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Split production Makefile from user Makefile #73

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Mar 17, 2023
Merged

Split production Makefile from user Makefile #73

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9bf2a1b
Dividing user makefile from release manager makefile, fixes #72
cmungall Mar 17, 2023
7d32f44
rebuild
cmungall Mar 17, 2023
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25 changes: 14 additions & 11 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
$(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='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@

$(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 $^ > $@


# ---
Expand Down
24 changes: 23 additions & 1 deletion ontologies.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
22 changes: 0 additions & 22 deletions src/semsql/builder/build.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@

$(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 $@

1 change: 1 addition & 0 deletions src/semsql/builder/prefixes/prefixes.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -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#
Expand Down
2 changes: 2 additions & 0 deletions src/semsql/builder/prefixes/prefixes_local.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -6,13 +6,15 @@ 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#
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_
Expand Down
11 changes: 10 additions & 1 deletion src/semsql/builder/registry/ontologies.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down