update odk 1.5 (#3242)

Co-authored-by: Anita Caron <anitacaron@users.noreply.github.com>

.github/workflows/qc.yml

@@ -1,4 +1,4 @@
-# This is a basic workflow to help you get started with Actions
+# Basic ODK workflow
 
 name: CI
 
@@ -23,14 +23,11 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4.3
-    permissions:
-      contents: read
-      pull-requests: write
+    container: obolibrary/odkfull:v1.5
     # 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
+      - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
         id: check
@@ -59,7 +56,7 @@ jobs:
           github_token: ${{secrets.GITHUB_TOKEN}}
           file: "../../comment.md"
           identifier: "TAXON_CONSTRAINTS_REASONING"
-
+  
       - name: Last rows of QC report
         if: steps.check.outcome == 'failure'
         run: |

docs/odk-workflows/RepoManagement.md

@@ -2,7 +2,7 @@
 
 ## Updating your ODK repository
 
-Your ODK repositories configuration is managed in `src/ontology/uberon-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
+Your ODK repositories configuration is managed in `src/ontology/uberon-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:
 
 
 ```

docs/odk-workflows/RepositoryFileStructure.md

@@ -18,14 +18,15 @@ These are the current imports in UBERON
 | ------ | --- | ---- |
 | pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | None |
 | cl | http://purl.obolibrary.org/obo/cl.owl | None |
-| go | http://purl.obolibrary.org/obo/go.owl | None |
+| go | http://purl.obolibrary.org/obo/go/go-base.owl | None |
 | envo | http://purl.obolibrary.org/obo/envo.owl | None |
 | ro | http://purl.obolibrary.org/obo/ro.owl | None |
 | bspo | http://purl.obolibrary.org/obo/bspo.owl | None |
 | chebi | https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.owl | None |
 | bfo | http://purl.obolibrary.org/obo/bfo.owl | None |
 | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
+| ncbitaxondisjoints | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl | None |
 | nbo | http://purl.obolibrary.org/obo/nbo.owl | None |
 | orcidio | https://w3id.org/orcidio/orcidio.owl | None |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
@@ -41,6 +42,7 @@ These are the components in UBERON
 
 | Filename | URL |
 | -------- | --- |
+| disjoint_union_over.owl | None |
 | mappings.owl | None |
 | in-subset.owl | None |
 | hra_subset.owl | None |