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Merge pull request #73 from INCATools/fix-custom-prefix-for-RG
Split production Makefile from user Makefile
2 parents c260aa4 + 7d32f44 commit 84fe170

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-35
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6 files changed

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‎Makefile‎

Lines changed: 14 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -81,22 +81,25 @@ realclean-%:
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# ---
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# Prefixes
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# ---
84-
# TODO: sync with bioregistry
85-
# NOTE: move this to build folder
8684

87-
build_prefixes: $(PREFIX_DIR)/prefixes.csv
85+
build_prefixes: $(PREFIX_DIR)/prefixes.csv $(PREFIX_DIR)/prefixes.yaml
8886

89-
#$(PREFIX_DIR)/obo_prefixes.owl:
90-
# robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
87+
$(PREFIX_DIR)/obo_prefixes.owl: $(STAMP)
88+
robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
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92-
#$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
93-
# sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
90+
$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
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sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $<
9492

95-
#$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
96-
# 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>'" > $@
93+
$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
94+
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>'" > $@
95+
96+
$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/prefixes_local.csv $(PREFIX_DIR)/obo_prefixes.csv
97+
cat $^ > $@
98+
99+
# see https://github.com/INCATools/relation-graph/issues/168
100+
$(PREFIX_YAML_PATH): $(PREFIX_CSV_PATH)
101+
grep -v ^prefix, $< | grep -v ^obo, | perl -npe 's@,(.*)@: "$$1"@' > $@.tmp && mv $@.tmp $@
97102

98-
#$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv#
99-
# cat $^ > $@
100103

101104

102105
# ---

‎ontologies.Makefile‎

Lines changed: 23 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -152,6 +152,17 @@ db/bcio.owl: download/bcio.owl
152152
cp $< $@
153153

154154

155+
download/oeo.owl: STAMP
156+
curl -L -s http://openenergy-platform.org/ontology/oeo/ > $@.tmp
157+
sha256sum -b $@.tmp > $@.sha256
158+
mv $@.tmp $@
159+
160+
.PRECIOUS: download/oeo.owl
161+
162+
db/oeo.owl: download/oeo.owl
163+
cp $< $@
164+
165+
155166
download/go.owl: STAMP
156167
curl -L -s http://purl.obolibrary.org/obo/go/extensions/go-plus.owl > $@.tmp
157168
sha256sum -b $@.tmp > $@.sha256
@@ -383,6 +394,17 @@ db/co_324.owl: download/co_324.owl
383394
cp $< $@
384395

385396

397+
download/interpro.owl: STAMP
398+
curl -L -s https://w3id.org/biopragmatics/resources/interpro/92.0/interpro.obo > $@.tmp
399+
sha256sum -b $@.tmp > $@.sha256
400+
mv $@.tmp $@
401+
402+
.PRECIOUS: download/interpro.owl
403+
404+
db/interpro.owl: download/interpro.owl
405+
robot merge -i $< -o $@
406+
407+
386408
download/hgnc.genegroup.owl: STAMP
387409
curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz | gzip -dc > $@.tmp
388410
sha256sum -b $@.tmp > $@.sha256
@@ -525,4 +547,4 @@ download/%.owl: STAMP
525547
db/%.owl: download/%.owl
526548
robot merge -i $< -o $@
527549

528-
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
550+
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

‎src/semsql/builder/build.Makefile‎

Lines changed: 0 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -86,25 +86,3 @@ PREFIX_YAML_PATH = $(PREFIX_DIR)/prefixes.yaml
8686
%-properties.txt:
8787
touch $@
8888

89-
# ---
90-
# Prefixes
91-
# ---
92-
93-
build_prefixes: $(PREFIX_DIR)/prefixes.csv $(PREFIX_DIR)/prefixes.yaml
94-
95-
$(PREFIX_DIR)/obo_prefixes.owl:
96-
robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
97-
98-
$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
99-
sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $<
100-
101-
$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
102-
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>'" > $@
103-
104-
$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/prefixes_local.csv $(PREFIX_DIR)/obo_prefixes.csv
105-
cat $^ > $@
106-
107-
# see https://github.com/INCATools/relation-graph/issues/168
108-
$(PREFIX_YAML_PATH): $(PREFIX_CSV_PATH)
109-
grep -v ^prefix, $< | grep -v ^obo, | perl -npe 's@,(.*)@: "$$1"@' > $@.tmp && mv $@.tmp $@
110-

‎src/semsql/builder/prefixes/prefixes.csv‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -58,6 +58,7 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library#
5858
biolink,https://w3id.org/biolink/vocab/
5959
loinc,https://loinc.org/
6060
BCIO,http://humanbehaviourchange.org/ontology/BCIO_
61+
OEO,http://openenergy-platform.org/ontology/oeo/OEO_
6162
orcid,https://orcid.org/
6263
evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
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old.fix,http://purl.org/obo/owl/FIX#

‎src/semsql/builder/prefixes/prefixes_local.csv‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -6,13 +6,15 @@ modl,https://archive.org/services/purl/purl/modular_ontology_design_library#
66
biolink,https://w3id.org/biolink/vocab/
77
loinc,https://loinc.org/
88
BCIO,http://humanbehaviourchange.org/ontology/BCIO_
9+
OEO,http://openenergy-platform.org/ontology/oeo/OEO_
910
orcid,https://orcid.org/
1011
evs.ncit,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
1112
old.fix,http://purl.org/obo/owl/FIX#
1213
mlo,http://www.a2rd.net.br/mlo#
1314
dbpediaont,http://dbpedia.org/ontology/
1415
dbpedia,http://dbpedia.org/
1516
co_324,https://cropontology.org/rdf/CO_324:
17+
InterPro,http://purl.obolibrary.org/obo/interpro_
1618
hgnc.genegroup,http://purl.obolibrary.org/obo/hgnc.genegroup_
1719
hgnc,http://purl.obolibrary.org/obo/hgnc_
1820
hgnc.genegroup,http://purl.obolibrary.org/obo/dictybase_

‎src/semsql/builder/registry/ontologies.yaml‎

Lines changed: 10 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -58,6 +58,10 @@ ontologies:
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url: http://humanbehaviourchange.org/ontology/bcio.owl
5959
prefixmap:
6060
BCIO: http://humanbehaviourchange.org/ontology/BCIO_
61+
oeo:
62+
url: http://openenergy-platform.org/ontology/oeo/
63+
prefixmap:
64+
OEO: http://openenergy-platform.org/ontology/oeo/OEO_
6165
go:
6266
url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
6367
go-lego:
@@ -91,7 +95,7 @@ ontologies:
9195
mlo: http://www.a2rd.net.br/mlo#
9296
ito:
9397
url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip
94-
zip_extract_file: ITO.owl
98+
zip_extract_file: ITO.owl
9599
reactome-Homo-sapiens:
96100
url: https://reactome.org/download/current/biopax.zip
97101
zip_extract_file: Homo_sapiens.owl
@@ -141,6 +145,11 @@ ontologies:
141145

142146
## PyOBO products
143147
## See https://github.com/INCATools/semantic-sql/issues/45
148+
interpro:
149+
url: https://w3id.org/biopragmatics/resources/interpro/92.0/interpro.obo
150+
format: obo
151+
prefixmap:
152+
InterPro: http://purl.obolibrary.org/obo/interpro_
144153
hgnc.genegroup:
145154
url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz
146155
compression: gzip

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