initial release

brain-bican · Aug 22, 2023 · 2d96987 · 2d96987
1 parent a528fa6
commit 2d96987
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Showing 13 changed files with 374 additions and 10 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,3 @@
+pandas
+ruamel.yaml
+linkml-owl
diff --git a/src/config/db_graph_atlas.yaml b/src/config/db_graph_atlas.yaml
@@ -0,0 +1,39 @@
+dhba:
+  species: human dev
+  graph: 16
+  atlases:
+    -
+      name: Human, 34 years, Cortex - Gyral
+      id: 138322605
+    -
+      name: Human, 34 years, Cortex - Mod. Brodmann
+      id: 265297126
+    -
+      name: Human, 21 pcw
+      id: 3
+    -
+      name: 287730656
+      id: 138322603
+
+mba:
+  species: mouse
+  graph: 1
+  atlases:
+    -
+      id: 602630314
+      name: Adult Mouse, 3D Coronal
+    -
+      id: 1
+      name: Mouse, P56, Coronal
+
+    - id: 2
+      name: Mouse, P56, Sagittal
+
+hba:
+  species: human
+  graph: 10
+  atlases:
+    -  
+      id: 265297125
+      name: Human Brain Atlas Guide
+
diff --git a/src/linkml/data/.gitignore b/src/linkml/data/.gitignore
diff --git a/src/linkml/structure_graph_schema.yaml b/src/linkml/structure_graph_schema.yaml
@@ -0,0 +1,44 @@
+id: http://purl.obolibrary.org/obo/ABA_Uberon
+name: structure_graph
+prefixes:
+  UBERON: 'http://purl.obolibrary.org/obo/UBERON_'
+
+default_curi_maps:
+- semweb_context
+- obo_context
+
+types:
+  string:
+    base: str
+    uri: xsd:string
+
+classes:
+  Class:
+    slots:
+      - id
+      - name
+      - acronym
+      - parent_structure_id
+      - subclass_of
+    class_uri: owl:Class
+
+slots:
+  id:
+    identifier: true
+#    range: uriorcurie
+  name:
+    slot_uri: rdfs:label
+    annotations:
+      owl: AnnotationAssertion
+  acronym:
+    slot_uri: oboInOwl:hasExactSynonym
+    annotations:
+      owl: AnnotationAssertion
+  parent_structure_id:
+    slot_uri: BFO:0000050
+    annotations:
+      owl: SubClassOf, ObjectSomeValuesFrom
+  subclass_of:
+    slot_uri: rdfs:subclass_of
+    annotations:
+      owl: SubClassOf
diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -9,7 +9,7 @@
   <uri name="https://purl.brain-bican.org/ontology/dhbao/imports/ncbitaxon_import.owl" uri="imports/ncbitaxon_import.owl"/>
   <uri name="https://purl.brain-bican.org/ontology/dhbao/imports/ncbitaxon_import.obo" uri="imports/ncbitaxon_import.obo"/>
 
-
+  <uri name="https://purl.brain-bican.org/ontology/dhbao/imports/merged_import.owl" uri="imports/merged_import.owl"/>
 
 
   <uri name="https://purl.brain-bican.org/ontology/dhbao/components/all_templates.owl" uri="components/all_templates.owl"/>

diff --git a/src/ontology/dhbao-edit.owl b/src/ontology/dhbao-edit.owl
@@ -11,13 +11,15 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
 
 Ontology(<https://purl.brain-bican.org/ontology/dhbao.owl>
 
-Import(<https://purl.brain-bican.org/ontology/dhbao/imports/uberon_import.owl>)
+# Import(<https://purl.brain-bican.org/ontology/dhbao/imports/uberon_import.owl>)
+# Import(<https://purl.brain-bican.org/ontology/dhbao/imports/ncbitaxon_import.owl>)
+
+Import(<https://purl.brain-bican.org/ontology/dhbao/imports/merged_import.owl>)
+Import(<https://purl.brain-bican.org/ontology/dhbao/components/all_templates.owl>)
 
-Import(<https://purl.brain-bican.org/ontology/dhbao/imports/ncbitaxon_import.owl>)
 
 
 Import(<https://purl.brain-bican.org/ontology/dhbao/patterns/definitions.owl>)
-Annotation(dcterms:description "None")
 Annotation(dcterms:license <https://creativecommons.org/licenses/unspecified>)
 Annotation(dcterms:title "Developing Human Brain Atlas Ontology")
 
@@ -39,10 +41,6 @@ AnnotationAssertion(rdfs:label dcterms:title "title")
 #   Classes
 ############################
 
-# Class: <https://purl.brain-bican.org/ontology/DHBAO_0000000> (root node)
-
-AnnotationAssertion(rdfs:label <https://purl.brain-bican.org/ontology/DHBAO_0000000> "root node"@en)
-
 
 )
 
diff --git a/src/ontology/dhbao.Makefile b/src/ontology/dhbao.Makefile
@@ -1,6 +1,166 @@
-## Customize Makefile settings for dhbao
-## 
+## Customize Makefile settings for mbao
+##
 ## If you need to customize your Makefile, make
 ## changes here rather than in the main Makefile
+#
+# sh ./run.sh make clean
+# sh ./run.sh make prepare_release
+#
+# MBA : 1
+# DMBA : 17
+# HBA : 10
+# DHBA : 16
+# PBA : 8
 
+URIBASE = https://purl.brain-bican.org/ontology
 
+JOBS = 16 # 1 17 10 8
+BRIDGES = aba dhba
+TARGETS = dhba
+
+LINKML = linkml-data2owl
+
+STRUCTURE_GRAPHS = $(patsubst %, sources/%.json, $(JOBS))
+ALL_GRAPH_ONTOLOGIES = $(patsubst sources/%.json,sources/%.ofn,$(STRUCTURE_GRAPHS))
+ALL_BRIDGES = $(patsubst %, sources/uberon-bridge-to-%.owl, $(BRIDGES))
+SOURCE_TEMPLATES = $(patsubst %, ../robot_templates/%_CCF_to_UBERON_source.tsv, $(TARGETS))
+NEW_BRIDGES = $(patsubst %, new-bridges/new-uberon-bridge-to-%.owl, $(TARGETS))
+
+
+.PHONY: $(COMPONENTSDIR)/all_templates.owl
+$(COMPONENTSDIR)/all_templates.owl: clean_files dependencies $(COMPONENTSDIR)/linkouts.owl $(COMPONENTSDIR)/sources_merged.owl
+	$(ROBOT) merge -i $(COMPONENTSDIR)/linkouts.owl -i $(COMPONENTSDIR)/sources_merged.owl annotate --ontology-iri $(URIBASE)/$@ convert -f ofn -o $@
+.PRECIOUS: $(COMPONENTSDIR)/all_templates.owl
+
+# Installing depedencies so it can run in ODK container
+.PHONY: dependencies
+dependencies:
+	pip3 install -r ../../requirements.txt
+
+
+LOCAL_CLEAN_FILES = $(ALL_GRAPH_ONTOLOGIES) $(ALL_BRIDGES) $(TMPDIR)/tmp.json $(TMPDIR)/tmp.owl $(COMPONENTSDIR)/sources_merged.owl $(COMPONENTSDIR)/linkouts.owl $(TEMPLATEDIR)/linkouts.tsv
+
+# clean previous build files
+.PHONY: clean_files
+clean_files:
+	rm -f $(LOCAL_CLEAN_FILES)
+
+sources/%.json:
+	curl -o $@ $(subst %,$(subst sources/,,$@),"http://api.brain-map.org/api/v2/structure_graph_download/%")
+
+../linkml/data/template_%.tsv: sources/%.json
+	python3 $(SCRIPTSDIR)/structure_graph_template.py -i $< -o $@
+.PRECIOUS: ../linkml/data/template_%.tsv:
+# TODO delete
+
+sources/%.ofn: ../linkml/data/template_%.tsv
+	$(LINKML) -C Class -s ../linkml/structure_graph_schema.yaml $< -o $@
+.PRECIOUS: sources/%.ofn
+
+# download bridges
+sources/uberon-bridge-to-aba.owl:
+	curl -o sources/uberon-bridge-to-aba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-aba.obo"
+	$(ROBOT) convert -i sources/uberon-bridge-to-aba.obo --format owl -o $@
+	sed -i 's|http://purl.obolibrary.org/obo/ABA_|https://purl.brain-bican.org/ontology/mbao/ABA_|g' $@
+
+sources/uberon-bridge-to-dhba.owl:
+	curl -o sources/uberon-bridge-to-dhba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-dhba.obo"
+	$(ROBOT) convert -i sources/uberon-bridge-to-dhba.obo --format owl -o $@
+	sed -i 's|http://purl.obolibrary.org/obo/DHBA_|https://purl.brain-bican.org/ontology/mbao/DHBA_|g' $@
+
+sources/uberon-bridge-to-dmba.owl:
+	curl -o sources/uberon-bridge-to-dmba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-dmba.obo"
+	$(ROBOT) convert -i sources/uberon-bridge-to-dmba.obo --format owl -o $@
+	sed -i 's|http://purl.obolibrary.org/obo/DMBA_|https://purl.brain-bican.org/ontology/mbao/DMBA_|g' $@
+
+sources/uberon-bridge-to-hba.owl:
+	curl -o sources/uberon-bridge-to-hba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-hba.obo"
+	$(ROBOT) convert -i sources/uberon-bridge-to-hba.obo --format owl -o $@
+	sed -i 's|http://purl.obolibrary.org/obo/HBA_|https://purl.brain-bican.org/ontology/mbao/HBA_|g' $@
+
+sources/uberon-bridge-to-mba.owl:
+	curl -o sources/uberon-bridge-to-mba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-mba.obo"
+	$(ROBOT) convert -i sources/uberon-bridge-to-mba.obo --format owl -o $@
+	sed -i 's|http://purl.obolibrary.org/obo/MBA_|https://purl.brain-bican.org/ontology/mbao/MBA_|g' $@
+
+sources/uberon-bridge-to-pba.owl:
+	curl -o sources/uberon-bridge-to-pba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-pba.obo"
+	$(ROBOT) convert -i sources/uberon-bridge-to-pba.obo --format owl -o $@
+	sed -i 's|http://purl.obolibrary.org/obo/PBA_|https://purl.brain-bican.org/ontology/mbao/PBA_|g' $@
+
+# TODO handle legacy mapings
+
+#all_bridges:
+#	make sources/uberon-bridge-to-aba.obo sources/uberon-bridge-to-dmba.obo -B
+
+# Merge sources. # crudely listing dependencies for now - but could switch to using pattern expansion
+#sources_merged.owl: all_bridges
+#	robot merge --input sources/1.ofn --input sources/17.ofn --input sources/10.ofn --input sources/16.ofn --input sources/8.ofn --input sources/uberon-bridge-to-aba.obo --input sources/uberon-bridge-to-dhba.obo --input sources/uberon-bridge-to-dmba.obo --input sources/uberon-bridge-to-hba.obo --input sources/uberon-bridge-to-mba.obo --input sources/uberon-bridge-to-pba.obo annotate --ontology-iri $(URIBASE)/$@ -o $@
+
+$(COMPONENTSDIR)/sources_merged.owl: $(ALL_GRAPH_ONTOLOGIES) $(ALL_BRIDGES)
+	$(ROBOT) merge $(patsubst %, -i %, $^) relax annotate --ontology-iri $(URIBASE)/$@ -o $@
+
+# merge uberon + sources, reason & relax (EC -> SC)
+$(TMPDIR)/tmp.owl: $(SRC) $(COMPONENTSDIR)/sources_merged.owl
+	robot merge $(patsubst %, -i %, $^) relax annotate --ontology-iri $(URIBASE)/$@ -o $@
+
+# Make a json file for use in generating ROBOT template
+$(TMPDIR)/tmp.json: $(TMPDIR)/tmp.owl
+	$(ROBOT) convert --input $< -f json -o $@
+
+# Build robot  template - with linkouts and prefLabels
+$(TEMPLATEDIR)/linkouts.tsv: $(TMPDIR)/tmp.json
+	python $(SCRIPTSDIR)/gen_linkout_template.py $<
+
+# generate OWL from template
+$(COMPONENTSDIR)/linkouts.owl: $(TMPDIR)/tmp.owl $(TEMPLATEDIR)/linkouts.tsv
+	$(ROBOT) template --template $(word 2, $^) --input $< --add-prefixes template_prefixes.json -o $@
+
+
+
+
+## ONTOLOGY: uberon (remove disjoint classes and properties, they are causing inconsistencies when merged with dhba bridge)
+.PHONY: mirror-uberon
+.PRECIOUS: $(MIRRORDIR)/uberon.owl
+mirror-uberon: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uberon/uberon-base.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 200 &&\
+		$(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --axioms disjoint -o $@.tmp.owl && \
+		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+#	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/subsets/human-view.owl -o [email protected] &&\
+#		$(ROBOT) remove -i [email protected] --axioms disjoint -o [email protected] && \
+#		mv [email protected] $(TMPDIR)/[email protected]; fi
+
+
+## Disable '--equivalent-classes-allowed asserted-only' due to DHBA inconsistencies
+.PHONY: reason_test
+reason_test: $(EDIT_PREPROCESSED)
+	# $(ROBOT) explain --input $< --reasoner ELK -M unsatisfiability --unsatisfiable all --explanation explanation.md
+	# $(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed asserted-only \
+	# 	--exclude-tautologies structural --output test.owl && rm test.owl
+	$(ROBOT) reason --input $< --reasoner ELK \
+		--exclude-tautologies structural --output test.owl && rm test.owl
+
+## Disable '--equivalent-classes-allowed asserted-only' due to DHBA inconsistencies
+# Full: The full artefacts with imports merged, reasoned.
+$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+		reason --reasoner ELK --exclude-tautologies structural \
+		relax \
+		reduce -r ELK \
+		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
+
+## Disable '--equivalent-classes-allowed asserted-only' due to DHBA inconsistencies
+# foo-simple: (edit->reason,relax,reduce,drop imports, drop every axiom which contains an entity outside the "namespaces of interest")
+# drop every axiom: filter --term-file keep_terms.txt --trim true
+#	remove --select imports --trim false
+$(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+		reason --reasoner ELK --exclude-tautologies structural \
+		relax \
+		remove --axioms equivalent \
+		relax \
+		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
+		reduce -r ELK \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
+		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl
diff --git a/src/ontology/template_prefixes.json b/src/ontology/template_prefixes.json
@@ -0,0 +1,7 @@
+{
+  "@context": {
+    "UBERON": "http://purl.obolibrary.org/obo/UBERON_",
+    "OboInOwl": "http://www.geneontology.org/formats/oboInOwl#",
+    "DHBA": "https://purl.brain-bican.org/ontology/mbao/DHBA_"
+  }
+}
diff --git a/src/ontology/template_prefixes.yaml b/src/ontology/template_prefixes.yaml
@@ -0,0 +1,3 @@
+UBERON: http://purl.obolibrary.org/obo/UBERON_
+OboInOwl: http://www.geneontology.org/formats/oboInOwl#
+DHBA: https://purl.brain-bican.org/ontology/mbao/DHBA_
diff --git a/src/scripts/gen_linkout_template.py b/src/scripts/gen_linkout_template.py
@@ -0,0 +1,51 @@
+import json
+from ruamel.yaml import YAML
+from string import Template
+import pandas as pd
+import argparse
+
+parser = argparse.ArgumentParser(description='Process some integers.')
+parser.add_argument('filepath',
+                    help='Path to json version of ontology for input')
+args = parser.parse_args()
+
+f = open(args.filepath, 'r')
+j = json.loads(f.read())
+g = j['graphs'][0]
+conf = open('../config/db_graph_atlas.yaml', 'r')
+yaml = YAML(typ='safe')
+mapping = yaml.load(conf.read())
+link = Template("http://atlas.brain-map.org/atlas?atlas="
+                "$atlas_id#structure=$structure_id")
+
+seed = {'ID': 'ID',
+        'xref': 'A OboInOwl:hasDbXref',
+        'prefLabel': 'A skos:prefLabel'}
+
+tab = [seed]
+
+for n in g['nodes']:
+    if 'type' in n.keys() and n['type'] == 'CLASS':
+        lstat = True
+        for k, v in mapping.items():
+            if str(n['id']).lower().startswith('http://purl.obolibrary.org/obo/%s' % k) and 'lbl' in n:
+                for a in v['atlases']:
+                    try:
+                        tab.append({'ID': n['id'],
+                                    'xref': link.substitute(atlas_id=a['id'],
+                                                            structure_id=str(n['id']).rsplit('_', 1)[-1]),
+                                    'prefLabel': ' '.join([n['lbl'],
+                                                           ' (',
+                                                           v['species'],
+                                                           ')'])})
+                    except Exception as e:
+                        print("ERROR: Exception occurred while processing: " + n['id'])
+                        raise e
+                lstat = False
+        if lstat and 'lbl' in n.keys():
+            tab.append({'ID': n['id'], 'xref': '', 'prefLabel': n['lbl']})
+
+
+r_temp = pd.DataFrame.from_records(tab)
+r_temp.to_csv('../templates/linkouts.tsv', sep='\t', index=False)
+
diff --git a/src/scripts/structure_graph_template.py b/src/scripts/structure_graph_template.py
@@ -0,0 +1,22 @@
+import argparse
+import pandas as pd
+import csv
+
+from structure_graph_utils import read_structure_graph
+
+
+def generate_template(graph_json, output):
+    data_list = read_structure_graph(graph_json)
+
+    data_template = pd.DataFrame.from_records(data_list)
+    data_template.to_csv(output, sep="\t", index=False, quoting=csv.QUOTE_NONE)
+
+
+parser = argparse.ArgumentParser(description='Cli interface structure graph linkml template generation.')
+
+parser.add_argument('-i', '--input', help="Path to input JSON file")
+parser.add_argument('-o', '--output', help="Path to output TSV file")
+
+args = parser.parse_args()
+
+generate_template(args.input, args.output)