Merge branch 'master' into Obsolete-neuronal-brush-cell

.github/workflows/diff.yml

@@ -53,7 +53,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -87,7 +87,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -103,19 +103,19 @@ jobs:
           ref: ${{ steps.comment-branch.outputs.head_ref }}
       - name: Classify ontology
         if: steps.check.outputs.triggered == 'true'
-        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-simple.owl
-      - name: Upload PR cl-simple.owl
+        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-base.owl
+      - name: Upload PR cl-base.owl
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4
         with:
-          name: cl-simple-pr.owl
-          path: src/ontology/cl-simple.owl
+          name: cl-base-pr.owl
+          path: src/ontology/cl-base.owl
           retention-days: 1
   classify_main:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -129,18 +129,18 @@ jobs:
           ref: master
       - name: Classify ontology
         if: steps.check.outputs.triggered == 'true'
-        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-simple.owl
-      - name: Upload master cl-simple.owl
+        run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-base.owl
+      - name: Upload master cl-base.owl
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4
         with:
-          name: cl-simple-master.owl
-          path: src/ontology/cl-simple.owl
+          name: cl-base-master.owl
+          path: src/ontology/cl-base.owl
           retention-days: 1
   diff_classification:
     needs:  [classify_branch, classify_main]
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.3
     steps:
       - uses: khan/[email protected]
         id: check
@@ -154,17 +154,17 @@ jobs:
         if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v4
         with:
-          name: cl-simple-master.owl
-          path: src/ontology/cl-simple-master.owl
+          name: cl-base-master.owl
+          path: src/ontology/cl-base-master.owl
       - name: Download PR classification
         if: steps.check.outputs.triggered == 'true'
         uses: actions/download-artifact@v4
         with:
-          name: cl-simple-pr.owl
-          path: src/ontology/cl-simple-pr.owl
+          name: cl-base-pr.owl
+          path: src/ontology/cl-base-pr.owl
       - name: Diff classification
         if: steps.check.outputs.triggered == 'true'
-        run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left cl-simple-master.owl/cl-simple.owl --left-catalog catalog-v001.xml --right cl-simple-pr.owl/cl-simple.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
+        run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left cl-base-master.owl/cl-base.owl --left-catalog catalog-v001.xml --right cl-base-pr.owl/cl-base.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
       - name: Upload diff
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4
@@ -191,7 +191,7 @@ jobs:
           path: classification-diff.md
       - name: Prepare reasoned comment
         if: steps.check.outputs.triggered == 'true'
-        run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -simple file): </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md"
+        run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology (on -base file): </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md"
       - name: Post reasoned comment
         if: steps.check.outputs.triggered == 'true'
         env:

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.2
+    container: obolibrary/odkfull:v1.5.3
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

.gitignore

@@ -56,10 +56,14 @@ subsets/BDS_subset.tsv
 subsets/BDS_subset.owl
 subsets/BDS_subset.obo
 subsets/BDS_subset.json
+subsets/*-view.*
+subsets/*-tags.*
 src/ontology/subsets/BDS_subset.tsv
 src/ontology/subsets/BDS_subset.owl
 src/ontology/subsets/BDS_subset.obo
 src/ontology/subsets/BDS_subset.json
+src/ontology/subsets/*-view.*
+src/ontology/subsets/*-tags.*
 src/mappings/cl-local.sssom.tsv
 src/mappings/cl.sssom.tsv
 cl.json

docs/odk-workflows/RepositoryFileStructure.md

@@ -22,6 +22,7 @@ These are the current imports in CL
 | ro | http://purl.obolibrary.org/obo/ro.owl | None |
 | pato | http://purl.obolibrary.org/obo/pato.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 |
 | omo | http://purl.obolibrary.org/obo/omo.owl | mirror |
 
 ## Components
@@ -42,3 +43,4 @@ These are the components in CL
 | general_cell_types_upper_slim.owl | None |
 | kidney_upper_slim.owl | None |
 | cellxgene_subset.owl | None |
+| clm-cl.owl | None |

images/README.md

@@ -0,0 +1 @@
+Folder for storing CL images.