Merge pull request #459 from materialdigital/reorganization-of-SDCs

Reorganization of SDCs

Author: joergwa

.github/workflow_resources/.DS_Store

@@ -24,8 +24,10 @@ bin/
 /pmdco-simple.*
 /pmdco-simple-non-classified.*
 /mappings/
+/patterns/
 /reports/
 /subsets/
+/bridges/
 
 src/ontology/mirror
 src/ontology/mirror/*
@@ -49,6 +51,7 @@ src/ontology/simple_seed.txt
 src/ontology/patterns
 src/ontology/merged-pmdco-edit.owl
 src/ontology/pmdco-edit.properties
+src/ontology/bridges
 
 src/ontology/target/
 src/ontology/tmp/*
@@ -75,3 +78,7 @@ docs/odk-workflows/RepositoryFileStructure.md
 /docs/odk-workflows
 /.cache
 /patterns/tmp
+._.DS_Store
+**/.DS_Store
+**/._.DS_Store
+patterns/.DS_Store

.gitignore

@@ -0,0 +1 @@
+# How to cite PMDCO

docs/cite.md

@@ -0,0 +1 @@
+# How to contribute to PMDCO

docs/contributing.md

@@ -6,7 +6,7 @@ Your ODK repositories configuration is managed in `src/ontology/pmdco-odk.yaml`.
 
 
 ```
-sh run.sh make update_repo
+sh run.sh update_repo
 ```
 
 There are a large number of options that can be set to configure your ODK, but we will only discuss a few of them here.
@@ -169,7 +169,7 @@ components:
     - filename: mycomp.owl
 ```
 
-When running `sh run.sh make update_repo`, a new file `src/ontology/components/mycomp.owl` will 
+When running `sh run.sh update_repo`, a new file `src/ontology/components/mycomp.owl` will 
 be created which you can edit as you see fit. Typical ways to edit:
 
 1. Using a ROBOT template to generate the component (see below)

docs/odk-workflows/RepoManagement.md

@@ -25,7 +25,7 @@ These are the current imports in PMDCO
 | uo | http://purl.obolibrary.org/obo/uo.owl | slme |
 | cob | http://purl.obolibrary.org/obo/cob.owl | custom |
 | nfdicore | https://raw.githubusercontent.com/ISE-FIZKarlsruhe/nfdicore/refs/tags/v3.0.4/nfdicore-base.owl | slme |
-| time | https://raw.githubusercontent.com/w3c/sdw/gh-pages/time/rdf/time.ttl | slme |
+| time | https://github.com/w3c/sdw-time/raw/refs/heads/gh-pages/rdf/time.ttl | slme |
 ## 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:
 

docs/odk-workflows/RepositoryFileStructure.md

@@ -51,4 +51,4 @@ shape:scalar_value_specification
     ] ;
 
    sh:closed true ;
-   sh:ignoredProperties ( rdf:type owl:topDataProperty owl:topObjectProperty obo:IAO_0000418 obo:IAO_0000219 obo:IAO_0000136 obo:BFO_0000051 obo:OBI_0002135 ) .
+   sh:ignoredProperties ( rdf:type owl:topDataProperty owl:topObjectProperty obo:IAO_0000418 obo:IAO_0000219 obo:IAO_0000136 obo:BFO_0000051 obo:OBI_0002135 rdfs:label <http://www.w3.org/2004/02/skos/core#definition>) .

patterns/scalar value specification/shape.ttl

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for pmdco
 # Generated using ontology-development-kit
-# ODK Version: "Unknown"
+# ODK Version: v1.6
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use pmdco.Makefile instead
 
@@ -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=                54072dc574a377048daa0be07494524ef16b0e62e4cbf5483bb9f4e1401d0586
+CONFIG_HASH=                f21fb6466e311206258e4626acb95498d16097f5c7c583eab894021c196a1441
 
 
 # ----------------------------------------
@@ -42,15 +42,14 @@ UPDATEREPODIR=              target
 SPARQLDIR =                 ../sparql
 EXTENDED_PREFIX_MAP=        $(TMPDIR)/obo.epm.json
 COMPONENTSDIR =             components
-ODK_RESOURCES_DIR ?=        /tools/resources
 ROBOT_PROFILE =             profile.txt
 REPORT_FAIL_ON =            ERROR
 REPORT_LABEL =              -l true
 REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        --clean-obo "strict drop-untranslatable-axioms"
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      "Unknown"
+ODK_VERSION_MAKEFILE =      v1.6
 RELAX_OPTIONS =             --include-subclass-of true
 REDUCE_OPTIONS =            --include-subproperties true
 
@@ -64,7 +63,6 @@ ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
 
-
 FORMATS = $(sort  owl ttl owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
 RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-minimal )
@@ -128,12 +126,12 @@ reason_test: $(EDIT_PREPROCESSED)
 .PHONY: odkversion
 odkversion:
 	@echo "ODK Makefile $(ODK_VERSION_MAKEFILE)"
-	@odk-helper info --tools
+	@odk-info --tools
 .PHONY: config_check
 config_check:
 	@if [ "$$(tr -d '\r' < $(ONT)-odk.yaml | sha256sum | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \
 		echo "Repository is up-to-date." ; else \
-		echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'sh run.sh update_repo'." ; fi
+		echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi
 
 
 $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR):
@@ -151,20 +149,23 @@ export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins
 custom_robot_plugins:
 
 
+.PHONY: extra_robot_plugins
+extra_robot_plugins: 
+
 
 # Install all ROBOT plugins to the runtime plugins directory
 .PHONY: all_robot_plugins
-all_robot_plugins: $(foreach plugin,$(notdir $(wildcard $(ODK_RESOURCES_DIR)/robot/plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
+all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
 		   $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
-		   custom_robot_plugins  \
+		   custom_robot_plugins extra_robot_plugins  \
 
 # Default rule to install plugins
 $(ROBOT_PLUGINS_DIRECTORY)/%.jar:
 	@mkdir -p $(ROBOT_PLUGINS_DIRECTORY)
 	@if [ -f ../../plugins/$*.jar ]; then        \
 		ln ../../plugins/$*.jar $@ ;         \
-	elif [ -f $(ODK_RESOURCES_DIR)/robot/plugins/$*.jar ]; then \
-		cp $(ODK_RESOURCES_DIR)/robot/plugins/$*.jar $@ ;  \
+	elif [ -f /tools/robot-plugins/$*.jar ]; then \
+		cp /tools/robot-plugins/$*.jar $@ ;  \
 	fi
 
 # Specific rules for supplementary plugins defined in configuration
@@ -224,11 +225,6 @@ RELEASED_MAPPING_FILES = $(foreach p, $(RELEASED_MAPPINGS), $(MAPPINGDIR)/$(p).s
 .PHONY: all_mappings
 all_mappings: $(MAPPING_FILES)
 
-# ----------------------------------------
-# Bridge assets
-# ----------------------------------------
-
-BRIDGE_FILES =
 
 # ----------------------------------------
 # QC Reports & Utilities
@@ -283,8 +279,13 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
 $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
 	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
 
-check_for_robot_updates:
-	@odk-helper check-robot-profile
+check_for_robot_updates:	
+	@cut -f2 "/tools/templates/src/ontology/profile.txt" | sort > $(TMPDIR)/sorted_tsv2.txt
+	@cut -f2 "$(ROBOT_PROFILE)" | sort > $(TMPDIR)/sorted_tsv1.txt
+	@comm -23 $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/sorted_tsv1.txt > $(TMPDIR)/missing.txt
+	@echo "Missing tests:"
+	@cat $(TMPDIR)/missing.txt
+	@rm $(TMPDIR)/sorted_tsv1.txt $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/missing.txt $(TMPDIR)/report_profile_robot.txt
 
 # ----------------------------------------
 # Release assets
@@ -295,13 +296,11 @@ ASSETS = \
   $(MAIN_FILES) \
   $(REPORT_FILES) \
   $(SUBSET_FILES) \
-  $(MAPPING_FILES) \
-  $(BRIDGE_FILES)
+  $(MAPPING_FILES)
 
 RELEASE_ASSETS = \
   $(MAIN_FILES) \
-  $(SUBSET_FILES)\
-  $(BRIDGE_FILES)
+  $(SUBSET_FILES)
 
 .PHONY: all_assets
 all_assets: $(ASSETS) check_rdfxml_assets
@@ -312,7 +311,7 @@ show_assets:
 	du -sh $(ASSETS)
 
 check_rdfxml_%: %
-	@odk-helper check-rdfxml $<
+	@check-rdfxml  $<
 
 .PHONY: check_rdfxml_assets
 check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl)
@@ -611,7 +610,7 @@ mirror-bfo: | $(TMPDIR)
 .PHONY: mirror-ro
 .PRECIOUS: $(MIRRORDIR)/ro.owl
 mirror-ro: | $(TMPDIR)
-	$(ROBOT) convert -I http://purl.obolibrary.org/obo/ro.owl -o $(TMPDIR)/$@.owl
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/ro/releases/2025-12-17/ro.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: iao
@@ -626,8 +625,7 @@ mirror-iao: | $(TMPDIR)
 .PHONY: mirror-obi
 .PRECIOUS: $(MIRRORDIR)/obi.owl
 mirror-obi: | $(TMPDIR)
-	curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/obi/2025-12-18/obi.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: chebi
@@ -665,14 +663,14 @@ mirror-cob: | $(TMPDIR)
 .PHONY: mirror-nfdicore
 .PRECIOUS: $(MIRRORDIR)/nfdicore.owl
 mirror-nfdicore: | $(TMPDIR)
-	$(ROBOT) convert -I https://raw.githubusercontent.com/ISE-FIZKarlsruhe/nfdicore/refs/tags/v3.0.4/nfdicore-base.owl -o $(TMPDIR)/$@.owl
+	$(ROBOT) convert -I https://raw.githubusercontent.com/ISE-FIZKarlsruhe/nfdicore/refs/tags/v3.0.5/nfdicore-base.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: time
 .PHONY: mirror-time
 .PRECIOUS: $(MIRRORDIR)/time.owl
 mirror-time: | $(TMPDIR)
-	$(ROBOT) convert -I https://raw.githubusercontent.com/w3c/sdw/gh-pages/time/rdf/time.ttl -o $(TMPDIR)/$@.owl
+	$(ROBOT) convert -I https://github.com/w3c/sdw-time/raw/refs/heads/gh-pages/rdf/time.ttl -o $(TMPDIR)/$@.owl
 
 
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
@@ -827,7 +825,7 @@ validate-all-tsv: $(ALL_TSV_FILES)
 # can use to pull the (currently inofficial) OBO EPM into the workspace.
 # Users are instructed to refer to the EPM only through the variable $(EXTENDED_PREFIX_MAP) as 
 # its location might change in a feature version of ODK.
-$(EXTENDED_PREFIX_MAP): $(ODK_RESOURCES_DIR)/obo.epm.json
+$(EXTENDED_PREFIX_MAP): /tools/obo.epm.json
 	cp $< $@
 
 

scripts/test_pr_checks.sh

@@ -21,8 +21,10 @@ Import(<https://w3id.org/pmd/co/imports/uo_import.owl>)
 Declaration(Class(obo:CHEBI_74236))
 Declaration(Class(qudt:QuantityValue))
 Declaration(Class(qudt:Unit))
+Declaration(Class(:PMD_0020259))
 Declaration(ObjectProperty(qudt:hasUnit))
 Declaration(DataProperty(qudt:numericValue))
+Declaration(NamedIndividual(<http://qudt.org/vocab/unit/PER-MOL>))
 Declaration(AnnotationProperty(:PMD_0000060))
 
 ############################
@@ -64,7 +66,7 @@ SubDataPropertyOf(qudt:numericValue obo:OBI_0001937)
 
 # Class: obo:CHEBI_74236 (polymerisation monomer)
 
-SubClassOf(obo:CHEBI_74236 obo:BFO_0000023)
+SubClassOf(obo:CHEBI_74236 :PMD_0020259)
 
 # Class: obo:NCBITaxon_9606 (homo sapiens)
 
@@ -90,6 +92,15 @@ For example, the meter is a quantity of length that has been rigorously defined
 More formally, the value of a physical quantity Q with respect to a unit (U) is expressed as the scalar multiple of a real number (n) and U, as  $Q = nU$."@en)
 
 
+############################
+#   Named Individuals
+############################
+
+# Individual: <http://qudt.org/vocab/unit/PER-MOL> (<http://qudt.org/vocab/unit/PER-MOL>)
+
+ClassAssertion(qudt:Unit <http://qudt.org/vocab/unit/PER-MOL>)
+
+
 SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000055 obo:RO_0000059) obo:STATO_0000102)
 AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000098 "you might consinder EDAM formats as sublasses here http://edamontology.org/format_1915")
 AnnotationAssertion(:PMD_0000060 obo:IAO_0020000 "true"^^xsd:boolean)