Merge pull request #155 from matentzn/odk20210217

Do not merge: Migration to ODK

We have resolved all remaining issues, answered final questions, and performed a final review. Therefore @matentzn @dillerm James Overton and I are all in agreement that it's ready to go.

.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:v1.2.26
+
+    # 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
+

.gitignore

@@ -1,7 +1,45 @@
-catalog-*.xml
 .DS_Store
-omrse/catalog*.xml
-omrse/language/catalog*.xml
-*~
-*.odba
+semantic.cache
+bin/
 
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/omrse.owl
+src/ontology/omrse.obo
+src/ontology/omrse.json
+src/ontology/omrse-base.*
+src/ontology/omrse-basic.*
+src/ontology/omrse-full.*
+src/ontology/omrse-simple.*
+src/ontology/omrse-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-omrse-edit.owl
+src/ontology/reports
+reports/
+
+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
+src/scripts/pull_changes_from_master.sh
+src/_patterns
+src/_sparql
+.cogs
+pull-request.md

.travis.yml

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+## REMEMBER TO SET UP YOUR GIT REPO FOR TRAVIS
+## Go to: https://travis-ci.org/matentzn for details
+sudo: required
+
+services:
+  - docker
+
+before_install:
+  - docker pull obolibrary/odkfull
+
+# command to run tests
+script: cd src/ontology && sh run.sh make test
+
+#after_success:
+#  coveralls
+
+# whitelist
+branches:
+  only:
+    - master
+    - test-travis
+
+### Add your own lists here
+### See https://github.com/INCATools/ontology-development-kit/issues/35
+notifications:
+  email:
+    - [email protected]

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/omrse)
+
+## 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 The Ontology of Medically Related Social Entities editorial team, Thanks!