rsc-ontologies#40 add files and folders seeded with ODK

NFDI4Chem · Apr 6, 2022 · eceb642 · eceb642
1 parent 9c0e070
commit eceb642
Show file tree

Hide file tree

Showing 48 changed files with 13,530 additions and 0 deletions.
diff --git a/rxno_odk/.github/workflows/diff.yml b/rxno_odk/.github/workflows/diff.yml
@@ -0,0 +1,117 @@
+name: 'Create ROBOT diffs on Pull requests'
+
+on:
+  # Triggers the workflow on pull request events for the master branch
+  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:
+  edit_file:
+    runs-on: ubuntu-latest
+    container: obolibrary/odklite:v1.3.0
+    steps:
+      - uses: actions/checkout@v2
+      # Checks-out main branch under "main" directory
+      - uses: actions/checkout@v2
+        with:
+          ref: master
+          path: master
+      - name: Diff classification
+        run: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/rxno-edit.owl --left-catalog master/src/ontology/catalog-v001.xml --right src/ontology/rxno-edit.owl --right-catalog src/ontology/catalog-v001.xml -f markdown -o edit-diff.md
+      - name: Upload diff
+        uses: actions/upload-artifact@v2
+        with:
+          name: edit-diff.md
+          path: edit-diff.md
+  classify_branch:
+    runs-on: ubuntu-latest
+    container: obolibrary/odklite:v1.3.0
+    steps:
+      - uses: actions/checkout@v2
+      - name: Classify ontology
+        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE rxno.owl
+      - name: Upload PR rxno.owl
+        uses: actions/upload-artifact@v2
+        with:
+          name: rxno-pr.owl
+          path: src/ontology/rxno.owl
+          retention-days: 1
+  classify_main:
+    runs-on: ubuntu-latest
+    container: obolibrary/odklite:v1.3.0
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          ref: master
+      - name: Classify ontology
+        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE rxno.owl
+      - name: Upload master rxno.owl
+        uses: actions/upload-artifact@v2
+        with:
+          name: rxno-master.owl
+          path: src/ontology/rxno.owl
+          retention-days: 1
+  diff_classification:
+    needs:
+      - classify_branch
+      - classify_main
+    runs-on: ubuntu-latest
+    container: obolibrary/odklite:v1.3.0
+    steps:
+      - uses: actions/checkout@v2
+      - name: Download master classification
+        uses: actions/download-artifact@v2
+        with:
+          name: rxno-master.owl
+          path: src/ontology/rxno-master.owl
+      - name: Download PR classification
+        uses: actions/download-artifact@v2
+        with:
+          name: rxno-pr.owl
+          path: src/ontology/rxno-pr.owl
+      - name: Diff classification
+        run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left rxno-master.owl/rxno.owl --left-catalog catalog-v001.xml --right rxno-pr.owl/rxno.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
+      - name: Upload diff
+        uses: actions/upload-artifact@v2
+        with:
+          name: classification-diff.md
+          path: src/ontology/classification-diff.md
+  post_comment:
+    needs: [diff_classification, edit_file]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Download reasoned diff
+        uses: actions/download-artifact@v2
+        with:
+          name: classification-diff.md
+          path: classification-diff.md
+      - name: Prepare reasoned comment
+        run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology: </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md"
+      - name: Post reasoned comment
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: NejcZdovc/[email protected]
+        with:
+          file: "../../comment.md"
+          identifier: "REASONED"
+      - uses: actions/checkout@v2
+      - name: Download edit diff
+        uses: actions/download-artifact@v2
+        with:
+          name: edit-diff.md
+          path: edit-diff.md
+      - name: Prepare edit file comment
+        run: "echo \"<details>\n <summary> Here's a diff of your edit file (unreasoned) </summary> \n\" >edit-comment.md; cat edit-diff.md/edit-diff.md >>edit-comment.md"
+      - name: Post comment
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: NejcZdovc/[email protected]
+        with:
+          file: "../../edit-comment.md"
+          identifier: "UNREASONED"
+
diff --git a/rxno_odk/.github/workflows/qc.yml b/rxno_odk/.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 main branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  # 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: main
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+
diff --git a/rxno_odk/.gitignore b/rxno_odk/.gitignore
@@ -0,0 +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/rxno.owl
+src/ontology/rxno.obo
+src/ontology/rxno.json
+src/ontology/rxno-base.*
+src/ontology/rxno-basic.*
+src/ontology/rxno-full.*
+src/ontology/rxno-simple.*
+src/ontology/rxno-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-rxno-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
diff --git a/rxno_odk/CONTRIBUTING.md b/rxno_odk/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/rxno)
+
+## 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 Named Reaction Ontology editorial team, Thanks!
diff --git a/rxno_odk/README.md b/rxno_odk/README.md
@@ -0,0 +1,29 @@
+
+![Build Status](https://github.com/rsc-ontologies/rxno/workflows/CI/badge.svg)
+# Named Reaction Ontology
+
+Description: None
+
+More information can be found at http://obofoundry.org/ontology/rxno
+
+## Versions
+
+### Stable release versions
+
+The latest version of the ontology can always be found at:
+
+http://purl.obolibrary.org/obo/rxno.owl
+
+(note this will not show up until the request has been approved by obofoundry.org)
+
+### Editors' version
+
+Editors of this ontology should use the edit version, [src/ontology/rxno-edit.owl](src/ontology/rxno-edit.owl)
+
+## Contact
+
+Please use this GitHub repository's [Issue tracker](https://github.com/rsc-ontologies/rxno/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
+
+## Acknowledgements
+
+This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).
diff --git a/rxno_odk/issue_template.md b/rxno_odk/issue_template.md
@@ -0,0 +1,21 @@
+For new term requests, please provide the following information:
+
+## Preferred term label
+
+(e.g., Asplenia)
+
+## Synonyms
+
+(e.g., Absent spleen)
+
+## Textual definition
+
+the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term.
+
+## Suggested parent term
+
+Please look in the hierarchy in a browser such as [OLS](http://www.ebi.ac.uk/ols/ontologies/rxno)
+
+## Attribution
+
+If you would like a nanoattribution, please indicate your ORCID id
diff --git a/rxno_odk/src/metadata/README.md b/rxno_odk/src/metadata/README.md
@@ -0,0 +1,24 @@
+Metadata files for the OBO Library
+
+ * [rxno.yml](rxno.yml)
+     * Determines how your purl.obolibrary.org/obo/rxno/ redirects will be handled
+     * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config
+     * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config)
+     * Paste in the contents of [rxno.yml](rxno.yml)
+     * Click "Commit new file"
+     * IMPORTANT: remember to make a pull request
+     * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
+ * [rxno.md](rxno.md)
+     * Determines how your metadata is shown on OBO Library, OLS and AberOWL
+     * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology
+     * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology)
+     * Paste in the contents of [rxno.md](rxno.md)
+     * Click "Commit new file"
+     * IMPORTANT: remember to make a pull request
+     * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
+
+For more background see:
+
+ * http://obofoundry.org/
+ * http://obofoundry.org/faq/how-do-i-edit-metadata.html
+
diff --git a/rxno_odk/src/metadata/rxno.md b/rxno_odk/src/metadata/rxno.md
@@ -0,0 +1,48 @@
+---
+layout: ontology_detail
+id: rxno
+title: Named Reaction Ontology
+jobs:
+  - id: https://travis-ci.org/rsc-ontologies/rxno
+    type: travis-ci
+build:
+  checkout: git clone https://github.com/rsc-ontologies/rxno.git
+  system: git
+  path: "."
+contact:
+  email: 
+  label: 
+  github: 
+description: Named Reaction Ontology is an ontology...
+domain: stuff
+homepage: https://github.com/rsc-ontologies/rxno
+products:
+  - id: rxno.owl
+    name: "Named Reaction Ontology main release in OWL format"
+  - id: rxno.obo
+    name: "Named Reaction Ontology additional release in OBO format"
+  - id: rxno.json
+    name: "Named Reaction Ontology additional release in OBOJSon format"
+  - id: rxno/rxno-base.owl
+    name: "Named Reaction Ontology main release in OWL format"
+  - id: rxno/rxno-base.obo
+    name: "Named Reaction Ontology additional release in OBO format"
+  - id: rxno/rxno-base.json
+    name: "Named Reaction Ontology additional release in OBOJSon format"
+dependencies:
+- id: ro
+- id: mop
+- id: bfo
+- id: obi
+- id: omo
+
+tracker: https://github.com/rsc-ontologies/rxno/issues
+license:
+  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
+activity_status: active
+---
+
+Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML.
+You can also embed images too.
+
diff --git a/rxno_odk/src/metadata/rxno.yml b/rxno_odk/src/metadata/rxno.yml
@@ -0,0 +1,27 @@
+# PURL configuration for http://purl.obolibrary.org/obo/rxno
+
+idspace: RXNO
+base_url: /obo/rxno
+
+products:
+- rxno.owl: https://raw.githubusercontent.com/rsc-ontologies/rxno/main/rxno.owl
+- rxno.obo: https://raw.githubusercontent.com/rsc-ontologies/rxno/main/rxno.obo
+
+term_browser: ontobee
+example_terms:
+- RXNO_0000000
+
+entries:
+
+- prefix: /releases/
+  replacement: https://raw.githubusercontent.com/rsc-ontologies/rxno/v
+
+- prefix: /tracker/
+  replacement: https://github.com/rsc-ontologies/rxno/issues
+
+- prefix: /about/
+  replacement: http://www.ontobee.org/ontology/RXNO?iri=http://purl.obolibrary.org/obo/
+
+## generic fall-through, serve direct from github by default
+- prefix: /
+  replacement: https://raw.githubusercontent.com/rsc-ontologies/rxno/main/