Make changes from Caroline comments

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.

src/ontology/Makefile

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                d4e868f8bbec3ce7b0d7656c824520ab0b96d8901a8c2b9cf400c27c3fb3dac2
+CONFIG_HASH=                fe26dd231ab531dab5609c794de598d2a28083168916941a3276fe672cfe8be2
 
 
 # ----------------------------------------
@@ -53,7 +53,7 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/blood_and_immune_upper_slim.owl $(COMPONENTSDIR)/eye_upper_slim.owl $(COMPONENTSDIR)/general_cell_types_upper_slim.owl $(COMPONENTSDIR)/kidney_upper_slim.owl $(COMPONENTSDIR)/cellxgene_subset.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/blood_and_immune_upper_slim.owl $(COMPONENTSDIR)/eye_upper_slim.owl $(COMPONENTSDIR)/general_cell_types_upper_slim.owl $(COMPONENTSDIR)/kidney_upper_slim.owl $(COMPONENTSDIR)/cellxgene_subset.owl $(COMPONENTSDIR)/clm-cl.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -513,6 +513,7 @@ $(COMPONENTSDIR)/cellxgene_subset.owl: $(TEMPLATEDIR)/cellxgene_subset.tsv
 		$(ANNOTATE_CONVERT_FILE); fi
 
 .PRECIOUS: $(COMPONENTSDIR)/cellxgene_subset.owl
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

src/ontology/catalog-v001.xml

@@ -16,6 +16,7 @@
     <uri id="User Entered Import Resolution" name="http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Cell.owl" uri="mirror/NIF-Cell.owl"/>
     <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/cl/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/hra_subset.owl" uri="components/hra_subset.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/cl/components/clm-cl.owl" uri="components/clm-cl.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/mappings.owl" uri="components/mappings.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/blood_and_immune_upper_slim.owl" uri="components/blood_and_immune_upper_slim.owl"/>
     <uri name="http://purl.obolibrary.org/obo/cl/components/eye_upper_slim.owl" uri="components/eye_upper_slim.owl"/>

src/ontology/cl-odk.yaml

@@ -9,6 +9,8 @@ use_dosdps: TRUE
 use_mappings: True
 use_edit_file_imports: FALSE
 release_diff: TRUE
+workflows:
+  - docs
 export_formats:
   - owl
   - obo
@@ -154,4 +156,5 @@ components:
       use_template: True
       templates:
         - cellxgene_subset.tsv
+    - filename: clm-cl.owl
 

src/ontology/cl.Makefile

@@ -95,8 +95,8 @@ $(MAPPINGDIR)/cl.sssom.tsv: $(MAPPINGDIR)/cl-local.sssom.tsv \
 EXTERNAL_SSSOM_PROVIDERS = fbbt zfa
 EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), $(MAPPINGDIR)/$(provider).sssom.tsv)
 
-# We only refresh external resources under IMP=true
-ifeq ($(strip $(IMP)),true)
+# We only refresh external resources under MIR=true
+ifeq ($(strip $(MIR)),true)
 
 # FBbt mapping set
 $(MAPPINGDIR)/fbbt.sssom.tsv: .FORCE
@@ -344,10 +344,9 @@ add-replacedby:
 # EXTERNAL RESOURCES
 # ----------------------------------------
 
+ifeq ($(strip $(MIR)),true)
+
 # Human reference atlas subset
-# FIXME: Refreshing of this resource should be uncoupled from the
-# release/QC pipelines.
-# See <https://github.com/obophenotype/cell-ontology/issues/2644>
 HRA_SUBSET_URL="https://raw.githubusercontent.com/hubmapconsortium/ccf-validation-tools/master/owl/CL_ASCTB_subset.owl"
 $(TMPDIR)/hra_subset.owl:
 	wget $(HRA_SUBSET_URL) -O $@
@@ -356,14 +355,20 @@ $(COMPONENTSDIR)/hra_subset.owl: $(TMPDIR)/hra_subset.owl
 	$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@
 
 # CellXGene reference subset
-# FIXME: Never actually downloaded again, unless the
-# $(TEMPLATEDIR)/cellxgene_subset.tsv file is manually removed; probably
-# not what was intended.
-# See <https://github.com/obophenotype/cell-ontology/issues/2644>
 CELLXGENE_SUBSET_URL="https://raw.githubusercontent.com/hkir-dev/cellxgene-cell-reporter/main/templates/cellxgene_subset.tsv"
-$(TEMPLATEDIR)/cellxgene_subset.tsv:
+$(TEMPLATEDIR)/cellxgene_subset.tsv: .FORCE
 	wget $(CELLXGENE_SUBSET_URL) -O $@
 
+# CellMark reference subset
+CLM_CL_URL="https://raw.githubusercontent.com/Cellular-Semantics/CellMark/main/clm-cl.owl"
+$(TMPDIR)/clm-cl.owl:
+	wget $(CLM_CL_URL) -O $@
+
+$(COMPONENTSDIR)/clm-cl.owl: $(TMPDIR)/clm-cl.owl
+	$(ROBOT) merge -i $< annotate --ontology-iri $(ONTBASE)/$@ --output $@
+
+endif
+
 
 # ----------------------------------------
 # RELEASE DEPLOYMENT

src/ontology/components/clm-cl.owl

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<rdf:RDF 
+     xml:base="http://purl.obolibrary.org/obo/"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:obo="http://purl.obolibrary.org/obo/">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cl/components/clm-cl.owl"/>
+
+    <!-- This is a placeholder, it will be regenerated when makefile is first executed -->
+</rdf:RDF>