First pass at revised version of COB

This revision is based on the results
of the September 2024 COB workshop.
Changes have not yet been vetted.

Author: jamesaoverton

cob-base.owl

@@ -16,8 +16,6 @@ These are the current imports in COB
 
 | Import | URL | Type |
 | ------ | --- | ---- |
-| ro | http://purl.obolibrary.org/obo/ro.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:
@@ -26,9 +24,4 @@ Components, in contrast to imports, are considered full members of the ontology.
 2. A part of the ontology is managed in ROBOT templates
 3. The expressivity of the component is higher than the format of the edit file. For example, people still choose to manage their ontology in OBO format (they should not) missing out on a lot of owl features. They may choose to manage logic that is beyond OBO in a specific OWL component.
 
-These are the components in COB
 
-| Filename | URL |
-| -------- | --- |
-| cob-annotations.owl | None |
-| cob-to-external.owl | None |

cob-full.owl

@@ -19,7 +19,7 @@
 # 6. [Run everything (COB products and release pipeline)](all)
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                5daef41d99e802417bd9ad0f378f72168e2d30f0488f5b2423330cbc561ec834
+CONFIG_HASH=                0cb0824fc712dd1bbe3e3067c8a9d6d4212a769da65f9ec96e0020e31e2cafb9
 
 
 # ----------------------------------------
@@ -62,13 +62,13 @@ 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 =                 $(COMPONENTSDIR)/cob-annotations.owl $(COMPONENTSDIR)/cob-to-external.owl 
+OTHER_SRC =                 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
 FORMATS = $(sort  owl owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full cob-base-reasoned cob-examples-reasoned cob-native )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-root )
 
 ifeq ($(ODK_DEBUG),yes)
 ODK_DEBUG_FILE = debug.log
@@ -168,7 +168,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  ro omo
+IMPORTS = 
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -375,16 +375,6 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt
 
 .PRECIOUS: $(IMPORTDIR)/%_import.owl
 
-## Module for ontology: ro
-
-$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl
-	echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in cob.Makefile!" && false
-## Module for ontology: omo
-
-$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combined.txt
-	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru  \
-    $(ANNOTATE_CONVERT_FILE); fi
-
 
 .PHONY: refresh-imports
 refresh-imports:
@@ -406,39 +396,6 @@ refresh-%:
 no-mirror-refresh-%:
 	$(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B
 
-
-# ----------------------------------------
-# Components
-# ----------------------------------------
-# Some ontologies contain external and internal components. A component is included in the ontology in its entirety.
-
-COMP=true # Global parameter to bypass component generation
-
-.PHONY: all_components
-all_components: $(OTHER_SRC)
-
-.PHONY: recreate-components
-recreate-components:
-	$(MAKE) COMP=true IMP=false MIR=true PAT=true IMP_LARGE=false all_components -B
-
-.PHONY: no-mirror-recreate-components
-no-mirror-recreate-components:
-	$(MAKE) COMP=true IMP=false MIR=false PAT=true IMP_LARGE=false all_components -B
-
-.PHONY: recreate-%
-recreate-%:
-	$(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B
-
-.PHONY: no-mirror-recreate-%
-no-mirror-recreate-%:
-	$(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B
-
-$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR)
-	test -f $@ || touch $@
-.PRECIOUS: $(COMPONENTSDIR)/%.owl
-
-
-
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------
@@ -450,22 +407,6 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
 ifeq ($(strip $(MIR)),true)
 
 
-## ONTOLOGY: ro
-.PHONY: mirror-ro
-.PRECIOUS: $(MIRRORDIR)/ro.owl
-mirror-ro: | $(TMPDIR)
-	curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl
-
-
-## ONTOLOGY: omo
-.PHONY: mirror-omo
-.PRECIOUS: $(MIRRORDIR)/omo.owl
-mirror-omo: | $(TMPDIR)
-	curl -L $(OBOBASE)/omo.owl --create-dirs -o $(TMPDIR)/omo-download.owl --retry 4 --max-time 200 && \
-	$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl
-
-
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
 	if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
@@ -549,15 +490,6 @@ $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 		relax \
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
-
-cob-base-reasoned.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false
-
-cob-examples-reasoned.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false
-
-cob-native.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false
 # ----------------------------------------
 # Debugging Tools
 # ----------------------------------------

cob-root.owl

@@ -10,27 +10,14 @@ workflows:
  - docs
 release_artefacts:
   - base
-  - full
-  - custom-cob-base-reasoned
-  - custom-cob-examples-reasoned
-  - custom-cob-native
+  - root
 import_group:
   module_type: filter
   annotation_properties:
     - rdfs:label
     - IAO:0000115
     - IAO:0000116
     - IAO:0000111
-  products:
-    - id: ro
-      module_type: custom
-      slme_individuals: exclude
-    - id: omo
-      module_type: mirror
-components:
-  products:
-    - filename: cob-annotations.owl
-    - filename: cob-to-external.owl
 robot_java_args: '-Xmx8G'
 custom_makefile_header: |
   ### Workflow
@@ -47,4 +34,4 @@ custom_makefile_header: |
   # 6. [Run everything (COB products and release pipeline)](all)
 create_obo_metadata: FALSE
 documentation:
-  documentation_system: mkdocs
+  documentation_system: mkdocs

cob.owl

@@ -10,16 +10,11 @@ SHELL := bash
 .SUFFIXES:
 .SECONDARY:
 
-COB_TO_EXTERNAL = $(COMPONENTSDIR)/cob-to-external.owl
-COB_ANNOTATIONS = $(COMPONENTSDIR)/cob-annotations.owl
-COB_EXAMPLES = $(COMPONENTSDIR)/cob-examples.owl
-
 .PHONY: prepare_release
-prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES) cob.tsv
-	rsync -R $(RELEASE_ASSETS) cob.tsv $(RELEASEDIR) &&\
-  rm -f $(CLEANFILES) &&\
-	rm -f cob.tsv &&\
-  echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab"
+prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES)
+	rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\
+	rm -f $(CLEANFILES) &&\
+	echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab"
 
 .PHONY: prepare_cob_products
 prepare_cob_products: test
@@ -36,88 +31,44 @@ products/:
 $(TMPDIR)/robot.jar: | $(TMPDIR)
 	if [ $(ROBOT_DOWNLOAD) = true ]; then curl -L -o $@ https://build.obolibrary.io/job/ontodev/job/robot/job/master/lastSuccessfulBuild/artifact/bin/robot.jar; fi
 
+
 ########################################
-# -- MAIN RELEASE PRODUCTS --
+# -- TEMPLATES --
 ########################################
 
-# build main release product
-REWIRE_PRECEDENCE = PR CHEBI
-cob.ttl: components/cob-to-external.tsv cob-native.owl
-	sssom rewire -I xml  -m $< $(patsubst %,--precedence %,$(REWIRE_PRECEDENCE)) cob-native.owl -o $@
+$(TMPDIR)/cob-%.tsv: $(SCRIPTSDIR)/split-cob-edit.py cob-edit.tsv
+	$^ $(TMPDIR)
 
-cob.owl: cob.ttl
-	robot merge --include-annotations true -i $< -i ontology-metadata.owl \
-	annotate --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-	--output $@.tmp.owl && mv $@.tmp.owl $@
-.PRECIOUS: cob.owl
 
-cob-native.owl: $(SRC)
-	$(ROBOT) remove --input $< --select imports --trim false \
-		reason -r HERMIT \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		--output $@.tmp.owl && mv $@.tmp.owl $@
+########################################
+# -- MAIN RELEASE PRODUCTS --
+########################################
 
-# base file is main cob plus linking axioms
-#cob-base.owl: cob.owl $(COB_TO_EXTERNAL)
-#	$(ROBOT) merge $(patsubst %, -i %, $^) -o $@
+$(ONT)-edit.owl: $(TMPDIR)/cob-root.tsv
+	$(ROBOT) template --template $< \
+	reason -r HERMIT \
+	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+	--output $@.tmp.owl && mv $@.tmp.owl $@
 
-$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
-	$(ROBOT_RELEASE_IMPORT_MODE_BASE) \
-	$(SHARED_ROBOT_COMMANDS) \
+# COB "Full"
+$(ONT).owl: $(TMPDIR)/cob-full.tsv
+	$(ROBOT) template --template $< \
+	reason -r HERMIT \
+	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+	--output $@.tmp.owl && mv $@.tmp.owl $@
+
+$(ONT)-base.owl: $(ONT).owl $(TMPDIR)/cob-base.tsv
+	$(ROBOT) template --input $< --template $(word 2,$^) \
 	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
 		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		--output $@.tmp.owl && mv $@.tmp.owl $@
 
-cob-base-reasoned.owl: cob-base.owl
-	$(ROBOT) remove --input $< --select imports --trim false \
-		reason -r HERMIT \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		--output $@.tmp.owl && mv $@.tmp.owl $@
-
-cob-examples-reasoned.owl: cob-base.owl $(COB_EXAMPLES)
-	$(ROBOT) remove --input $< --select imports --trim false \
-		merge $(patsubst %, -i %, $^) \
-		reason -r HERMIT \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		--output $@.tmp.owl && mv $@.tmp.owl $@
-
-# TSV export (may depend on dev version of robot export)
-cob.tsv: cob.owl
-	$(ROBOT) export -i $<  -c "ID|ID [LABEL]|definition|subClassOf [ID NAMED]|subClassOf [LABEL NAMED]|subClassOf [ID ANON]|subClassOf [LABEL ANON]" -e $@
-#	$(ROBOT) export -i $< --entity-select NAMED -c "ID|ID [LABEL]|definition|subClassOf [ID]|subClassOf [LABEL]|subClassOf [ID ANON]|subClassOf [LABEL ANON]" -e $@
-
-# -- BRIDGING AXIOMS TO OBO ROOTS --
-#
-#  the source file is cob-to-external.tsv
-#
-#  OWL is generated from this
-#
-
-$(TMPDIR)/cob-to-external.sssom.owl: $(COMPONENTSDIR)/cob-to-external.tsv | $(TMPDIR)
-	sssom convert $< --output-format owl -o $@
-
-$(COB_TO_EXTERNAL): $(TMPDIR)/cob-to-external.sssom.owl
-	$(ROBOT) merge -i $< \
+$(ONT)-root.owl: $(TMPDIR)/cob-root.tsv
+	$(ROBOT) template --template $< \
+	reason -r HERMIT \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-	convert -f owl -o $@
-
-$(TMPDIR)/cob-annotations.ttl: $(COB_TO_EXTERNAL) $(SPARQLDIR)/external-links.rq | $(TMPDIR)
-	$(ROBOT) query --input $< --query $(word 2,$^) $@
-
-$(COB_ANNOTATIONS): $(TMPDIR)/cob-annotations.ttl
-	$(ROBOT) annotate --input $< \
-	--ontology-iri "http://purl.obolibrary.org/obo/cob/$@" \
-	--annotation owl:versionInfo $(TODAY) \
-	--output $@
-
-# This is the custom import: removing all COB related axioms from RO, but otherwise pulling in logical dependencies.
+	--output $@.tmp.owl && mv $@.tmp.owl $@
 
-$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms_combined.txt
-	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
-		extract -T $(IMPORTDIR)/ro_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --method BOT \
-		remove --base-iri http://purl.obolibrary.org/obo/COB_ --axioms internal --preserve-structure false --trim false \
-		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
-		$(ANNOTATE_CONVERT_FILE); fi
 
 ########################################
 # -- TESTING --
@@ -151,7 +102,7 @@ cob_test: main_test itest
 # main test: should be run via CI on every PR
 # this tests COB's internal consistency
 .PHONY: main_test
-main_test: $(REPORTDIR)/$(SRC)-obo-report.tsv cob.owl cob-base-reasoned.owl cob-examples-reasoned.owl
+main_test: $(REPORTDIR)/$(SRC)-obo-report.tsv $(RELEASEDIR)/cob-root.owl
 test: main_test
 
 # integration tests: for now, run these on commmand line

docs/odk-workflows/RepositoryFileStructure.md

@@ -0,0 +1,92 @@
+#!/usr/bin/env python3
+#
+# Split the cob-edit.tsv file into three ROBOT templates:
+# cob-base.tsv cob-full.tsv cob-root.tsv
+
+import argparse
+import csv
+import os
+import re
+
+
+def initialize_tsv(output_dir, filename, fieldnames, robot_row):
+    '''Initialize and return a DictWriter for a ROBOT template.'''
+    path = os.path.join(output_dir, filename)
+    path_fh = open(path, 'w')
+    writer = csv.DictWriter(path_fh, fieldnames, delimiter='\t', lineterminator='\n', extrasaction='ignore')
+    writer.writeheader()
+    writer.writerow(robot_row)
+    return writer
+
+
+def split(input_path, output_dir):
+    '''Split the COB term template into base, full, and root templates.'''
+    fieldnames = None
+    robot_row, terms, replacements = {}, {}, {}
+
+    with open(input_path) as f:
+        rows = csv.DictReader(f, delimiter='\t')
+        for row in rows:
+            if not fieldnames:
+                # Ignore the last three columns
+                fieldnames = list(row.keys())[0:-3]
+            id = row['Ontology ID'].strip()
+            if id == '':
+                continue
+            if id == 'ID':
+                robot_row = row
+                continue
+
+            # Handle the Replacement columns
+            # by collecting a dictionary of replacements.
+            replacement_id = row['Replacement ID'].strip()
+            replacement_label = row['Replacement Label'].strip()
+            if replacement_label and replacement_label != '':
+                # removed exception for non-base IDs... TBD if needed/wanted
+                replacements[row['Label'].strip()] = {
+                    'ID': id,
+                    'Replacement Label': replacement_label,
+                    'Replacement ID': replacement_id,
+                }
+            # Otherwise just add this row to 'terms'.
+            else:
+                terms[id] = row
+
+    # Apply replacements to the axioms in all the logical columns
+    axiom_cols = [
+        'Parent Class', 'Subclass Axiom', 'Equivalent Class Axiom',
+        'Disjoint Class', 'Parent Property', 'Domain', 'Range',
+        'Inverse Property'
+    ]
+    for id, row in terms.items():
+        for repl_label, repl_dict in replacements.items():
+            for col in axiom_cols:
+                if col not in row:
+                    continue
+                row[col] = re.sub(repl_label, repl_dict['Replacement Label'], row[col])
+
+    base_writer = initialize_tsv(output_dir, 'cob-base.tsv', fieldnames, robot_row)
+    full_writer = initialize_tsv(output_dir, 'cob-full.tsv', fieldnames, robot_row)
+    root_writer = initialize_tsv(output_dir, 'cob-root.tsv', fieldnames, robot_row)
+
+    for id, row in terms.items():
+        module = row['COB Module'].strip()
+        if module == 'BASE':
+            base_writer.writerow(row)
+        if module not in ['', 'ROOT']:
+            full_writer.writerow(row)
+        if module != '':
+            root_writer.writerow(row)
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Split the main COB term template into multiple module templates')
+    parser.add_argument('input', type=str, help='The input COB term template')
+    parser.add_argument('outdir', type=str, help='The output directory')
+    args = parser.parse_args()
+
+    split(args.input, args.outdir)
+
+
+if __name__ == '__main__':
+    main()