First pass at PyOBO ingest.

See #45
INCATools · Nov 23, 2022 · 019f211 · 019f211
1 parent 0178c2d
commit 019f211
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Showing 6 changed files with 108 additions and 8 deletions.
diff --git a/Makefile b/Makefile
@@ -6,6 +6,7 @@ BUILDER_DIR = src/semsql/builder
 DDL_DIR = $(BUILDER_DIR)/sql_schema
 YAML_DIR = src/semsql/linkml
 SQLA_DIR = src/semsql/sqla
+ONT_REGISTRY = src/semsql/builder/registry/ontologies.yaml 
 
 PREFIX_DIR = $(BUILDER_DIR)/prefixes
 
@@ -141,7 +142,7 @@ download/reactome-biopax.zip:
 src/semsql/builder/registry/registry_schema.py: src/semsql/builder/registry/registry_schema.yaml
 	$(RUN) gen-python $< > $@
 
-ontologies.Makefile: src/semsql/builder/registry/ontologies.yaml 
+ontologies.Makefile: $(ONT_REGISTRY)
 	$(RUN) semsql generate-makefile -P src/semsql/builder/prefixes/prefixes_local.csv $< > $@.tmp && mv $@.tmp $@
 
 include ontologies.Makefile

diff --git a/ontologies.Makefile b/ontologies.Makefile
@@ -208,7 +208,7 @@ db/mlo.owl: download/mlo.owl
 
 
 download/ito.owl: STAMP
-	curl -L -s https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip > $@.zip.tmp && unzip -p $@.zip.tmp ITO.owl > $@.tmp && rm $@.zip.tmp
+	curl -L -s https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip > $@.zip.tmp && unzip -p $@.zip.tmp {ont.zip_extract_file} > $@.tmp && rm $@.zip.tmp
 	sha256sum -b $@.tmp > $@.sha256
 	mv $@.tmp $@
 
@@ -219,7 +219,7 @@ db/ito.owl: download/ito.owl
 
 
 download/reactome-Homo-sapiens.owl: STAMP
-	curl -L -s https://reactome.org/download/current/biopax.zip > $@.zip.tmp && unzip -p $@.zip.tmp Homo_sapiens.owl > $@.tmp && rm $@.zip.tmp
+	curl -L -s https://reactome.org/download/current/biopax.zip > $@.zip.tmp && unzip -p $@.zip.tmp {ont.zip_extract_file} > $@.tmp && rm $@.zip.tmp
 	sha256sum -b $@.tmp > $@.sha256
 	mv $@.tmp $@
 
@@ -263,7 +263,7 @@ db/sweetAll.owl: download/sweetAll.owl
 
 
 download/lov.owl: STAMP
-	curl -L -s https://lov.linkeddata.es/lov.n3.gz > $@.tmp
+	curl -L -s https://lov.linkeddata.es/lov.n3.gz | gzip -dc > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
 	mv $@.tmp $@
 
@@ -306,6 +306,61 @@ db/co_324.owl: download/co_324.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
+	mv $@.tmp $@
+
+.PRECIOUS: download/hgnc.genegroup.owl
+
+db/hgnc.genegroup.owl: download/hgnc.genegroup.owl
+	cp $< $@
+
+
+download/hgnc.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc/2022-06-01/hgnc.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/hgnc.owl
+
+db/hgnc.owl: download/hgnc.owl
+	cp $< $@
+
+
+download/dictybase.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/dictybase/dictybase.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/dictybase.owl
+
+db/dictybase.owl: download/dictybase.owl
+	cp $< $@
+
+
+download/eccode.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/eccode/25-May-2022/eccode.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/eccode.owl
+
+db/eccode.owl: download/eccode.owl
+	cp $< $@
+
+
+download/uniprot.owl: STAMP
+	curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/uniprot/2022_02/uniprot.owl.gz | gzip -dc > $@.tmp
+	sha256sum -b $@.tmp > $@.sha256
+	mv $@.tmp $@
+
+.PRECIOUS: download/uniprot.owl
+
+db/uniprot.owl: download/uniprot.owl
+	cp $< $@
+
+
 download/%.owl: STAMP
 	curl -L -s http://purl.obolibrary.org/obo/$*.owl > $@.tmp
 	sha256sum -b $@.tmp > $@.sha256
@@ -316,4 +371,4 @@ download/%.owl: STAMP
 db/%.owl: download/%.owl
 	robot merge -i $< -o $@
 
-EXTRA_ONTOLOGIES = chiro ncit foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324
+EXTRA_ONTOLOGIES = chiro ncit foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot
diff --git a/src/semsql/builder/builder.py b/src/semsql/builder/builder.py
@@ -13,7 +13,7 @@
 
 from semsql.builder.registry import registry_schema
 from semsql.builder.registry.registry_schema import (Makefile, MakefileRule,
-                                                     Ontology)
+                                                     Ontology, CompressionEnum)
 from semsql.utils.makefile_utils import makefile_to_string
 
 this_path = Path(__file__).parent
@@ -137,6 +137,11 @@ def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> st
                 "unzip -p [email protected] {ont.zip_extract_file} "
                 "> [email protected] && rm [email protected]"
             )
+        elif ont.compression:
+            if str(ont.compression) == str(CompressionEnum.gzip.text):
+                command = f"curl -L -s {ont.url} | gzip -dc > [email protected]"
+            else:
+                raise ValueError(f"Unknown compression: '{ont.compression}'")
         else:
             command = f"curl -L -s {ont.url} > [email protected]"
         download_rule = MakefileRule(

diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv
@@ -59,6 +59,12 @@ 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#
 co_324,https://cropontology.org/rdf/CO_324:
+hgnc.genegroup,http://purl.obolibrary.org/obo/hgnc.genegroup_
+hgnc,http://purl.obolibrary.org/obo/hgnc_
+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_
 RBO,http://purl.obolibrary.org/obo/RBO_
 CLYH,http://purl.obolibrary.org/obo/CLYH_
 RO,http://purl.obolibrary.org/obo/RO_

diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv
@@ -7,3 +7,9 @@ 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#
 co_324,https://cropontology.org/rdf/CO_324:
+hgnc.genegroup,http://purl.obolibrary.org/obo/hgnc.genegroup_
+hgnc,http://purl.obolibrary.org/obo/hgnc_
+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_
diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml
@@ -110,5 +110,32 @@ ontologies:
     url: https://cropontology.org/ontology/CO_324/rdf
     prefixmap:
       co_324: "https://cropontology.org/rdf/CO_324:"
-
-
+
+## PyOBO products      
+## See https://github.com/INCATools/semantic-sql/issues/45
+  hgnc.genegroup:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc.genegroup/hgnc.genegroup.owl.gz
+    compression: gzip
+    prefixmap:
+      hgnc.genegroup: http://purl.obolibrary.org/obo/hgnc.genegroup_
+  hgnc:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/hgnc/2022-06-01/hgnc.owl.gz
+    compression: gzip
+    prefixmap:
+      hgnc: http://purl.obolibrary.org/obo/hgnc_
+  dictybase:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/dictybase/dictybase.owl.gz
+    compression: gzip
+    prefixmap:
+      hgnc.genegroup: http://purl.obolibrary.org/obo/dictybase_
+  eccode:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/eccode/25-May-2022/eccode.owl.gz
+    compression: gzip
+    prefixmap:
+      EC: http://purl.obolibrary.org/obo/eccode_
+      uniprot.obo: http://purl.obolibrary.org/obo/uniprot_
+  uniprot:
+    url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/uniprot/2022_02/uniprot.owl.gz
+    compression: gzip
+    prefixmap:
+      uniprot.obo: http://purl.obolibrary.org/obo/uniprot_