Merge pull request #94 from INCATools/new-entries-and-uri-resolution

Adding new entries for kbase

Author: cmungall

ontologies.Makefile

@@ -559,6 +559,17 @@ db/orcid.owl: download/orcid.owl
 	cp $< $@
 
 
+download/ror.owl: STAMP
+	curl -L -s https://w3id.org/biopragmatics/resources/ror/ror.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/ror.owl
+
+db/ror.owl: download/ror.owl
+	cp $< $@
+
+
 download/cpont.owl: STAMP
 	curl -L -s https://w3id.org/cpont/cpont.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -977,6 +988,17 @@ db/interpro.owl: download/interpro.owl
 	perl -npe 's@ go:@ GO:@g;s@ ro:@ RO:@g;s@ interpro:@ InterPro:@g' $< > $@.tmp && robot convert -i $@.tmp -o $@
 
 
+download/pfam.owl: STAMP
+	curl -L -s https://w3id.org/biopragmatics/resources/pfam/pfam.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/pfam.owl
+
+db/pfam.owl: download/pfam.owl
+	cp $< $@
+
+
 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
@@ -1010,14 +1032,14 @@ db/sgd.owl: download/sgd.owl
 	robot merge -i $< -o $@
 
 
-download/dictybase.owl: STAMP
-	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/dictybase/dictybase.owl.gz | gzip -dc > $@.tmp
+download/gtdb.owl: STAMP
+	curl -L -s https://w3id.org/biopragmatics/resources/gtdb/gtdb.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
 	mv $@.tmp $@
 
-.PRECIOUS: download/dictybase.owl
+.PRECIOUS: download/gtdb.owl
 
-db/dictybase.owl: download/dictybase.owl
+db/gtdb.owl: download/gtdb.owl
 	cp $< $@
 
 
@@ -1033,7 +1055,7 @@ db/eccode.owl: download/eccode.owl
 
 
 download/uniprot.owl: STAMP
-	curl -L -s https://w3id.org/biopragmatics/resources/uniprot/2022_02/uniprot.owl.gz | gzip -dc > $@.tmp
+	curl -L -s https://w3id.org/biopragmatics/resources/uniprot/uniprot.owl.gz | gzip -dc > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
 	mv $@.tmp $@
 
@@ -1043,15 +1065,37 @@ db/uniprot.owl: download/uniprot.owl
 	cp $< $@
 
 
+download/uniprot.ptm.owl: STAMP
+	curl -L -s https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/uniprot.ptm.owl
+
+db/uniprot.ptm.owl: download/uniprot.ptm.owl
+	cp $< $@
+
+
+download/credit.owl: STAMP
+	curl -L -s https://raw.githubusercontent.com/biopragmatics/obo-db-ingest/main/export/credit/credit.owl > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/credit.owl
+
+db/credit.owl: download/credit.owl
+	cp $< $@
+
+
 download/rhea.owl: STAMP
-	curl -L -s https://w3id.org/biopragmatics/resources/rhea/rhea.obo > $@.tmp
+	curl -L -s https://w3id.org/biopragmatics/resources/rhea/rhea.owl.gz | gzip -dc > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
 	mv $@.tmp $@
 
 .PRECIOUS: download/rhea.owl
 
 db/rhea.owl: download/rhea.owl
-	robot merge -i $<  -o $@
+	perl -npe 's@https://www.ebi.ac.uk/.*ec=@https://bioregistry.io/eccode:@g' $< > $@.tmp && robot convert -i $@.tmp -o $@
 
 
 download/swisslipid.owl: STAMP
@@ -1328,4 +1372,4 @@ download/%.owl: STAMP
 db/%.owl: download/%.owl
 	robot merge -i $< -o $@
 
-EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio pride modl phenio phenio_test comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who ordo gard mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito chemont molgenie cso obiws biopragmatics-reactome reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll oboe-core oboe-standards lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm omim co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time
+EXTRA_ONTOLOGIES = swo chiro pcl chemessence ogco ncit fma maxo foodon chebiplus msio pride modl phenio phenio_test comploinc hba mba dmba dhba pba bero aio reacto xsmo bcio sio icd10who ordo gard mondo-ingest oeo envthes wifire taxslim goldterms sdgio kin biovoices omop comet cco occo iof upa go go-lego go-amigo neo bao orcid ror cpont biolink biopax enanomapper mlo ito chemont molgenie cso obiws biopragmatics-reactome reactome-hs reactome-mm efo hcao hpinternational edam chr sweetAll oboe-core oboe-standards lov schema-dot-org prov dtype vaem qudtunit quantitykind cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm omim co_324 ppeo interpro pfam hgnc.genegroup hgnc sgd gtdb eccode uniprot uniprot.ptm credit rhea swisslipid drugbank drugcentral complexportal wikipathways pathbank kegg.genome drugmechdb rxnorm vccf ontobiotope nando ecso enigma_context ontie ecosim nmdc_schema mixs kgcl fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time

src/semsql/builder/prefixes/prefixes.csv

@@ -118,6 +118,7 @@ OccO,http://purl.obolibrary.org/obo/OccO_
 IOFcore,https://spec.industrialontologies.org/ontology/
 UPa,http://purl.obolibrary.org/obo/UPa_
 orcid,https://orcid.org/
+ror,https://ror.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#
@@ -151,15 +152,20 @@ OMIMPS,https://www.omim.org/phenotypicSeries/PS
 co_324,https://cropontology.org/rdf/CO_324:
 PPEO,http://purl.org/ppeo/PPEO.owl#
 InterPro,http://purl.obolibrary.org/obo/InterPro_
+PFAM,https://www.ebi.ac.uk/interpro/entry/pfam/
+PFAM.CLAN,https://www.ebi.ac.uk/interpro/set/pfam/
 hgnc.genegroup,http://purl.obolibrary.org/obo/hgnc.genegroup_
 hgnc,http://purl.obolibrary.org/obo/hgnc_
-SGD,http://purl.obolibrary.org/obo/sgd_
-hgnc.genegroup,http://purl.obolibrary.org/obo/dictybase_
-EC,http://purl.obolibrary.org/obo/eccode_
-uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
-uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
-RHEA,http://purl.obolibrary.org/obo/rhea_
-uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
+SGD,https://www.yeastgenome.org/locus/
+gtdb,https://gtdb.ecogenomic.org/tree?r=
+EC,https://bioregistry.io/eccode:
+UniProtKB,https://bioregistry.io/uniprot:
+UniProtKB,https://bioregistry.io/uniprot:
+RESID,https://proteininformationresource.org/cgi-bin/resid?id=
+UNIMOD,http://www.unimod.org/modifications_view.php?editid1=
+uniprot.ptm,https://biopragmatics.github.io/providers/uniprot.ptm/
+credit,https://credit.niso.org/contributor-roles/
+RHEA,https://www.rhea-db.org/rhea/
 swisslipid,http://purl.obolibrary.org/obo/swisslipid_
 drugbank,http://purl.obolibrary.org/obo/drugbank_
 drugbank,http://purl.obolibrary.org/obo/drugcentral_

src/semsql/builder/prefixes/prefixes_local.csv

@@ -55,6 +55,7 @@ OccO,http://purl.obolibrary.org/obo/OccO_
 IOFcore,https://spec.industrialontologies.org/ontology/
 UPa,http://purl.obolibrary.org/obo/UPa_
 orcid,https://orcid.org/
+ror,https://ror.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#
@@ -88,15 +89,20 @@ OMIMPS,https://www.omim.org/phenotypicSeries/PS
 co_324,https://cropontology.org/rdf/CO_324:
 PPEO,http://purl.org/ppeo/PPEO.owl#
 InterPro,http://purl.obolibrary.org/obo/InterPro_
+PFAM,https://www.ebi.ac.uk/interpro/entry/pfam/
+PFAM.CLAN,https://www.ebi.ac.uk/interpro/set/pfam/
 hgnc.genegroup,http://purl.obolibrary.org/obo/hgnc.genegroup_
 hgnc,http://purl.obolibrary.org/obo/hgnc_
-SGD,http://purl.obolibrary.org/obo/sgd_
-hgnc.genegroup,http://purl.obolibrary.org/obo/dictybase_
-EC,http://purl.obolibrary.org/obo/eccode_
-uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
-uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
-RHEA,http://purl.obolibrary.org/obo/rhea_
-uniprot.obo,http://purl.obolibrary.org/obo/uniprot_
+SGD,https://www.yeastgenome.org/locus/
+gtdb,https://gtdb.ecogenomic.org/tree?r=
+EC,https://bioregistry.io/eccode:
+UniProtKB,https://bioregistry.io/uniprot:
+UniProtKB,https://bioregistry.io/uniprot:
+RESID,https://proteininformationresource.org/cgi-bin/resid?id=
+UNIMOD,http://www.unimod.org/modifications_view.php?editid1=
+uniprot.ptm,https://biopragmatics.github.io/providers/uniprot.ptm/
+credit,https://credit.niso.org/contributor-roles/
+RHEA,https://www.rhea-db.org/rhea/
 swisslipid,http://purl.obolibrary.org/obo/swisslipid_
 drugbank,http://purl.obolibrary.org/obo/drugbank_
 drugbank,http://purl.obolibrary.org/obo/drugcentral_

src/semsql/builder/registry/ontologies.yaml

@@ -243,6 +243,11 @@ ontologies:
     url: https://w3id.org/orcidio/orcidio.owl
     prefixmap:
       orcid: https://orcid.org/
+  ror:
+    url: https://w3id.org/biopragmatics/resources/ror/ror.owl.gz
+    compression: gzip
+    prefixmap:
+      ror: https://ror.org/
   cpont:
     url: https://w3id.org/cpont/cpont.owl
   biolink:
@@ -307,6 +312,7 @@ ontologies:
     zip_extract_file: Mus_musculus.owl
     post_processing_steps:
       - "sqlite3 {db} < views/reactome.sql"
+  
   efo:
     url: http://www.ebi.ac.uk/efo/efo.owl
     has_imports: true
@@ -426,6 +432,11 @@ ontologies:
     format: obo
     prefixmap:
       InterPro: http://purl.obolibrary.org/obo/InterPro_
+  pfam:
+    url: https://w3id.org/biopragmatics/resources/pfam/pfam.owl
+    prefixmap:
+      PFAM: https://www.ebi.ac.uk/interpro/entry/pfam/
+      PFAM.CLAN: https://www.ebi.ac.uk/interpro/set/pfam/
   hgnc.genegroup:
     url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz
     compression: gzip
@@ -441,29 +452,40 @@ ontologies:
     url: https://w3id.org/biopragmatics/resources/sgd/sgd.obo
     format: obo
     prefixmap:
-      SGD: http://purl.obolibrary.org/obo/sgd_
-  dictybase:
-    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/dictybase/dictybase.owl.gz
-    compression: gzip
+      SGD: https://www.yeastgenome.org/locus/
+  gtdb:
+    url: https://w3id.org/biopragmatics/resources/gtdb/gtdb.owl
     prefixmap:
-      hgnc.genegroup: http://purl.obolibrary.org/obo/dictybase_
+      gtdb: https://gtdb.ecogenomic.org/tree?r=
   eccode:
     url: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz
     compression: gzip
     prefixmap:
-      EC: http://purl.obolibrary.org/obo/eccode_
-      uniprot.obo: http://purl.obolibrary.org/obo/uniprot_
+      EC: "https://bioregistry.io/eccode:"
+      UniProtKB: "https://bioregistry.io/uniprot:"
   uniprot:
-    url: https://w3id.org/biopragmatics/resources/uniprot/2022_02/uniprot.owl.gz
+    url: https://w3id.org/biopragmatics/resources/uniprot/uniprot.owl.gz
     compression: gzip
     prefixmap:
-      uniprot.obo: http://purl.obolibrary.org/obo/uniprot_
+      UniProtKB: "https://bioregistry.io/uniprot:"
+  uniprot.ptm:
+    url: https://w3id.org/biopragmatics/resources/uniprot.ptm/uniprot.ptm.owl
+    prefixmap:
+      RESID: https://proteininformationresource.org/cgi-bin/resid?id=
+      UNIMOD: http://www.unimod.org/modifications_view.php?editid1=
+      uniprot.ptm: https://biopragmatics.github.io/providers/uniprot.ptm/
+  credit:
+    url: https://raw.githubusercontent.com/biopragmatics/obo-db-ingest/main/export/credit/credit.owl
+    prefixmap:
+      credit: https://credit.niso.org/contributor-roles/
   rhea:
-    url: https://w3id.org/biopragmatics/resources/rhea/rhea.obo
-    build_command: "robot merge -i $<  -o $@"
+    url: https://w3id.org/biopragmatics/resources/rhea/rhea.owl.gz
+    # https://github.com/biopragmatics/obo-db-ingest/issues/15
+    build_command: "perl -npe 's@https://www.ebi.ac.uk/.*ec=@https://bioregistry.io/eccode:@g' $< > [email protected] && robot convert -i [email protected] -o $@"
+    compression: gzip
+    # build_command: "robot merge -i $<  -o $@"
     prefixmap:
-      RHEA: http://purl.obolibrary.org/obo/rhea_
-      uniprot.obo: http://purl.obolibrary.org/obo/uniprot_
+      RHEA: https://www.rhea-db.org/rhea/
   swisslipid:
     url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/swisslipid/2023-02-03/swisslipid.obo.gz
     format: obo