DO NOT MERGE: 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:v1.2.32
+
+    # 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

@@ -1,8 +1,40 @@
 cache
 *-merged.owl
 *-merged-*.owl
-*-catalog.xml
+.DS_Store
 *.tmp
 *.old
 monarch-merged*
-.DS_Store
+*.tmp
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/mo.owl
+src/ontology/mo.obo
+src/ontology/mo.json
+src/ontology/mo-base.*
+src/ontology/mo-basic.*
+src/ontology/mo-full.*
+src/ontology/mo-simple.*
+src/ontology/mo-simple-non-classified.*
+semantic.cache
+bin/
+src/ontology/seed.txt
+src/ontology/target/
+src/ontology/dosdp-tools.log
+src/patterns/imports/seed_sorted.txt
+src/ontology/ed_definitions_merged.owl
+src/ontology/patterns 
+*.tmp.obo
+*.tmp.owl
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt
+src/ontology/simple_seed.txt
+src/ontology/merged-mo-edit.owl
+/imports/
+reports/
+components/
+/mo-*
+/mo.*
+src/ontology/monarch-pre.owl
+src/ontology/monarch-inferred.owl
+src/ontology/monarch-pre-nothing.owl

.travis.yml

@@ -0,0 +1,27 @@
+## REMEMBER TO SET UP YOUR GITHUB REPO FOR TRAVIS
+## Go to: https://travis-ci.org/monarch-initiative for details
+sudo: required
+
+services:
+  - docker
+
+before_install:
+  - docker pull obolibrary/odkfull
+
+# command to run tests
+script: cd src/ontology && sh run.sh make preprocess_release -B
+
+#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:
+    - obo-ci-reports-all@groups.io

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/mo)
+
+## 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 Monarch Ontology editorial team, Thanks!

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/mo)
+
+## Attribution
+
+If you would like a nanoattribution, please indicate your ORCID id

src/archive/mammal.owl

@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/x-bfo.owl#"
+     xml:base="http://purl.obolibrary.org/obo/x-bfo.owl"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/upheno/mammal.owl">
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/mp/mp-importer.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/hp/hp-importer.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/upheno/hp-mp/mp_hp-align-equiv.owl"/>
+
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/upheno/imports/go_phenotype.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/upheno/imports/mpath_phenotype.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/upheno/imports/nbo_phenotype.owl"/>
+        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/upheno/imports/uberon_phenotype.owl"/>
+
+        <!-- <owl:imports rdf:resource="http://purl.obolibrary.org/obo/mp/mp-to-hp-match-best.owl"/> -->
+    </owl:Ontology>
+
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 0.5.1-SNAPSHOT) http://owlapi.sourceforge.net -->
+

src/archive/project.yaml

@@ -0,0 +1,166 @@
+allow_equivalents: all
+catalog_file: catalog-v001.xml
+components:
+  directory: components/
+  filename: null
+  products:
+  - filename: upheno.owl
+  - filename: mondo.owl
+  - filename: eco.owl
+  - filename: so.owl
+contact: null
+contributors: null
+creators: null
+description: None
+dosdp_tools_options: --obo-prefixes=true
+edit_format: owl
+export_formats:
+- owl
+- obo
+- json
+github_org: monarch-initiative
+gzip_main: false
+id: mo
+import_group:
+  directory: imports/
+  disabled: false
+  ids: null
+  products:
+  - description: null
+    id: nbo
+    mirror_from: http://purl.obolibrary.org/obo/nbo/nbo-base.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: pr
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: go
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: ro
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: chebi
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: hsapdv
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: cl
+    mirror_from: http://purl.obolibrary.org/obo/cl/cl-base.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: mpath
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: ncbitaxon-taxslim.owl
+    mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: go-plus
+    mirror_from: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: so
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: eco
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon-ext
+    mirror_from: http://purl.obolibrary.org/obo/uberon/ext.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon-bridge-to-zfa.owl
+    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon/bridge/uberon-bridge-to-ma.owl
+    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon/bridge/uberon-bridge-to-fma.owl
+    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon/bridge/cl-bridge-to-zfa.owl
+    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon/bridge/cl-bridge-to-ma.owl
+    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon/bridge/cl-bridge-to-fma.owl
+    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: uberon/bridge/uberon-bridge-to-nifstd.owl
+    mirror_from: http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-nifstd.owl
+    rebuild_if_source_changes: true
+    robot_settings: null
+  - description: null
+    id: pato
+    mirror_from: null
+    rebuild_if_source_changes: true
+    robot_settings: null
+  rebuild_if_source_changes: true
+import_pattern_ontology: false
+license: Unspecified
+namespaces:
+- http://purl.obolibrary.org/obo/HP_
+- http://purl.obolibrary.org/obo/hp
+obo_format_options: ''
+pattern_group: null
+pattern_pipelines_group: null
+primary_release: full
+reasoner: ELK
+release_artefacts:
+- base
+- simple-non-classified
+- full
+- simple
+repo: monarch-ontology
+report_fail_on: none
+robot_java_args: -Xmx8G
+robot_settings: null
+robot_version: null
+robotemplate_group: null
+subset_group: null
+title: Monarch Ontology
+travis_emails: null
+uribase: http://purl.obolibrary.org/obo
+use_dosdps: true
+use_external_date: false