Merge branch 'master' into issue-3480

Author: dosumis

.github/workflows/docs.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout main
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Deploy docs
         uses: mhausenblas/mkdocs-deploy-gh-pages@master

.github/workflows/qc.yml

@@ -23,11 +23,11 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.4
+    container: obolibrary/odkfull:v1.6
     # 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@v3
+      - uses: actions/checkout@v4
 
       - name: Run ontology QC checks
         id: check

.gitignore

@@ -1,19 +1,81 @@
-
-!src/ontology/tmp/README.md
+# ODK-managed rules, do not modify
+# If you need to add your own ignore rules, you may do so below
+# the "End ODK-managed rules" marker at the end of this file.
 .DS_Store
+semantic.cache
+bin/
+
 *.tmp
-*.tmp2
-*.tmp.json
 *.tmp.obo
 *.tmp.owl
+*.tmp.json
+*-relation-graph.tsv.gz
+.template.db
+
+.github/token.txt
+
+/uberon.owl
+/uberon.obo
+/uberon.json
+/uberon.db
+/uberon-base.*
+/uberon-basic.*
+/uberon-full.*
+/uberon-simple.*
+/uberon-simple-non-classified.*
+/mappings/
+/patterns/
+/reports/
+/subsets/
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+!src/ontology/reports/release-diff.md
+src/ontology/uberon.owl
+src/ontology/uberon.obo
+src/ontology/uberon.json
+src/ontology/uberon.db
+src/ontology/uberon-base.*
+src/ontology/uberon-basic.*
+src/ontology/uberon-full.*
+src/ontology/uberon-simple.*
+src/ontology/uberon-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-uberon-edit.owl
+src/ontology/uberon-edit.properties
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/.gitkeep
+!src/ontology/tmp/README.md
+
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
+
+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
+
+# End of ODK-managed rules
+
+*.tmp2
 aminoacid.owl
 basic-allcycles
 basic-orphans
 basic-orphans.tmp
 basic.obo.tmp1
 bfo-check.owl
 bfo-check.txt
-bin/
 bridge-check-caro.owl
 bridge-check-caro.txt
 bridge-check-caro.txt.tmp
@@ -107,38 +169,12 @@ robot_main_diff.md
 seed.obo
 seed.obo.tmp
 seed.owl
-semantic.cache
-src/ontology/dosdp-tools.log
-src/ontology/ed_definitions_merged.owl
 src/ontology/imports/*.obo
 imports/*.obo
 uberon-lastbuild.owl
 uberon-lastbuild.obo
 src/mappings/uberon-local.sssom.tsv
 src/mappings/uberon.sssom.tsv
-src/ontology/imports/*_terms_combined.txt
-src/ontology/merged-uberon-edit.owl
-src/ontology/mirror
-src/ontology/mirror/*
-src/ontology/ontologyterms.txt
-src/ontology/patterns
-src/ontology/reports/*
-src/ontology/seed.txt
-src/ontology/simple_seed.txt
-src/ontology/target/
-src/ontology/tmp/*
-src/ontology/uberon-base.*
-src/ontology/uberon-basic.*
-src/ontology/uberon-full.*
-src/ontology/uberon-simple-non-classified.*
-src/ontology/uberon-simple.*
-src/ontology/uberon.json
-src/ontology/uberon.obo
-src/ontology/uberon.owl
-src/patterns/all_pattern_terms.txt
-src/patterns/data/**/*.ofn
-src/patterns/data/**/*.txt
-src/patterns/pattern_owl_seed.txt
 taxon-constraint-check.txt
 tmp/
 trunk/
@@ -187,7 +223,6 @@ src/ontology/basic.json
 src/ontology/basic.obo
 src/ontology/basic.owl
 src/ontology/test_obo_serialiser.sh
-src/ontology/uberon-edit.properties
 src/ontology/.token
 imports/*
 basic.json

docs/odk-workflows/ManageAutomatedTest.md

@@ -25,4 +25,3 @@ We can define custom checks using [SPARQL](https://www.w3.org/TR/rdf-sparql-quer
 ```shell
 sh run.sh make update_repo
 ```
-

docs/odk-workflows/RepositoryFileStructure.md

@@ -16,21 +16,20 @@ These are the current imports in UBERON
 
 | Import | URL | Type |
 | ------ | --- | ---- |
-| 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/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 |
+| pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | slme |
+| cl | http://purl.obolibrary.org/obo/cl.owl | slme |
+| go | http://purl.obolibrary.org/obo/go/go-base.owl | slme |
+| envo | http://purl.obolibrary.org/obo/envo.owl | slme |
+| ro | http://purl.obolibrary.org/obo/ro.owl | slme |
+| bspo | http://purl.obolibrary.org/obo/bspo.owl | slme |
+| chebi | https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl | slme |
+| pato | http://purl.obolibrary.org/obo/pato.owl | slme |
+| bfo | http://purl.obolibrary.org/obo/bfo.owl | slme |
+| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | slme |
+| ncbitaxondisjoints | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl | slme |
+| nbo | http://purl.obolibrary.org/obo/nbo.owl | slme |
 | orcidio | https://w3id.org/orcidio/orcidio.owl | custom |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
-
 ## 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:
 
@@ -45,6 +44,6 @@ These are the components in UBERON
 | disjoint_union_over.owl | None |
 | mappings.owl | None |
 | in-subset.owl | None |
-| hra_subset.owl | None |
+| hra_subset.owl | https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/UB_ASCTB_subset.owl |
 | vasculature_class.owl | None |
-| hra_depiction_3d_images.owl | None |
+| hra_depiction_3d_images.owl | https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/hra_uberon_3d_images.owl |

docs/odk-workflows/components.md

@@ -14,35 +14,46 @@ components:
     - filename: your-component-name.owl
 ```
 
-3) Add the component to your catalog file (src/ontology/catalog-v001.xml)
+3) Refresh your repo by running `sh run update_repo`. This will automatically (1) create a new file in `src/ontology/components/`, (2) update the `-edit` file so that it imports `http://purl.obolibrary.org/obo/uberon/components/your-component-name.owl` (the IRI of your new component), and (3) update the XML catalog file (`src/ontology/catalog-v001.xml`) to redirect that IRI to the file in the `src/ontology/components` directory, so that the new component can be found by tools such as Protégé or ROBOT, when they load the `-edit` file.
+
+If your component is to be generated by some automated process, add a goal in your custom Makefile (`src/ontology/uberon.Makefile`) and make it perform any task needed to generate the component:
 
 ```
-  <uri name="http://purl.obolibrary.org/obo/uberon/components/your-component-name.owl" uri="components/your-component-name.owl"/>
+$(COMPONENTSDIR)/your-component-name.owl: $(SRC)
+	<Insert here the code to produce the component>
 ```
 
-4) Add the component to the edit file (src/ontology/uberon-edit.obo)
-for .obo formats: 
+If the component is to be generated from a ROBOT template, the ODK can generate the appropriate code for you. For that, when adding the component fo the ODK configuration file (step 2 above), explicitly indicate that the component should be derived from template(s) and list the source templates:
 
 ```
-import: http://purl.obolibrary.org/obo/uberon/components/your-component-name.owl
+components:
+  products:
+    - filename: your-component-name.owl
+      use_template: true
+      templates:
+        - template1.tsv
+        - template2.tsv
 ```
 
-for .owl formats: 
+In this example, the component will be derived from the templates found in `src/templates/template1.tsv` and `src/templates/template2.tsv`. Initial empty templates will automatically be generated when the repository is refreshed (step 3).
+
+Likewise, the ODK can generate the required code for the case where the component is to be derived from SSSOM mappings:
 
 ```
-Import(<http://purl.obolibrary.org/obo/uberon/components/your-component-name.owl>)
+components:
+  products:
+    - filename: your-component-name.owl
+      use_mappings: true
+      mappings:
+        - my-mappings.sssom.tsv
 ```
 
-5) Refresh your repo by running `sh run.sh make update_repo` - this should create a new file in src/ontology/components.
-6) In your custom makefile (src/ontology/uberon.Makefile) add a goal for your custom make file. In this example, the goal is a ROBOT template.
+and for the case where the component is to be fetched from a remote resource:
 
 ```
-$(COMPONENTSDIR)/your-component-name.owl: $(SRC) ../templates/your-component-template.tsv 
-	$(ROBOT) template --template ../templates/your-component-template.tsv \
-  annotate --ontology-iri $(ONTBASE)/$@ --output $(COMPONENTSDIR)/your-component-name.owl
+components:
+  products:
+    - filename: your-component-name.owl
+      source: https://example.org/component-source.owl
 ```
 
-(If using a ROBOT template, do not forget to add your template tsv in src/templates/)
-
-7) Make the file by running `sh run.sh make components/your-component-name.owl`
-