From 9bf2a1b780feeee1f262d08a710bfe9c73c73c51 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 17 Mar 2023 07:57:22 -0700 Subject: [PATCH 1/2] Dividing user makefile from release manager makefile, fixes #72 --- Makefile | 25 ++++++++++++++----------- src/semsql/builder/build.Makefile | 22 ---------------------- 2 files changed, 14 insertions(+), 33 deletions(-) diff --git a/Makefile b/Makefile index c5daece..ba3664c 100644 --- a/Makefile +++ b/Makefile @@ -81,22 +81,25 @@ realclean-%: # --- # Prefixes # --- -# TODO: sync with bioregistry -# NOTE: move this to build folder -build_prefixes: $(PREFIX_DIR)/prefixes.csv +build_prefixes: $(PREFIX_DIR)/prefixes.csv $(PREFIX_DIR)/prefixes.yaml -#$(PREFIX_DIR)/obo_prefixes.owl: -# robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@ +$(PREFIX_DIR)/obo_prefixes.owl: $(STAMP) + robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@ -#$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl -# sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $< +$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl + sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $< -#$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db -# sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='' AND ns.predicate=''" > $@ +$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db + sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='' AND ns.predicate=''" > $@ + +$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/prefixes_local.csv $(PREFIX_DIR)/obo_prefixes.csv + cat $^ > $@ + +# see https://github.com/INCATools/relation-graph/issues/168 +$(PREFIX_YAML_PATH): $(PREFIX_CSV_PATH) + grep -v ^prefix, $< | grep -v ^obo, | perl -npe 's@,(.*)@: "$$1"@' > $@.tmp && mv $@.tmp $@ -#$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv# -# cat $^ > $@ # --- diff --git a/src/semsql/builder/build.Makefile b/src/semsql/builder/build.Makefile index ce1d1fe..1d53d51 100644 --- a/src/semsql/builder/build.Makefile +++ b/src/semsql/builder/build.Makefile @@ -86,25 +86,3 @@ PREFIX_YAML_PATH = $(PREFIX_DIR)/prefixes.yaml %-properties.txt: touch $@ -# --- -# Prefixes -# --- - -build_prefixes: $(PREFIX_DIR)/prefixes.csv $(PREFIX_DIR)/prefixes.yaml - -$(PREFIX_DIR)/obo_prefixes.owl: - robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@ - -$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl - sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $< - -$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db - sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='' AND ns.predicate=''" > $@ - -$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/prefixes_local.csv $(PREFIX_DIR)/obo_prefixes.csv - cat $^ > $@ - -# see https://github.com/INCATools/relation-graph/issues/168 -$(PREFIX_YAML_PATH): $(PREFIX_CSV_PATH) - grep -v ^prefix, $< | grep -v ^obo, | perl -npe 's@,(.*)@: "$$1"@' > $@.tmp && mv $@.tmp $@ - From 7d32f44bddcd60dca50082181e27ac94c3add774 Mon Sep 17 00:00:00 2001 From: cmungall Date: Fri, 17 Mar 2023 09:16:08 -0700 Subject: [PATCH 2/2] rebuild --- ontologies.Makefile | 24 ++++++++++++++++++- src/semsql/builder/prefixes/prefixes.csv | 1 + .../builder/prefixes/prefixes_local.csv | 2 ++ src/semsql/builder/registry/ontologies.yaml | 11 ++++++++- 4 files changed, 36 insertions(+), 2 deletions(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index a064ed3..9a820e3 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -152,6 +152,17 @@ db/bcio.owl: download/bcio.owl cp $< $@ +download/oeo.owl: STAMP + curl -L -s http://openenergy-platform.org/ontology/oeo/ > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/oeo.owl + +db/oeo.owl: download/oeo.owl + cp $< $@ + + download/go.owl: STAMP curl -L -s http://purl.obolibrary.org/obo/go/extensions/go-plus.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -383,6 +394,17 @@ db/co_324.owl: download/co_324.owl cp $< $@ +download/interpro.owl: STAMP + curl -L -s https://w3id.org/biopragmatics/resources/interpro/92.0/interpro.obo > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/interpro.owl + +db/interpro.owl: download/interpro.owl + robot merge -i $< -o $@ + + download/hgnc.genegroup.owl: STAMP curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz | gzip -dc > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -525,4 +547,4 @@ download/%.owl: STAMP db/%.owl: download/%.owl robot merge -i $< -o $@ -EXTRA_ONTOLOGIES = chiro ncit fma maxo foodon chebiplus msio modl phenio comploinc bero aio reacto bcio go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao edam sweetAll lov schema-dot-org cellosaurus cosmo dbpendiaont co_324 hgnc.genegroup hgnc dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal drugmechdb rxnorm +EXTRA_ONTOLOGIES = chiro ncit fma maxo foodon chebiplus msio modl phenio comploinc bero aio reacto bcio oeo go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao edam sweetAll lov schema-dot-org cellosaurus cosmo dbpendiaont co_324 interpro hgnc.genegroup hgnc dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal drugmechdb rxnorm diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index 45dcdc2..6bc5834 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -58,6 +58,7 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library# biolink,https://w3id.org/biolink/vocab/ loinc,https://loinc.org/ BCIO,http://humanbehaviourchange.org/ontology/BCIO_ +OEO,http://openenergy-platform.org/ontology/oeo/OEO_ orcid,https://orcid.org/ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# old.fix,http://purl.org/obo/owl/FIX# diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index 1cd6567..bee36b6 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -6,6 +6,7 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library# biolink,https://w3id.org/biolink/vocab/ loinc,https://loinc.org/ BCIO,http://humanbehaviourchange.org/ontology/BCIO_ +OEO,http://openenergy-platform.org/ontology/oeo/OEO_ orcid,https://orcid.org/ evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# old.fix,http://purl.org/obo/owl/FIX# @@ -13,6 +14,7 @@ mlo,http://www.a2rd.net.br/mlo# dbpediaont,http://dbpedia.org/ontology/ dbpedia,http://dbpedia.org/ co_324,https://cropontology.org/rdf/CO_324: +InterPro,http://purl.obolibrary.org/obo/interpro_ hgnc.genegroup,http://purl.obolibrary.org/obo/hgnc.genegroup_ hgnc,http://purl.obolibrary.org/obo/hgnc_ hgnc.genegroup,http://purl.obolibrary.org/obo/dictybase_ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index d9f3171..e3aff7f 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -58,6 +58,10 @@ ontologies: url: http://humanbehaviourchange.org/ontology/bcio.owl prefixmap: BCIO: http://humanbehaviourchange.org/ontology/BCIO_ + oeo: + url: http://openenergy-platform.org/ontology/oeo/ + prefixmap: + OEO: http://openenergy-platform.org/ontology/oeo/OEO_ go: url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl go-lego: @@ -91,7 +95,7 @@ ontologies: mlo: http://www.a2rd.net.br/mlo# ito: url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip - zip_extract_file: ITO.owl + zip_extract_file: ITO.owl reactome-Homo-sapiens: url: https://reactome.org/download/current/biopax.zip zip_extract_file: Homo_sapiens.owl @@ -141,6 +145,11 @@ ontologies: ## PyOBO products ## See https://github.com/INCATools/semantic-sql/issues/45 + interpro: + url: https://w3id.org/biopragmatics/resources/interpro/92.0/interpro.obo + format: obo + prefixmap: + InterPro: http://purl.obolibrary.org/obo/interpro_ hgnc.genegroup: url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz compression: gzip