relation-graph config.

additional ontologies

Author: cmungall

ontologies.Makefile

@@ -2,7 +2,7 @@ db/msio.owl: STAMP
 	curl -L -s https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl > $@.tmp && mv $@.tmp $@
 
 db/phenio.owl: STAMP
-	curl -L -s https://github.com/monarch-initiative/phenio/releases/download/latest/phenio.owl > $@.tmp && mv $@.tmp $@
+	curl -L -s https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl > $@.tmp && mv $@.tmp $@
 
 db/bero.owl: STAMP
 	curl -L -s https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl > $@.tmp && mv $@.tmp $@
@@ -28,6 +28,9 @@ db/biopax.owl: STAMP
 db/enanomapper.owl: STAMP
 	robot merge -I http://enanomapper.github.io/ontologies/enanomapper.owl -o $@
 
+db/mlo.owl: STAMP
+	robot merge -I https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/external/ml-ontology-202010021305.owl -o $@
+
 db/efo.owl: STAMP
 	robot merge -I http://www.ebi.ac.uk/efo/efo.owl -o $@
 
@@ -49,4 +52,4 @@ 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 efo edam sweetAll lov schema-dot-org cosmo co_324
+EXTRA_ONTOLOGIES = msio phenio bero aio reacto go-lego bao biolink biopax enanomapper mlo efo edam sweetAll lov schema-dot-org cosmo co_324

src/semsql/builder/build.Makefile

@@ -40,7 +40,10 @@ $(TEMPLATE): $(THIS_DIR)/sql_schema/semsql.sql build_prefixes
 .PRECIOUS: $(TEMPLATE)
 
 %-min.owl: %.owl
-	robot remove -i $< --axioms "equivalent disjoint annotation" -o $@
+	robot \
+	  remove -i $< --axioms "equivalent disjoint annotation" \
+	  filter --exclude-terms $(THIS_DIR)/exclude-terms.txt \
+	  -o $@
 
 # -- MAIN TARGET --
 # A db is constructed from
@@ -65,9 +68,10 @@ $(TEMPLATE): $(THIS_DIR)/sql_schema/semsql.sql build_prefixes
 # will be simplified in future. See:
 #  - https://github.com/balhoff/relation-graph/issues/123
 #  - https://github.com/balhoff/relation-graph/issues/25
-%-$(RGSUFFIX).tsv: %-min.owl
+%-$(RGSUFFIX).tsv: %-min.owl %-properties.txt
 	$(RG) --disable-owl-nothing true \
                        --ontology-file $<\
+		       $(RG_PROPERTIES) \
                        --output-file [email protected] \
                        --equivalence-as-subclass true \
 	               --output-individuals true \
@@ -81,6 +85,9 @@ $(TEMPLATE): $(THIS_DIR)/sql_schema/semsql.sql build_prefixes
 	rm $@.*.tmp
 .PRECIOUS: %-$(RGSUFFIX).tsv
 
+%-properties.txt:
+	touch $@
+
 # ---
 # Prefixes
 # ---

src/semsql/builder/builder.py

@@ -85,6 +85,7 @@ def download_obo_sqlite(ontology: str, destination: str):
     """
     db = f"{ontology}.db"
     url = f"https://s3.amazonaws.com/bbop-sqlite/{db}.gz"
+    logging.info(f"Downloading from {url}")
     r = requests.get(url, allow_redirects=True)
     destination_gzip = f"{destination}.gz"
     open(destination_gzip, "wb").write(r.content)

src/semsql/builder/exclude-terms.txt

@@ -0,0 +1,23 @@
+RO:0002222
+RO:0002244
+RO:0002320
+RO:0002321
+RO:0002323
+RO:0002324
+RO:0002330
+RO:0002337
+RO:0002375
+RO:0002410
+RO:0002487
+RO:0002501
+RO:0002506
+RO:0002514
+RO:0002567
+RO:0002595
+RO:0002609
+RO:0002616
+RO:0004000
+RO:0004010
+RO:0004023
+RO:0016001
+RO:0040035

src/semsql/builder/prefixes/prefixes.csv

@@ -49,6 +49,13 @@ wikidata,http://www.wikidata.org/entity/
 schema,https://schema.org/
 ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/
 ICD10WHO,https://icd.who.int/browse10/2019/en#/
+prefix,base
+MSIO,http://purl.obolibrary.org/obo/MSIO_
+nmrCV,http://nmrML.org/nmrCV#NMR:
+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:
 RBO,http://purl.obolibrary.org/obo/RBO_
 CLYH,http://purl.obolibrary.org/obo/CLYH_
 RO,http://purl.obolibrary.org/obo/RO_

src/semsql/builder/prefixes/prefixes_local.csv

@@ -3,4 +3,5 @@ MSIO,http://purl.obolibrary.org/obo/MSIO_
 nmrCV,http://nmrML.org/nmrCV#NMR:
 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:

src/semsql/builder/registry/ontologies.yaml

@@ -9,7 +9,14 @@ ontologies:
       nmrCV: "http://nmrML.org/nmrCV#NMR:"
   phenio:
     description: Monarch Phenomics Integrated Ontology
-    url: https://github.com/monarch-initiative/phenio/releases/download/latest/phenio.owl
+    url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio.owl
+    relation_graph_settings:
+      properties:
+        - BFO:0000050
+        - BFO:0000051
+        - UPHENO:0000001
+        - UPHENO:0000003
+        - RO:0002202
   bero:
     url: https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl
   aio:

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: 2022-09-17T15:44:28
+# Generation date: 2022-10-15T14:23:31
 # Schema: ontology_registry
 #
 # id: https://w3id.org/semsql/registry
@@ -22,8 +22,8 @@
 from linkml_runtime.utils.enumerations import EnumDefinitionImpl
 from rdflib import Namespace, URIRef
 from linkml_runtime.utils.curienamespace import CurieNamespace
-from linkml_runtime.linkml_model.types import Boolean, Integer, String
-from linkml_runtime.utils.metamodelcore import Bool
+from linkml_runtime.linkml_model.types import Boolean, Integer, String, Uriorcurie
+from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE
 
 metamodel_version = "1.7.0"
 version = None
@@ -92,6 +92,7 @@ class Ontology(YAMLRoot):
     format: Optional[str] = None
     compression: Optional[Union[str, "CompressionEnum"]] = None
     suppress: Optional[Union[bool, Bool]] = None
+    relation_graph_settings: Optional[Union[dict, "RelationGraphConfiguration"]] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):
@@ -126,6 +127,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.suppress is not None and not isinstance(self.suppress, Bool):
             self.suppress = Bool(self.suppress)
 
+        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))
+
         super().__post_init__(**kwargs)
 
 
@@ -184,6 +188,25 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
+@dataclass
+class RelationGraphConfiguration(YAMLRoot):
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.RelationGraphConfiguration
+    class_class_curie: ClassVar[str] = "semsql_registry:RelationGraphConfiguration"
+    class_name: ClassVar[str] = "RelationGraphConfiguration"
+    class_model_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.RelationGraphConfiguration
+
+    properties: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = empty_list()
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        if not isinstance(self.properties, list):
+            self.properties = [self.properties] if self.properties is not None else []
+        self.properties = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.properties]
+
+        super().__post_init__(**kwargs)
+
+
 # Enumerations
 class FormatEnum(EnumDefinitionImpl):
 
@@ -207,14 +230,17 @@ class CompressionEnum(EnumDefinitionImpl):
 class slots:
     pass
 
+slots.id = Slot(uri=SEMSQL_REGISTRY.id, name="id", curie=SEMSQL_REGISTRY.curie('id'),
+                   model_uri=SEMSQL_REGISTRY.id, domain=None, range=URIRef)
+
 slots.description = Slot(uri=SEMSQL_REGISTRY.description, name="description", curie=SEMSQL_REGISTRY.curie('description'),
                    model_uri=SEMSQL_REGISTRY.description, domain=None, range=Optional[str])
 
 slots.url = Slot(uri=SEMSQL_REGISTRY.url, name="url", curie=SEMSQL_REGISTRY.curie('url'),
                    model_uri=SEMSQL_REGISTRY.url, domain=None, range=Optional[Union[str, Identifier]])
 
-slots.id = Slot(uri=SEMSQL_REGISTRY.id, name="id", curie=SEMSQL_REGISTRY.curie('id'),
-                   model_uri=SEMSQL_REGISTRY.id, domain=None, range=URIRef)
+slots.relation_graph_settings = Slot(uri=SEMSQL_REGISTRY.relation_graph_settings, name="relation_graph_settings", curie=SEMSQL_REGISTRY.curie('relation_graph_settings'),
+                   model_uri=SEMSQL_REGISTRY.relation_graph_settings, domain=None, range=Optional[Union[dict, RelationGraphConfiguration]])
 
 slots.has_imports = Slot(uri=SEMSQL_REGISTRY.has_imports, name="has_imports", curie=SEMSQL_REGISTRY.curie('has_imports'),
                    model_uri=SEMSQL_REGISTRY.has_imports, domain=None, range=Optional[int])
@@ -248,3 +274,6 @@ class slots:
 
 slots.suppress = Slot(uri=SEMSQL_REGISTRY.suppress, name="suppress", curie=SEMSQL_REGISTRY.curie('suppress'),
                    model_uri=SEMSQL_REGISTRY.suppress, domain=None, range=Optional[Union[bool, Bool]])
+
+slots.relationGraphConfiguration__properties = Slot(uri=SEMSQL_REGISTRY.properties, name="relationGraphConfiguration__properties", curie=SEMSQL_REGISTRY.curie('properties'),
+                   model_uri=SEMSQL_REGISTRY.relationGraphConfiguration__properties, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]])

src/semsql/builder/registry/registry_schema.yaml

@@ -24,6 +24,11 @@ enums:
       gzip:
         description: gzip
 slots:
+  id:
+    examples:
+    - value: lov
+    identifier: true
+    range: string
   description:
     examples:
     - value: Monarch Phenomics Integrated Ontology
@@ -32,11 +37,8 @@ slots:
     examples:
     - value: https://lov.linkeddata.es/lov.n3.gz
     range: identifier
-  id:
-    examples:
-    - value: lov
-    identifier: true
-    range: string
+  relation_graph_settings:
+    range: RelationGraphConfiguration
   has_imports:
     examples:
     - value: 'True'
@@ -102,6 +104,7 @@ classes:
     - format
     - compression
     - suppress
+    - relation_graph_settings
   PrefixMap:
     slots:
     - prefix
@@ -113,4 +116,8 @@ classes:
     - license
     - ontologies
     tree_root: true
-
+  RelationGraphConfiguration:
+    attributes:
+      properties:
+        range: uriorcurie
+        multivalued: true