +1. You prefer to manage all your imported terms in a single file (rather than multiple files like in the "Using term files" workflow above). +2. You wish to augment your imported ontologies with additional information. This requires a cautionary discussion. + +To enable this workflow, you add the following to your ODK config file (`src/ontology/omo-odk.yaml`), and [update the repository](RepoManagement.md): + +``` +use_custom_import_module: TRUE +``` + +Now you can manage your imported terms directly in the custom external terms template, which is located at `src/templates/external_import.owl`. Note that this file is a [ROBOT template](http://robot.obolibrary.org/template), and can, in principle, be extended to include any axioms you like. Before extending the template, however, read the following carefully. + +The main purpose of the custom import template is to enable the management off all terms to be imported in a centralised place. To enable that, you do not have to do anything other than maintaining the template. So if you, say current import `APOLLO_SV:00000480`, and you wish to import `APOLLO_SV:00000532`, you simply add a row like this: + +``` +ID Entity Type +ID TYPE +APOLLO_SV:00000480 owl:Class +APOLLO_SV:00000532 owl:Class +``` + +When the imports are refreshed [see imports refresh workflow](#Refresh-imports), the term(s) will simply be imported from the configured ontologies. + +Now, if you wish to extent the Makefile (which is beyond these instructions) and add, say, synonyms to the imported terms, you can do that, but you need to (a) preserve the `ID` and `ENTITY` columns and (b) ensure that the ROBOT template is valid otherwise, [see here](http://robot.obolibrary.org/template). + +_WARNING_. Note that doing this is a _widespread antipattern_ (see related [issue](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1443)). You should not change the axioms of terms that do not belong into your ontology unless necessary - such changes should always be pushed into the ontology where they belong. However, since people are doing it, whether the OBO Foundry likes it or not, at least using the _custom imports module_ as described here localises the changes to a single simple template and ensures that none of the annotations added this way are merged into the [base file](https://github.com/INCATools/ontology-development-kit/blob/master/docs/ReleaseArtefacts.md#release-artefact-1-base-required). + +### Refresh imports + +If you want to refresh the import yourself (this may be necessary to pass the travis tests), and you have the ODK installed, you can do the following (using go as an example): + +First, you navigate in your terminal to the ontology directory (underneath src in your hpo root directory). +``` +cd src/ontology +``` + +Then, you regenerate the import that will now include any new terms you have added. Note: You must have [docker installed](SettingUpDockerForODK.md). + +``` +sh run.sh make PAT=false imports/go_import.owl -B +``` + +Since ODK 1.2.27, it is also possible to simply run the following, which is the same as the above: + +``` +sh run.sh make refresh-go +``` + +Note that in case you changed the defaults, you need to add `IMP=true` and/or `MIR=true` to the command below: + +``` +sh run.sh make IMP=true MIR=true PAT=false imports/go_import.owl -B +``` + +If you wish to skip refreshing the mirror, i.e. skip downloading the latest version of the source ontology for your import (e.g. `go.owl` for your go import) you can set `MIR=false` instead, which will do the exact same thing as the above, but is easier to remember: + +``` +sh run.sh make IMP=true MIR=false PAT=false imports/go_import.owl -B +``` + +## Using the Base Module approach + +Since ODK 1.2.31, we support an entirely new approach to generate modules: Using base files. +The idea is to only import axioms from ontologies that _actually belong to it_. +A base file is a subset of the ontology that only contains those axioms that nominally +belong there. In other words, the base file does not contain any axioms that belong +to another ontology. An example would be this: + +Imagine this being the full Uberon ontology: + +``` +Axiom 1: BFO:123 SubClassOf BFO:124 +Axiom 1: UBERON:123 SubClassOf BFO:123 +Axiom 1: UBERON:124 SubClassOf UBERON 123 +``` + +The base file is the set of all axioms that are about UBERON terms: + +``` +Axiom 1: UBERON:123 SubClassOf BFO:123 +Axiom 1: UBERON:124 SubClassOf UBERON 123 +``` + +I.e. + +``` +Axiom 1: BFO:123 SubClassOf BFO:124 +``` + +Gets removed. + +The base file pipeline is a bit more complex then the normal pipelines, because +of the logical interactions between the imported ontologies. This is solved by _first +merging all mirrors into one huge file and then extracting one mega module from it. + +Example: Let's say we are importing terms from Uberon, GO and RO in our ontologies. +When we use the base pipelines, we + +1) First obtain the base (ususally by simply downloading it, but there is also an option now to create it with ROBOT) +2) We merge all base files into one big pile +3) Then we extract a single module `imports/merged_import.owl` + +The first implementation of this pipeline is PATO, see https://github.com/pato-ontology/pato/blob/master/src/ontology/pato-odk.yaml. + +To check if your ontology uses this method, check src/ontology/omo-odk.yaml to see if `use_base_merging: TRUE` is declared under `import_group` + +If your ontology uses Base Module approach, please use the following steps: + +First, add the term to be imported to the term file associated with it (see above "Using term files" section if this is not clear to you) + +Next, you navigate in your terminal to the ontology directory (underneath src in your hpo root directory). +``` +cd src/ontology +``` + +Then refresh imports by running + +``` +sh run.sh make imports/merged_import.owl +``` +Note: if your mirrors are updated, you can run `sh run.sh make no-mirror-refresh-merged` + +This requires quite a bit of memory on your local machine, so if you encounter an error, it might be a lack of memory on your computer. A solution would be to create a ticket in an issue tracker requesting for the term to be imported, and your one of the local devs should pick this up and run the import for you. + +Lastly, restart Protege, and the term should be imported in ready to be used. + diff --git a/docs/odk-workflows/index.md b/docs/odk-workflows/index.md new file mode 100644 index 0000000..7fd9471 --- /dev/null +++ b/docs/odk-workflows/index.md @@ -0,0 +1,9 @@ +# Default ODK Workflows + +- [Daily Editors Workflow](EditorsWorkflow.md) +- [Release Workflow](ReleaseWorkflow.md) +- [Manage your ODK Repository](RepoManagement.md) +- [Setting up Docker for ODK](SettingUpDockerForODK.md) +- [Imports management](UpdateImports.md) +- [Managing the documentation](ManageDocumentation.md) + diff --git a/docs/templates/dosdp.md b/docs/templates/dosdp.md new file mode 100644 index 0000000..cb105f0 --- /dev/null +++ b/docs/templates/dosdp.md @@ -0,0 +1,3 @@ +# DOSDP documentation stub + +Do not overwrite, contents will be generated automatically, diff --git a/mkdocs.yaml b/mkdocs.yaml new file mode 100644 index 0000000..86fc9d8 --- /dev/null +++ b/mkdocs.yaml @@ -0,0 +1,19 @@ +site_name: OBO Metadata Ontology +theme: material +nav: + - Getting started: index.md + - Cite: cite.md + - History: history.md + - How-to guides: + - Standard ODK workflows: + - Overview: odk-workflows/index.md + - Editors Workflow: odk-workflows/EditorsWorkflow.md + - Release Workflow: odk-workflows/ReleaseWorkflow.md + - Manage your ODK Repository: odk-workflows/RepoManagement.md + - Setting up Docker for ODK: odk-workflows/SettingUpDockerForODK.md + - Imports management: odk-workflows/UpdateImports.md + - Managing the documentation: odk-workflows/ManageDocumentation.md + - Continuous Integration: odk-workflows/ContinuousIntegration.md + - Your ODK Repository Overview: odk-workflows/RepositoryFileStructure.md + - Contributing: contributing.md + diff --git a/omo-base.json b/omo-base.json new file mode 100644 index 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Overton" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "James Malone" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Jennifer Fostel" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Jie Zheng" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Jonathan Rees" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Larisa Soldatova" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Lawrence Hunter" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Mathias Brochhausen" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Matt Brush" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Melanie Courtot" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Michel Dumontier" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Paolo Ciccarese" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Pat Hayes" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Philippe Rocca-Serra" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Randy Dipert" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Ron Rudnicki" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Satya Sahoo" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Sivaram Arabandi" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Werner Ceusters" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "William Duncan" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "William Hogan" + }, + { + "pred": "http://purl.org/dc/elements/1.1/contributor", + "val": "Yongqun (Oliver) He" + }, + { + "pred": "http://purl.org/dc/elements/1.1/description", + "val": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)." + }, + { + "pred": "http://purl.org/dc/elements/1.1/title", + "val": "OBO Metadata Ontology" + }, + { + "pred": "http://purl.org/dc/elements/1.1/type", + "val": "http://purl.obolibrary.org/obo/IAO_8000001" + }, + { + "pred": "http://purl.org/dc/terms/license", + "val": "https://creativecommons.org/publicdomain/zero/1.0/" + }, + { + "pred": "http://www.w3.org/2002/07/owl#versionInfo", + "val": "2022-04-27" + } + ], + "subsets": [], + "version": "http://purl.obolibrary.org/obo/omo/releases/2022-04-27/omo-base.json", + "xrefs": [] + }, + "nodes": [ + { + "id": "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl": "example to be eventually removed", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "example to be eventually removed" + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000027", + "lbl": "data item", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "data item" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000030", + "lbl": "information content entity", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "information content entity" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000078", + "lbl": "curation status specification", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "curation status specification" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Bill Bug" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "OBI_0000266" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000102", + "lbl": "data about an ontology part", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "data about an ontology part" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "Data about an ontology part is a data item about a part of an ontology, for example a term", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl": "failed exploratory term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "failed exploratory term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000111", + "lbl": "editor preferred term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "editor preferred term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl": "example of usage", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "example of usage" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl": "in branch", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "in branch" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "GROUP:OBI" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "OBI_0000277" + } + ], + "definition": { + "val": "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl": "has curation status", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has curation status" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Bill Bug" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl": "definition", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "definition" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl": "editor note", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "editor note" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl": "term editor", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term editor" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl": "alternative label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "alternative label" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "OBO Operations committee" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "comments": [ + "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." + ], + "definition": { + "val": "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl": "definition source", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "definition source" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl": "metadata complete", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "metadata complete" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl": "organizational term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "organizational term" + } + ], + "definition": { + "val": "Term created to ease viewing/sort terms for development purpose, and will not be included in a release", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl": "ready for release", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ready for release" + } + ], + "definition": { + "val": "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.\"", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl": "metadata incomplete", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "metadata incomplete" + } + ], + "definition": { + "val": "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl": "uncurated", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "uncurated" + } + ], + "definition": { + "val": "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl": "pending final vetting", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "pending final vetting" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000224", + "lbl": "obsolete_core", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000231", + "val": "http://purl.obolibrary.org/obo/IAO_0000226" + } + ], + "definition": { + "val": "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", + "xrefs": [] + }, + "deprecated": true + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl": "obsolescence reason specification", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "obsolescence reason specification" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Melanie Courtot" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl": "placeholder removed", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "placeholder removed" + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl": "terms merged", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "terms merged" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "An editor note should explain what were the merged terms and the reason for the merge." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl": "term imported", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term imported" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl": "term split", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term split" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl": "has obsolescence reason", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has obsolescence reason" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl": "curator note", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "curator note" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ], + "definition": { + "val": "An administrative note of use for a curator but of no use for a user", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl": "term tracker item", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term tracker item" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } + ], + "comments": [ + "The 'tracker item' can associate a tracker with a specific ontology term." + ], + "definition": { + "val": "An IRI or similar locator for a request or discussion of an ontology term.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl": "ontology term requester", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology term requester" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } + ], + "comments": [ + "The 'term requester' can credit the person, organization or project who request the ontology term." + ], + "definition": { + "val": "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl": "denotator type", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "denotator type" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Barry Smith, Werner Ceusters" + } + ], + "definition": { + "val": "A denotator type indicates how a term should be interpreted from an ontological perspective.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl": "universal", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "universal" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl": "is denotator type", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is denotator type" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "Relates an class defined in an ontology, to the type of it's denotator", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl": "imported from", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "imported from" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "For external terms/classes, the ontology from which the term was imported", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl": "defined class", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "defined class" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "\"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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl": "named class expression", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "named class expression" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl": "to be replaced with external ontology term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "to be replaced with external ontology term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "group:OBI" + } + ], + "definition": { + "val": "Terms with this status should eventually replaced with a term from another ontology.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl": "expand expression to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "expand expression to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: 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)\"\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl": "expand assertion to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "expand assertion to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + } + ], + "definition": { + "val": "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl": "first order logic expression", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "first order logic expression" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl": "antisymmetric property", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "antisymmetric property" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "part_of antisymmetric property xsd:true" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "Use boolean value xsd:true to indicate that the property is an antisymmetric property", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl": "requires discussion", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "requires discussion" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "group:OBI" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl": "OBO foundry unique label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "OBO foundry unique label" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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 ." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Bjoern Peters" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBO Foundry " + } + ], + "definition": { + "val": "An alternative name for a class or property which is unique across the OBO Foundry.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl": "has ID digit count", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID digit count" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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)", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl": "has ID range allocated to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID range allocated" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl": "has ID policy for", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID policy for" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "Relating an ontology used to record id policy to the ontology namespace whose policy it manages", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl": "has ID prefix", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID prefix" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl": "elucidation", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "elucidation" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Barry Smith" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "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" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl": "has associated axiom(nl)", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has associated axiom(nl)" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "An axiom associated with a term expressed using natural language" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl": "has associated axiom(fol)", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has associated axiom(fol)" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "An axiom expressed in first order logic using CLIF syntax" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl": "is allocated id range", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is allocated id range" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ], + "comments": [ + "Add as annotation triples in the granting ontology" + ], + "definition": { + "val": "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\"", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl": "has ontology root term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ontology root term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Nicolas Matentzoglu" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl": "may be identical to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "may be identical to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "David Osumi-Sutherland" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "#40" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "VFB" + } + ], + "comments": [ + "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl": "scheduled for obsoletion on or after", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "scheduled for obsoletion on or after" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall, Jie Zheng" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/geneontology/go-ontology/issues/15532" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "GO ontology" + } + ], + "definition": { + "val": "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl": "has axiom label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has axiom id" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "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" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl": "term replaced by", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term replaced by" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + } + ], + "comments": [ + "Add as annotation triples in the granting ontology" + ], + "definition": { + "val": "Use on obsolete terms, relating the term to another term that can be used as a substitute", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl": "ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ontology file" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000232", + "val": "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." + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl": "base ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "base ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/INCATools/ontology-starter-kit/issues/50" + } + ], + "definition": { + "val": "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl": "editors ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "editors ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "source ontology module" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl": "main release ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "main release ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } + ], + "definition": { + "val": "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl": "bridge ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "bridge ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + } + ], + "definition": { + "val": "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000005", + "lbl": "import ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "import ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: add axioms that indicate this is the output of a module extraction process." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "import file" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/extract" + } + ], + "definition": { + "val": "A subset ontology module that is intended to be imported from another ontology.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000006", + "lbl": "subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ontology slim" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "subset ontology" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/filter" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://www.geneontology.org/page/go-slim-and-subset-guide" + } + ], + "definition": { + "val": "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000007", + "lbl": "curation subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "curation subset ontology module" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000008", + "lbl": "analysis subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "analysis ontology module" + } + ], + "definition": { + "val": "An ontology module that is intended for usage in analysis or discovery applications.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000009", + "lbl": "single layer subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "single layer ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ribbon subset" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl": "exclusion subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "exclusion subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "antislim" + } + ], + "definition": { + "val": "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl": "external import ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "external import ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "external import" + } + ], + "definition": { + "val": "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl": "species subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "species subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "taxon subset" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } + ], + "definition": { + "val": "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl": "reasoned ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "reasoned ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/reason" + } + ], + "definition": { + "val": "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl": "generated ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "generated ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } + ], + "definition": { + "val": "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl": "template generated ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "template generated ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/template" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://doi.org/10.1186/s13326-017-0126-0" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/dosumis/dead_simple_owl_design_patterns/" + } + ], + "definition": { + "val": "An ontology module that is automatically generated from a template specification and fillers for slots in that template.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl": "taxonomic bridge ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "taxonomic bridge ontology module" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl": "ontology module subsetted by expressivity", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module subsetted by expressivity" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl": "obo basic subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "obo basic subset ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + } + ], + "definition": { + "val": "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl": "ontology module subsetted by OWL profile", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module subsetted by OWL profile" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl": "EL++ ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "EL++ ontology module" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl": "out of scope", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "http://orcid.org/0000-0001-5208-3432" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "https://orcid.org/0000-0001-5208-3432" + } + ], + "definition": { + "val": "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0001001", + "lbl": "logical characteristic of object property", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "OBO Operations call" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "http://orcid.org/0000-0001-5208-3432" + } + ], + "definition": { + "val": "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl": "defined by construct", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data about an ontology part" xsd:string +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "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." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "denotator type" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "ontology module" xsd:string +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "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." xsd:string + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "base ontology module" xsd:string +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "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." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "editors ontology module" xsd:string +property_value: IAO:0000118 "source ontology module" xsd:string + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "main release ontology module" xsd:string +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "bridge ontology module" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "import ontology module" xsd:string +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "subset ontology module" xsd:string +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "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." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "curation subset ontology module" xsd:string + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "analysis ontology module" xsd:string + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "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." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "single layer ontology module" xsd:string +property_value: IAO:0000118 "ribbon subset" xsd:string + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "exclusion subset ontology module" xsd:string +property_value: IAO:0000118 "antislim" xsd:string + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000111 "external import ontology module" xsd:string +property_value: IAO:0000118 "external import" xsd:string + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "species subset ontology module" xsd:string +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "reasoned ontology module" xsd:string +property_value: seeAlso http://robot.obolibrary.org/reason + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "generated ontology module" xsd:string +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: IAO:0000111 "template generated ontology module" xsd:string +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "obo basic subset ontology module" xsd:string +property_value: seeAlso "6.2" + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +property_value: IAO:0000111 "EL++ ontology module" xsd:string + diff --git a/omo-base.owl b/omo-base.owl new file mode 100644 index 0000000..4f44298 --- /dev/null +++ b/omo-base.owl @@ -0,0 +1,1412 @@ + + + + + en + Adam Goldstein + Alan Ruttenberg + Albert Goldfain + Barry Smith + Bjoern Peters + Carlo Torniai + Chris Mungall + Chris Stoeckert + Christian A. Boelling + Darren Natale + David Osumi-Sutherland + Gwen Frishkoff + Holger Stenzhorn + James A. Overton + James Malone + Jennifer Fostel + Jie Zheng + Jonathan Rees + Larisa Soldatova + Lawrence Hunter + Mathias Brochhausen + Matt Brush + Melanie Courtot + Michel Dumontier + Paolo Ciccarese + Pat Hayes + Philippe Rocca-Serra + Randy Dipert + Ron Rudnicki + Satya Sahoo + Sivaram Arabandi + Werner Ceusters + William Duncan + William Hogan + Yongqun (Oliver) He + An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). + OBO Metadata Ontology + + + 2022-04-27 + + + + + + + + + + + + + + + + + + + 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 label + + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label + + + + + + + + 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 + + + + + + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + + + + + + + + + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + + + + + + + + + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + + + + + + + + + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + + + + + + + + + + + + + + + + + + + + + data item + data item + + + + + + + + + information content entity + information content 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 + + + + + + + + + + + + + + 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 + + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/omo-full.json b/omo-full.json new file mode 100644 index 0000000..e18d81b --- /dev/null +++ b/omo-full.json @@ -0,0 +1,2447 @@ +{ + "graphs": [ + { + "domainRangeAxioms": [], + "edges": [ + { + "obj": "http://purl.obolibrary.org/obo/BFO_0000031", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000030" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000027", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000102" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000030", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000027" + }, + { + "obj": 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(US-English)", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000112", + "lbl": "example of usage", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "example of usage" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl": "in branch", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "in branch" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "GROUP:OBI" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "OBI_0000277" + } + ], + "definition": { + "val": "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl": "has curation status", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has curation status" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Bill Bug" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl": "definition", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "definition" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl": "editor note", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "editor note" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl": "term editor", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term editor" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl": "alternative label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "alternative label" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "OBO Operations committee" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "comments": [ + "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." + ], + "definition": { + "val": "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl": "definition source", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "definition source" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl": "metadata complete", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "metadata complete" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl": "organizational term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "organizational term" + } + ], + "definition": { + "val": "Term created to ease viewing/sort terms for development purpose, and will not be included in a release", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl": "ready for release", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ready for release" + } + ], + "definition": { + "val": "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.\"", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl": "metadata incomplete", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "metadata incomplete" + } + ], + "definition": { + "val": "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl": "uncurated", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "uncurated" + } + ], + "definition": { + "val": "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl": "pending final vetting", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "pending final vetting" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000224", + "lbl": "obsolete_core", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000231", + "val": "http://purl.obolibrary.org/obo/IAO_0000226" + } + ], + "definition": { + "val": "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", + "xrefs": [] + }, + "deprecated": true + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl": "obsolescence reason specification", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "obsolescence reason specification" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Melanie Courtot" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl": "placeholder removed", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "placeholder removed" + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl": "terms merged", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "terms merged" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "An editor note should explain what were the merged terms and the reason for the merge." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl": "term imported", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term imported" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl": "term split", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term split" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl": "has obsolescence reason", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has obsolescence reason" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl": "curator note", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "curator note" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ], + "definition": { + "val": "An administrative note of use for a curator but of no use for a user", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl": "term tracker item", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term tracker item" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } + ], + "comments": [ + "The 'tracker item' can associate a tracker with a specific ontology term." + ], + "definition": { + "val": "An IRI or similar locator for a request or discussion of an ontology term.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl": "ontology term requester", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology term requester" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } + ], + "comments": [ + "The 'term requester' can credit the person, organization or project who request the ontology term." + ], + "definition": { + "val": "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl": "denotator type", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "denotator type" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Barry Smith, Werner Ceusters" + } + ], + "definition": { + "val": "A denotator type indicates how a term should be interpreted from an ontological perspective.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl": "universal", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "universal" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl": "is denotator type", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is denotator type" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "Relates an class defined in an ontology, to the type of it's denotator", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl": "imported from", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "imported from" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "For external terms/classes, the ontology from which the term was imported", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl": "defined class", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "defined class" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "\"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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl": "named class expression", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "named class expression" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl": "to be replaced with external ontology term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "to be replaced with external ontology term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "group:OBI" + } + ], + "definition": { + "val": "Terms with this status should eventually replaced with a term from another ontology.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl": "expand expression to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "expand expression to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: 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)\"\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl": "expand assertion to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "expand assertion to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + } + ], + "definition": { + "val": "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl": "first order logic expression", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "first order logic expression" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl": "antisymmetric property", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "antisymmetric property" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "part_of antisymmetric property xsd:true" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "Use boolean value xsd:true to indicate that the property is an antisymmetric property", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl": "requires discussion", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "requires discussion" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "group:OBI" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl": "OBO foundry unique label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "OBO foundry unique label" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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 ." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Bjoern Peters" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBO Foundry " + } + ], + "definition": { + "val": "An alternative name for a class or property which is unique across the OBO Foundry.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl": "has ID digit count", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID digit count" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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)", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl": "has ID range allocated to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID range allocated" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl": "has ID policy for", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID policy for" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "Relating an ontology used to record id policy to the ontology namespace whose policy it manages", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl": "has ID prefix", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID prefix" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl": "elucidation", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "elucidation" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Barry Smith" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "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" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl": "has associated axiom(nl)", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has associated axiom(nl)" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "An axiom associated with a term expressed using natural language" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl": "has associated axiom(fol)", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has associated axiom(fol)" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "An axiom expressed in first order logic using CLIF syntax" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl": "is allocated id range", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is allocated id range" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ], + "comments": [ + "Add as annotation triples in the granting ontology" + ], + "definition": { + "val": "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\"", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl": "has ontology root term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ontology root term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Nicolas Matentzoglu" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl": "may be identical to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "may be identical to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "David Osumi-Sutherland" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "#40" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "VFB" + } + ], + "comments": [ + "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl": "scheduled for obsoletion on or after", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "scheduled for obsoletion on or after" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall, Jie Zheng" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/geneontology/go-ontology/issues/15532" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "GO ontology" + } + ], + "definition": { + "val": "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl": "has axiom label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has axiom id" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "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" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl": "term replaced by", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term replaced by" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + } + ], + "comments": [ + "Add as annotation triples in the granting ontology" + ], + "definition": { + "val": "Use on obsolete terms, relating the term to another term that can be used as a substitute", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl": "ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ontology file" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000232", + "val": "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." + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl": "base ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "base ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/INCATools/ontology-starter-kit/issues/50" + } + ], + "definition": { + "val": "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl": "editors ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "editors ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "source ontology module" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl": "main release ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "main release ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } + ], + "definition": { + "val": "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl": "bridge ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "bridge ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + } + ], + "definition": { + "val": "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000005", + "lbl": "import ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "import ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: add axioms that indicate this is the output of a module extraction process." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "import file" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/extract" + } + ], + "definition": { + "val": "A subset ontology module that is intended to be imported from another ontology.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000006", + "lbl": "subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ontology slim" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "subset ontology" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/filter" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://www.geneontology.org/page/go-slim-and-subset-guide" + } + ], + "definition": { + "val": "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000007", + "lbl": "curation subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "curation subset ontology module" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000008", + "lbl": "analysis subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "analysis ontology module" + } + ], + "definition": { + "val": "An ontology module that is intended for usage in analysis or discovery applications.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000009", + "lbl": "single layer subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "single layer ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ribbon subset" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl": "exclusion subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "exclusion subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "antislim" + } + ], + "definition": { + "val": "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl": "external import ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "external import ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "external import" + } + ], + "definition": { + "val": "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl": "species subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "species subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "taxon subset" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } + ], + "definition": { + "val": "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl": "reasoned ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "reasoned ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/reason" + } + ], + "definition": { + "val": "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl": "generated ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "generated ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } + ], + "definition": { + "val": "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl": "template generated ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "template generated ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/template" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://doi.org/10.1186/s13326-017-0126-0" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/dosumis/dead_simple_owl_design_patterns/" + } + ], + "definition": { + "val": "An ontology module that is automatically generated from a template specification and fillers for slots in that template.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl": "taxonomic bridge ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "taxonomic bridge ontology module" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl": "ontology module subsetted by expressivity", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module subsetted by expressivity" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl": "obo basic subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "obo basic subset ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + } + ], + "definition": { + "val": "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl": "ontology module subsetted by OWL profile", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module subsetted by OWL profile" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl": "EL++ ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "EL++ ontology module" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl": "out of scope", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "http://orcid.org/0000-0001-5208-3432" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "https://orcid.org/0000-0001-5208-3432" + } + ], + "definition": { + "val": "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0001001", + "lbl": "logical characteristic of object property", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "OBO Operations call" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "http://orcid.org/0000-0001-5208-3432" + } + ], + "definition": { + "val": "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl": "defined by construct", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data about an ontology part" xsd:string +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "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." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "denotator type" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "ontology module" xsd:string +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "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." xsd:string + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "base ontology module" xsd:string +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "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." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "editors ontology module" xsd:string +property_value: IAO:0000118 "source ontology module" xsd:string + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "main release ontology module" xsd:string +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "bridge ontology module" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "import ontology module" xsd:string +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "subset ontology module" xsd:string +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "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." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "curation subset ontology module" xsd:string + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "analysis ontology module" xsd:string + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "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." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "single layer ontology module" xsd:string +property_value: IAO:0000118 "ribbon subset" xsd:string + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "exclusion subset ontology module" xsd:string +property_value: IAO:0000118 "antislim" xsd:string + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000111 "external import ontology module" xsd:string +property_value: IAO:0000118 "external import" xsd:string + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "species subset ontology module" xsd:string +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "reasoned ontology module" xsd:string +property_value: seeAlso http://robot.obolibrary.org/reason + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "generated ontology module" xsd:string +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: IAO:0000111 "template generated ontology module" xsd:string +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "obo basic subset ontology module" xsd:string +property_value: seeAlso "6.2" + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +property_value: IAO:0000111 "EL++ ontology module" xsd:string + diff --git a/omo-full.owl b/omo-full.owl new file mode 100644 index 0000000..acc2abf --- /dev/null +++ b/omo-full.owl @@ -0,0 +1,1411 @@ + + + + + en + Adam Goldstein + Alan Ruttenberg + Albert Goldfain + Barry Smith + Bjoern Peters + Carlo Torniai + Chris Mungall + Chris Stoeckert + Christian A. Boelling + Darren Natale + David Osumi-Sutherland + Gwen Frishkoff + Holger Stenzhorn + James A. Overton + James Malone + Jennifer Fostel + Jie Zheng + Jonathan Rees + Larisa Soldatova + Lawrence Hunter + Mathias Brochhausen + Matt Brush + Melanie Courtot + Michel Dumontier + Paolo Ciccarese + Pat Hayes + Philippe Rocca-Serra + Randy Dipert + Ron Rudnicki + Satya Sahoo + Sivaram Arabandi + Werner Ceusters + William Duncan + William Hogan + Yongqun (Oliver) He + An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). + OBO Metadata Ontology + + 2022-04-27 + + + + + + + + + + + + + + + + + + + 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 label + + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label + + + + + + + + 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 + + + + + + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + + + + + + + + + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + + + + + + + + + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + + + + + + + + + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + + + + + + + + + + + + + + + + + + + + + data item + data item + + + + + + + + + information content entity + information content 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 + + + + + + + + + + + + + + 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 + + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/omo-odk.yaml b/omo-odk.yaml new file mode 100644 index 0000000..a08ddb3 --- /dev/null +++ b/omo-odk.yaml @@ -0,0 +1,30 @@ +id: omo +title: "OBO Metadata Ontology" +github_org: information-artifact-ontology +repo: ontology-metadata +git_main_branch: master +edit_format: owl +export_formats: + - owl + - obo + - json +release_artefacts: + - full + - custom-disease +primary_release: full +documentation: + documentation_system: mkdocs +robot_java_args: '-Xmx12G' +namespaces: + - http://purl.obolibrary.org/obo/OMO_ + - http://purl.obolibrary.org/obo/IAO_ + - http://www.geneontology.org/formats/oboInOwl# +robot_report: + release_reports: False + fail_on : ERROR + use_labels : False + custom_profile : True + report_on : + - omo-full.owl + custom_sparql_exports : + - basic-report \ No newline at end of file diff --git a/omo.json b/omo.json new file mode 100644 index 0000000..a253c03 --- /dev/null +++ b/omo.json @@ -0,0 +1,2447 @@ +{ + "graphs": [ + { + "domainRangeAxioms": [], + "edges": [ + { + "obj": "http://purl.obolibrary.org/obo/BFO_0000031", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000030" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000027", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000102" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000030", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000027" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000002" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000120" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000121" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000123" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000124" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000423" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000078", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000428" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000102", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000078" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000102", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000225" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000102", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_0000409" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000102", + "pred": "is_a", + "sub": "http://purl.obolibrary.org/obo/IAO_8000000" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000225", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000103" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000225", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000226" + }, + { + "obj": "http://purl.obolibrary.org/obo/IAO_0000225", + "pred": "type", + "sub": "http://purl.obolibrary.org/obo/IAO_0000227" + }, + { + "obj": 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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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000113", + "lbl": "in branch", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "in branch" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "GROUP:OBI" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "OBI_0000277" + } + ], + "definition": { + "val": "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000114", + "lbl": "has curation status", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has curation status" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Bill Bug" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl": "definition", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "definition" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl": "editor note", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "editor note" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000117", + "lbl": "term editor", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term editor" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000118", + "lbl": "alternative label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "alternative label" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "OBO Operations committee" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "comments": [ + "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related)." + ], + "definition": { + "val": "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000119", + "lbl": "definition source", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "definition source" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Daniel Schober" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl": "metadata complete", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "metadata complete" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl": "organizational term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "organizational term" + } + ], + "definition": { + "val": "Term created to ease viewing/sort terms for development purpose, and will not be included in a release", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl": "ready for release", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ready for release" + } + ], + "definition": { + "val": "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.\"", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl": "metadata incomplete", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "metadata incomplete" + } + ], + "definition": { + "val": "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl": "uncurated", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "uncurated" + } + ], + "definition": { + "val": "Nothing done yet beyond assigning a unique class ID and proposing a preferred term.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl": "pending final vetting", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "pending final vetting" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000224", + "lbl": "obsolete_core", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000231", + "val": "http://purl.obolibrary.org/obo/IAO_0000226" + } + ], + "definition": { + "val": "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.", + "xrefs": [] + }, + "deprecated": true + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl": "obsolescence reason specification", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "obsolescence reason specification" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON: Melanie Courtot" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl": "placeholder removed", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "placeholder removed" + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl": "terms merged", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "terms merged" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "An editor note should explain what were the merged terms and the reason for the merge." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl": "term imported", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term imported" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl": "term split", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term split" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl": "has obsolescence reason", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has obsolescence reason" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000232", + "lbl": "curator note", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "curator note" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000122" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ], + "definition": { + "val": "An administrative note of use for a curator but of no use for a user", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl": "term tracker item", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term tracker item" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } + ], + "comments": [ + "The 'tracker item' can associate a tracker with a specific ontology term." + ], + "definition": { + "val": "An IRI or similar locator for a request or discussion of an ontology term.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000234", + "lbl": "ontology term requester", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology term requester" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" + } + ], + "comments": [ + "The 'term requester' can credit the person, organization or project who request the ontology term." + ], + "definition": { + "val": "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000409", + "lbl": "denotator type", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "denotator type" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Barry Smith, Werner Ceusters" + } + ], + "definition": { + "val": "A denotator type indicates how a term should be interpreted from an ontological perspective.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl": "universal", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "universal" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" + } + ] + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000411", + "lbl": "is denotator type", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is denotator type" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "Relates an class defined in an ontology, to the type of it's denotator", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000412", + "lbl": "imported from", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "imported from" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBI:" + } + ], + "definition": { + "val": "For external terms/classes, the ontology from which the term was imported", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl": "defined class", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "defined class" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "\"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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl": "named class expression", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "named class expression" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "A named class expression is a logical expression that is given a name. The name can be used in place of the expression.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl": "to be replaced with external ontology term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "to be replaced with external ontology term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "group:OBI" + } + ], + "definition": { + "val": "Terms with this status should eventually replaced with a term from another ontology.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl": "expand expression to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "expand expression to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: 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)\"\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000425", + "lbl": "expand assertion to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "expand assertion to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall" + } + ], + "definition": { + "val": "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000426", + "lbl": "first order logic expression", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "first order logic expression" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000427", + "lbl": "antisymmetric property", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "antisymmetric property" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "part_of antisymmetric property xsd:true" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + } + ], + "definition": { + "val": "Use boolean value xsd:true to indicate that the property is an antisymmetric property", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl": "requires discussion", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "requires discussion" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "group:OBI" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl": "OBO foundry unique label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "OBO foundry unique label" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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 ." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Bjoern Peters" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Chris Mungall" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Melanie Courtot" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "GROUP:OBO Foundry " + } + ], + "definition": { + "val": "An alternative name for a class or property which is unique across the OBO Foundry.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000596", + "lbl": "has ID digit count", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID digit count" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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)", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000597", + "lbl": "has ID range allocated to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID range allocated" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000598", + "lbl": "has ID policy for", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID policy for" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "Relating an ontology used to record id policy to the ontology namespace whose policy it manages", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000599", + "lbl": "has ID prefix", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ID prefix" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000600", + "lbl": "elucidation", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "elucidation" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Barry Smith" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "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" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000601", + "lbl": "has associated axiom(nl)", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has associated axiom(nl)" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "An axiom associated with a term expressed using natural language" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000602", + "lbl": "has associated axiom(fol)", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has associated axiom(fol)" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "An axiom expressed in first order logic using CLIF syntax" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000603", + "lbl": "is allocated id range", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "is allocated id range" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "PERSON:Alan Ruttenberg" + } + ], + "comments": [ + "Add as annotation triples in the granting ontology" + ], + "definition": { + "val": "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\"", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl": "has ontology root term", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has ontology root term" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Nicolas Matentzoglu" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0006011", + "lbl": "may be identical to", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "may be identical to" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "David Osumi-Sutherland" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "#40" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "VFB" + } + ], + "comments": [ + "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0006012", + "lbl": "scheduled for obsoletion on or after", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "scheduled for obsoletion on or after" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Chris Mungall, Jie Zheng" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/geneontology/go-ontology/issues/15532" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "GO ontology" + } + ], + "definition": { + "val": "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0010000", + "lbl": "has axiom label", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "has axiom id" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000600", + "val": "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" + } + ] + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl": "term replaced by", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "term replaced by" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000114", + "val": "http://purl.obolibrary.org/obo/IAO_0000125" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "Person:Alan Ruttenberg" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "Person:Alan Ruttenberg" + } + ], + "comments": [ + "Add as annotation triples in the granting ontology" + ], + "definition": { + "val": "Use on obsolete terms, relating the term to another term that can be used as a substitute", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000000", + "lbl": "ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "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." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ontology file" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000232", + "val": "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." + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000001", + "lbl": "base ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "base ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/INCATools/ontology-starter-kit/issues/50" + } + ], + "definition": { + "val": "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000002", + "lbl": "editors ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "editors ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "source ontology module" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000003", + "lbl": "main release ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "main release ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" + } + ], + "definition": { + "val": "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000004", + "lbl": "bridge ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "bridge ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" + } + ], + "definition": { + "val": "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000005", + "lbl": "import ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "import ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: add axioms that indicate this is the output of a module extraction process." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "import file" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/extract" + } + ], + "definition": { + "val": "A subset ontology module that is intended to be imported from another ontology.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000006", + "lbl": "subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ontology slim" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "subset ontology" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/filter" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://www.geneontology.org/page/go-slim-and-subset-guide" + } + ], + "definition": { + "val": "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000007", + "lbl": "curation subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "curation subset ontology module" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000008", + "lbl": "analysis subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "analysis ontology module" + } + ], + "definition": { + "val": "An ontology module that is intended for usage in analysis or discovery applications.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000009", + "lbl": "single layer subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "single layer ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "ribbon subset" + } + ], + "definition": { + "val": "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.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000010", + "lbl": "exclusion subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "exclusion subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "antislim" + } + ], + "definition": { + "val": "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000011", + "lbl": "external import ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "external import ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "external import" + } + ], + "definition": { + "val": "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000012", + "lbl": "species subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "species subset ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000118", + "val": "taxon subset" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } + ], + "definition": { + "val": "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000013", + "lbl": "reasoned ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "reasoned ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/reason" + } + ], + "definition": { + "val": "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000014", + "lbl": "generated ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "generated ontology module" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" + } + ], + "definition": { + "val": "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000015", + "lbl": "template generated ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "template generated ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://robot.obolibrary.org/template" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://doi.org/10.1186/s13326-017-0126-0" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "https://github.com/dosumis/dead_simple_owl_design_patterns/" + } + ], + "definition": { + "val": "An ontology module that is automatically generated from a template specification and fillers for slots in that template.", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000016", + "lbl": "taxonomic bridge ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "taxonomic bridge ontology module" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000017", + "lbl": "ontology module subsetted by expressivity", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module subsetted by expressivity" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000018", + "lbl": "obo basic subset ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "obo basic subset ontology module" + }, + { + "pred": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val": "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" + } + ], + "definition": { + "val": "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports", + "xrefs": [] + } + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000019", + "lbl": "ontology module subsetted by OWL profile", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "ontology module subsetted by OWL profile" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/IAO_8000020", + "lbl": "EL++ ontology module", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000111", + "val": "EL++ ontology module" + } + ] + }, + "type": "CLASS" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl": "out of scope", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000116", + "val": "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000117", + "val": "http://orcid.org/0000-0001-5208-3432" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000233", + "val": "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" + }, + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000234", + "val": "https://orcid.org/0000-0001-5208-3432" + } + ], + "definition": { + "val": "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.", + "xrefs": [] + } + }, + "type": "INDIVIDUAL" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0001001", + "lbl": "logical characteristic of object property", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000119", + "val": "OBO Operations call" + }, + { + "pred": "http://www.geneontology.org/formats/oboInOwl#created_by", + "val": "http://orcid.org/0000-0001-5208-3432" + } + ], + "definition": { + "val": "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.", + "xrefs": [] + } + }, + "type": "PROPERTY" + }, + { + "id": "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl": "defined by construct", + "meta": { + "basicPropertyValues": [ + { + "pred": "http://purl.obolibrary.org/obo/IAO_0000112", + "val": "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000111 "data about an ontology part" xsd:string +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "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." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "denotator type" xsd:string +property_value: IAO:0000112 "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." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: IAO:8000000 +name: ontology module +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "ontology module" xsd:string +property_value: IAO:0000116 "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." xsd:string +property_value: IAO:0000118 "ontology file" xsd:string +property_value: IAO:0000232 "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." xsd:string + +[Term] +id: IAO:8000001 +name: base ontology module +def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "base ontology module" xsd:string +property_value: seeAlso https://github.com/INCATools/ontology-starter-kit/issues/50 + +[Term] +id: IAO:8000002 +name: editors ontology module +def: "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." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "editors ontology module" xsd:string +property_value: IAO:0000118 "source ontology module" xsd:string + +[Term] +id: IAO:8000003 +name: main release ontology module +def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "main release ontology module" xsd:string +property_value: IAO:0000116 "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" xsd:string + +[Term] +id: IAO:8000004 +name: bridge ontology module +def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "bridge ontology module" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies + +[Term] +id: IAO:8000005 +name: import ontology module +def: "A subset ontology module that is intended to be imported from another ontology." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "import ontology module" xsd:string +property_value: IAO:0000116 "TODO: add axioms that indicate this is the output of a module extraction process." xsd:string +property_value: IAO:0000118 "import file" xsd:string +property_value: seeAlso http://robot.obolibrary.org/extract + +[Term] +id: IAO:8000006 +name: subset ontology module +def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "subset ontology module" xsd:string +property_value: IAO:0000118 "ontology slim" xsd:string +property_value: IAO:0000118 "subset ontology" xsd:string +property_value: seeAlso http://robot.obolibrary.org/filter +property_value: seeAlso http://www.geneontology.org/page/go-slim-and-subset-guide + +[Term] +id: IAO:8000007 +name: curation subset ontology module +def: "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." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "curation subset ontology module" xsd:string + +[Term] +id: IAO:8000008 +name: analysis subset ontology module +def: "An ontology module that is intended for usage in analysis or discovery applications." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "analysis ontology module" xsd:string + +[Term] +id: IAO:8000009 +name: single layer subset ontology module +def: "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." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "single layer ontology module" xsd:string +property_value: IAO:0000118 "ribbon subset" xsd:string + +[Term] +id: IAO:8000010 +name: exclusion subset ontology module +def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "exclusion subset ontology module" xsd:string +property_value: IAO:0000118 "antislim" xsd:string + +[Term] +id: IAO:8000011 +name: external import ontology module +def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] +is_a: IAO:8000005 ! import ontology module +property_value: IAO:0000111 "external import ontology module" xsd:string +property_value: IAO:0000118 "external import" xsd:string + +[Term] +id: IAO:8000012 +name: species subset ontology module +def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "species subset ontology module" xsd:string +property_value: IAO:0000118 "taxon subset" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints + +[Term] +id: IAO:8000013 +name: reasoned ontology module +def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "reasoned ontology module" xsd:string +property_value: seeAlso http://robot.obolibrary.org/reason + +[Term] +id: IAO:8000014 +name: generated ontology module +def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] +is_a: IAO:8000000 ! ontology module +property_value: IAO:0000111 "generated ontology module" xsd:string +property_value: IAO:0000116 "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" xsd:string + +[Term] +id: IAO:8000015 +name: template generated ontology module +def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] +is_a: IAO:8000014 ! generated ontology module +property_value: IAO:0000111 "template generated ontology module" xsd:string +property_value: seeAlso http://robot.obolibrary.org/template +property_value: seeAlso https://doi.org/10.1186/s13326-017-0126-0 +property_value: seeAlso https://github.com/dosumis/dead_simple_owl_design_patterns/ + +[Term] +id: IAO:8000016 +name: taxonomic bridge ontology module +is_a: IAO:8000004 ! bridge ontology module +property_value: IAO:0000111 "taxonomic bridge ontology module" xsd:string + +[Term] +id: IAO:8000017 +name: ontology module subsetted by expressivity +is_a: IAO:8000006 ! subset ontology module +property_value: IAO:0000111 "ontology module subsetted by expressivity" xsd:string + +[Term] +id: IAO:8000018 +name: obo basic subset ontology module +def: "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.\n\nExamples 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).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "obo basic subset ontology module" xsd:string +property_value: seeAlso "6.2" + +[Term] +id: IAO:8000019 +name: ontology module subsetted by OWL profile +is_a: IAO:8000017 ! ontology module subsetted by expressivity +property_value: IAO:0000111 "ontology module subsetted by OWL profile" xsd:string + +[Term] +id: IAO:8000020 +name: EL++ ontology module +is_a: IAO:8000019 ! ontology module subsetted by OWL profile +property_value: IAO:0000111 "EL++ ontology module" xsd:string + diff --git a/omo.owl b/omo.owl index e2c1a1f..7975653 100644 --- a/omo.owl +++ b/omo.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Adam Goldstein Alan Ruttenberg @@ -52,6 +52,7 @@ An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). OBO Metadata Ontology + 2022-04-27 @@ -186,12 +187,14 @@ We also have the outstanding issue of how to aim different definitions to differ - alternative term + alternative label - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. + OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - alternative term + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label @@ -337,6 +340,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property + @@ -538,6 +542,47 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. + OBO Operations call + + logical characteristic of object property + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + + defined by construct + + + + @@ -646,6 +691,58 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + An alternative label for a class or property which has a more general meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + has broad synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/18 + + + + + + + + + An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + has exact synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/20 + + + + + + + + + An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + has narrow synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/19 + + + + + + + + + An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + has related synonym + https://github.com/information-artifact-ontology/ontology-metadata/issues/21 + + + + + + + + + The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. + This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + + https://github.com/information-artifact-ontology/ontology-metadata/issues/77 + https://orcid.org/0000-0001-5208-3432 + out of scope + + + +