Add SSSOM sets for mappings with the Alliance’s ontologies and vocabularies

.gitignore

@@ -67,6 +67,7 @@ src/patterns/pattern_owl_seed.txt
 src/patterns/all_pattern_terms.txt
 
 # End of ODK-managed rules
+src/mappings/fbcv.sssom.tsv
 src/ontology/oort
 src/ontology/oort/*
 src/ontology/oort_test

src/mappings/README.md

@@ -0,0 +1,2 @@
+# Directory for managing SSSOM mappings files
+

src/mappings/agr-vocabs.sssom.tsv

@@ -0,0 +1,27 @@
+#curie_map:
+#  FBcv: http://purl.obolibrary.org/obo/FBcv_
+#  ORCID: https://orcid.org/
+#  obo: http://purl.obolibrary.org/obo/
+#mapping_set_id: http://purl.obolibrary.org/obo/fbcv/agr-vocabs.sssom.tsv
+#mapping_set_description: Mappings between the FlyBase Controlled Vocabulary (FBcv) and vocabulary terms from the Alliance of Genome Resources.
+#creator_id:
+#  - ORCID:0000-0002-6095-8718
+#license: https://creativecommons.org/licenses/by/4.0/
+#subject_source: obo:fbcv.owl
+#object_type: rdfs literal
+#mapping_date: 2025-10-02
+subject_id	subject_label	predicate_id	object_label	object_category	mapping_justification	comment
+FBcv:0000222	male	skos:exactMatch	male	Genetic Sex	semapv:ManualMappingCuration	
+FBcv:0000334	female	skos:exactMatch	female	Genetic Sex	semapv:ManualMappingCuration	
+FBcv:0003124	species study	skos:exactMatch	species	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003125	strain study	skos:exactMatch	genome variation	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003127	developmental stage study	skos:exactMatch	developmental stage	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003128	circadian rhythm study	skos:narrowMatch	time of day	Data Set Category Tags	semapv:ManualMappingCuration	The Alliance term is specifically about a study that compares samples collected at specified times of the day, while the FBcv term is more broadly about any study of the circadian rhythm (which would likely involve collecting samples at specified times of the day but not necessarily).
+FBcv:0003129	cell cycle study	skos:exactMatch	cell cycle	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003130	tissue type study	skos:narrowMatch	anatomical structure	Data Set Category Tags	semapv:ManualMappingCuration	The Alliance term is specifically about studying gene expression in tissues, while the FBcv term is more broadly about studying the form or function of tissues (including but not limited to gene expression).
+FBcv:0003131	cell type study	skos:exactMatch	cell type	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003132	subcellular component study	skos:exactMatch	subcellular component	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003133	gene study	skos:narrowMatch	gene	Data Set Category Tags	semapv:ManualMappingCuration	The Alliance term is specifically about studying the effects of gene perturbation, while the FBcv term is more broadly about studying the properties of a gene, whether in perturbed conditions or not.
+FBcv:0003134	biotic stimulus study	skos:exactMatch	biotic stimulus	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003135	chemical stimulus study	skos:exactMatch	chemical stimulus	Data Set Category Tags	semapv:ManualMappingCuration	
+FBcv:0003136	physical stimulus study	skos:exactMatch	physical stimulus	Data Set Category Tags	semapv:ManualMappingCuration	

src/mappings/agr.sssom.tsv

@@ -0,0 +1,42 @@
+#curie_map:
+#  FBcv: http://purl.obolibrary.org/obo/FBcv_
+#  MMO: http://purl.obolibrary.org/obo/MMO_
+#  OBI: http://purl.obolibrary.org/obo/OBI_
+#  ORCID: https://orcid.org/
+#  obo: http://purl.obolibrary.org/obo/
+#mapping_set_id: http://purl.obolibrary.org/obo/fbcv/agr.sssom.tsv
+#mapping_set_description: Mappings between the FlyBase Controlled Vocabulary (FBcv) and some of the ontologies used by the Alliance of Genome Resources (AGR).
+#creator_id:
+#  - ORCID:0000-0002-6095-8718
+#license: https://creativecommons.org/licenses/by/4.0/
+#subject_source: obo:fbcv.owl
+#mapping_date: 2025-10-02
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	object_source
+FBcv:0003047	isolated cells	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003068	RNA-Seq	skos:exactMatch	MMO:0000658	ribonucleic acid in situ hybridization assay	semapv:ManualMappingCuration	obo:mmo.owl
+FBcv:0003127	developmental stage study	skos:exactMatch	OBI:0003713	organism development assay	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003130	tissue type study	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003133	gene study	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003134	biotic stimulus study	skos:broadMatch	OBI:0001396	stimulus or stress design	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003135	chemical stimulus study	skos:broadMatch	OBI:0001396	stimulus or stress design	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003141	multi-individual sample	skos:exactMatch	OBI:0302716	pool of specimens	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003166	biotic treatment	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003167	chemical treatment	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003169	tissue dissection	skos:exactMatch	OBI:0001504	dissection	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003170	cell isolation	skos:exactMatch	OBI:0000512	isolation of cell population	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0003213	Illumina sequencing	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009000	single-cell RNA-Seq	skos:exactMatch	MMO:0000862	single cell RNA-seq assay	semapv:ManualMappingCuration	obo:mmo.owl
+FBcv:0009000	single-cell RNA-Seq	skos:exactMatch	OBI:0002631	single-cell RNA sequencing assay	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009001	single-nucleus RNA-Seq	skos:exactMatch	OBI:0003109	single-nucleus RNA sequencing assay	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009001	single-nucleus RNA-Seq	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:mmo.owl
+FBcv:0009002	cell clustering analysis	skos:broadMatch	OBI:0200175	class discovery data transformation	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009004	isolated nuclei	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009006	DROP-Seq	skos:broadMatch	OBI:0002631	single-cell RNA sequencing assay	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009007	Smart-seq2	skos:broadMatch	OBI:0002631	single-cell RNA sequencing assay	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009008	10x sequencing	skos:broadMatch	OBI:0002631	single-cell RNA sequencing assay	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009009	starvation	skos:broadMatch	OBI:0600030	experimental disease induction	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009011	mechanical cell dissociation	skos:broadMatch	OBI:0000512	isolation of cell population	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009012	enzymatic cell dissociation	skos:broadMatch	OBI:0000512	isolation of cell population	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009013	chemical cell dissociation	skos:broadMatch	OBI:0000512	isolation of cell population	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009056	single-cell combinatorial indexing RNA sequencing	skos:exactMatch	OBI:0003105	single-cell combinatorial indexing RNA sequencing assay	semapv:ManualMappingCuration	obo:obi.owl
+FBcv:0009058	EMBL-EBI SCEA standard analysis method	skos:exactMatch	sssom:NoTermFound		semapv:ManualMappingCuration	obo:obi.owl

src/mappings/common.sssom.tsv

@@ -0,0 +1,8 @@
+#curie_map:
+#  ORCID: https://orcid.org/
+#mapping_set_id: http://purl.obolibrary.org/obo/fbcv/fbcv.sssom.tsv
+#mapping_set_description: Mappings between the FlyBase Controlled Vocabulary (FBcv) and foreign ontologies and vocabularies.
+#creator_id:
+#  - ORCID:0000-0002-6095-8718
+#license: https://creativecommons.org/licenses/by/4.0/
+subject_id	predicate_id	object_id	mapping_justification	object_source

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=                e8f37b5150af876d5eb7dc695969a933dbcb0c2fae0c59f7be440e67efbcc410
+CONFIG_HASH=                615898f6bc894bac8c75d184cd2460494f7ca7ec3abb6bbed8243ed1b05dc1e3
 
 
 # ----------------------------------------
@@ -61,6 +61,12 @@ OTHER_SRC =                 $(COMPONENTSDIR)/dpo-simple.owl
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
+MAPPINGDIR=                 ../mappings
+MAPPING_TESTER=             sssom validate
+SSSOMPY=                    sssom
+MAPPINGS=                   agr agr-vocabs common fbcv 
+MAPPING_RELEASE_FILES=      $(foreach n,$(MAPPINGS), $(MAPPINGDIR)/$(n).sssom.tsv)
+
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
@@ -218,8 +224,9 @@ all_subsets: $(SUBSET_FILES)
 # ----------------------------------------
 
 
-MAPPINGS = 
+MAPPINGS =  agr agr-vocabs common fbcv
 
+RELEASED_MAPPINGS =  fbcv
 
 MAPPING_FILES = $(foreach p, $(MAPPINGS), $(MAPPINGDIR)/$(p).sssom.tsv)
 RELEASED_MAPPING_FILES = $(foreach p, $(RELEASED_MAPPINGS), $(MAPPINGDIR)/$(p).sssom.tsv)
@@ -339,9 +346,12 @@ prepare_release_fast:
 .PHONY: copy_release_files
 copy_release_files:
 	rsync -R $(RELEASE_ASSETS) $(RELEASEDIR)
+	mkdir -p $(RELEASEDIR)/mappings
+	cp -rf $(RELEASED_MAPPING_FILES) $(RELEASEDIR)/mappings
 
 # All released assets, in their final location within the release
-RELEASE_ASSETS_AFTER_RELEASE=$(foreach n,$(RELEASE_ASSETS), $(RELEASEDIR)/$(n))
+RELEASE_ASSETS_AFTER_RELEASE=$(foreach n,$(RELEASE_ASSETS), $(RELEASEDIR)/$(n)) \
+			     $(foreach n,$(RELEASED_MAPPINGS), $(RELEASEDIR)/mappings/$(n).sssom.tsv)
 
 .PHONY: show_release_assets
 show_release_assets:
@@ -559,6 +569,38 @@ ifneq ($(SPARQL_EXPORTS_ARGS),)
 	$(ROBOT) query -f tsv --use-graphs true -i $< $(SPARQL_EXPORTS_ARGS)
 endif
 
+# ----------------------------------------
+# SSSOM Mapping Files
+# ----------------------------------------
+
+validate-sssom-%:
+	tsvalid $(MAPPINGDIR)/$*.sssom.tsv --comment "#"
+	sssom validate $(MAPPINGDIR)/$*.sssom.tsv
+
+validate_mappings:
+	$(MAKE_FAST) $(foreach n,$(MAPPINGS),validate-sssom-$(n))
+
+normalize-sssom-%:
+	sssom-cli --output $(MAPPINGDIR)/$*.sssom.tsv $(MAPPINGDIR)/$*.sssom.tsv
+
+normalize_mappings:
+	$(MAKE_FAST) $(foreach n,$(MAPPINGS),normalize-sssom-$(n))
+
+# This mappingset is manually curated, so we only check that the file actually exists.
+$(MAPPINGDIR)/agr.sssom.tsv:
+	test -f $@
+
+# This mappingset is manually curated, so we only check that the file actually exists.
+$(MAPPINGDIR)/agr-vocabs.sssom.tsv:
+	test -f $@
+
+# This mappingset is manually curated, so we only check that the file actually exists.
+$(MAPPINGDIR)/common.sssom.tsv:
+	test -f $@
+
+$(MAPPINGDIR)/fbcv.sssom.tsv: $(MAPPINGDIR)/common.sssom.tsv $(MAPPINGDIR)/agr.sssom.tsv $(MAPPINGDIR)/agr-vocabs.sssom.tsv
+	sssom-cli --output $@ $^
+
 # ----------------------------------------
 # Release artefacts: export formats
 # ----------------------------------------

src/ontology/fbcv-odk.yaml

@@ -48,3 +48,19 @@ release_date: TRUE
 components:
   products:
     - filename: dpo-simple.owl
+use_mappings: true
+sssom_mappingset_group:
+  products:
+    - id: agr
+      maintenance: manual
+    - id: agr-vocabs
+      maintenance: manual
+    - id: common
+      maintenance: manual
+    - id: fbcv
+      maintenance: merged
+      source_mappings:
+        - common
+        - agr
+        - agr-vocabs
+      release_mappings: true