ito

Author: cmungall

ontologies.Makefile

@@ -31,6 +31,9 @@ db/enanomapper.owl: STAMP
 db/mlo.owl: STAMP
 	robot merge -I https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl -o $@
 
+db/ito.owl: STAMP
+	curl -L -s https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip > $@.tmp && unzip -p $@.tmp ITO.owl > $@.tmp2 && mv $@.tmp2 $@ && rm $@.tmp
+
 db/efo.owl: STAMP
 	robot merge -I http://www.ebi.ac.uk/efo/efo.owl -o $@
 
@@ -52,4 +55,4 @@ db/cosmo.owl: STAMP
 db/co_324.owl: STAMP
 	curl -L -s https://cropontology.org/ontology/CO_324/rdf > $@.tmp && mv $@.tmp $@
 
-EXTRA_ONTOLOGIES = msio phenio bero aio reacto go-lego bao biolink biopax enanomapper mlo efo edam sweetAll lov schema-dot-org cosmo co_324
+EXTRA_ONTOLOGIES = msio phenio bero aio reacto go-lego bao biolink biopax enanomapper mlo ito efo edam sweetAll lov schema-dot-org cosmo co_324

src/semsql/builder/builder.py

@@ -125,7 +125,9 @@ def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> st
     for ont in registry.ontologies.values():
         target = f"db/{ont.id}.owl"
         dependencies = ["STAMP"]
-        if ont.has_imports or (ont.format and ont.format != 'rdfxml'):
+        if ont.zip_extract_file:
+            command = f"curl -L -s {ont.url} > [email protected] && unzip -p [email protected] {ont.zip_extract_file} > [email protected] && mv [email protected] $@ && rm [email protected]"
+        elif ont.has_imports or (ont.format and ont.format != 'rdfxml'):
             command = f"robot merge -I {ont.url} -o $@"
         else:
             command = f"curl -L -s {ont.url} > [email protected] && mv [email protected] $@"

src/semsql/builder/registry/ontologies.yaml

@@ -46,6 +46,9 @@ ontologies:
     has_imports: true
     prefixmap:
       mlo: http://www.a2rd.net.br/mlo#
+  ito:
+    url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip
+    zip_extract_file: ITO.owl
   efo:
     url: http://www.ebi.ac.uk/efo/efo.owl
     has_imports: true

src/semsql/builder/registry/registry_schema.py

@@ -1,5 +1,5 @@
 # Auto generated from registry_schema.yaml by pythongen.py version: 0.9.0
-# Generation date: 2022-10-15T14:23:31
+# Generation date: 2022-10-18T18:20:11
 # Schema: ontology_registry
 #
 # id: https://w3id.org/semsql/registry
@@ -93,6 +93,7 @@ class Ontology(YAMLRoot):
     compression: Optional[Union[str, "CompressionEnum"]] = None
     suppress: Optional[Union[bool, Bool]] = None
     relation_graph_settings: Optional[Union[dict, "RelationGraphConfiguration"]] = None
+    zip_extract_file: Optional[str] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -130,6 +131,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.relation_graph_settings is not None and not isinstance(self.relation_graph_settings, RelationGraphConfiguration):
             self.relation_graph_settings = RelationGraphConfiguration(**as_dict(self.relation_graph_settings))
 
+        if self.zip_extract_file is not None and not isinstance(self.zip_extract_file, str):
+            self.zip_extract_file = str(self.zip_extract_file)
+
         super().__post_init__(**kwargs)
 
 
@@ -251,6 +255,9 @@ class slots:
 slots.prefixmap = Slot(uri=SEMSQL_REGISTRY.prefixmap, name="prefixmap", curie=SEMSQL_REGISTRY.curie('prefixmap'),
                    model_uri=SEMSQL_REGISTRY.prefixmap, domain=None, range=Optional[Union[Dict[Union[str, PrefixMapPrefix], Union[dict, PrefixMap]], List[Union[dict, PrefixMap]]]])
 
+slots.zip_extract_file = Slot(uri=SEMSQL_REGISTRY.zip_extract_file, name="zip_extract_file", curie=SEMSQL_REGISTRY.curie('zip_extract_file'),
+                   model_uri=SEMSQL_REGISTRY.zip_extract_file, domain=None, range=Optional[str])
+
 slots.named_prefixmaps = Slot(uri=SEMSQL_REGISTRY.named_prefixmaps, name="named_prefixmaps", curie=SEMSQL_REGISTRY.curie('named_prefixmaps'),
                    model_uri=SEMSQL_REGISTRY.named_prefixmaps, domain=None, range=Optional[Union[str, List[str]]])
 

src/semsql/builder/registry/registry_schema.yaml

@@ -53,6 +53,8 @@ slots:
     multivalued: true
     range: PrefixMap
     inlined: true
+  zip_extract_file:
+    description: file to extract in a zip download
   named_prefixmaps:
     examples:
     - value: '[''sweet'', ''prefixcc'']'
@@ -105,6 +107,7 @@ classes:
     - compression
     - suppress
     - relation_graph_settings
+    - zip_extract_file
   PrefixMap:
     slots:
     - prefix