Generalize is_metadata_tag (#520)

From the OBO data model, this is just a boolean. This PR generalizes the
TypeDef object to keep track of an enumeration of the three
possibilities (annotation, data, or object) for properties.

This also makes much nicer i/o with OFN and OBO Graphs

Author: cthoyt

src/pyobo/constants.py

@@ -28,6 +28,7 @@
     "OntologyFormat",
     "OntologyPathPack",
     "SlimGetOntologyKwargs",
+    "TypeDefType",
     "check_should_cache",
     "check_should_force",
     "check_should_use_tqdm",
@@ -319,3 +320,7 @@ def get_semantic_mapping_metadata(
         confidence=confidence,
         version=version,
     )
+
+
+#: The type of a typedef.
+TypeDefType = Literal["object", "annotation", "data"]

src/pyobo/sources/civic_gene.py

@@ -20,8 +20,8 @@
 FACTOR = Term(reference=default_reference(PREFIX, "factor", name="factor"))
 FUSION = Term(reference=default_reference(PREFIX, "fusion", name="fusion"))
 REGION = Term(reference=default_reference(PREFIX, "region", name="region"))
-HAS_3P = TypeDef.default(PREFIX, "has3p", name="has 3' gene", is_metadata_tag=False)
-HAS_5P = TypeDef.default(PREFIX, "has5p", name="has 5' gene", is_metadata_tag=False)
+HAS_3P = TypeDef.default(PREFIX, "has3p", name="has 3' gene", predicate_type="object")
+HAS_5P = TypeDef.default(PREFIX, "has5p", name="has 5' gene", predicate_type="object")
 
 TYPES = {
     "Gene": GENE,

src/pyobo/sources/clinicaltrials.py

@@ -19,13 +19,13 @@
     reference=default_reference(
         prefix=PREFIX, identifier="investigates_condition", name="investigates condition"
     ),
-    is_metadata_tag=True,
+    predicate_type="annotation",
 )
 HAS_INTERVENTION = TypeDef(
     reference=default_reference(
         prefix=PREFIX, identifier="has_intervention", name="has intervention"
     ),
-    is_metadata_tag=True,
+    predicate_type="annotation",
 )
 
 INVESTIGATION_TERM = Term(

src/pyobo/sources/cvx.py

@@ -16,9 +16,9 @@
 cvx_url = "https://www2a.cdc.gov/vaccines/iis/iisstandards/downloads/cvx.txt"
 PREFIX = "cvx"
 STATUS = TypeDef(
-    reference=default_reference(PREFIX, "status", name="has status"), is_metadata_tag=True
+    reference=default_reference(PREFIX, "status", name="has status"), predicate_type="annotation"
 )
-NONVACCINE = TypeDef(reference=default_reference(PREFIX, "nonvaccine"), is_metadata_tag=True)
+NONVACCINE = TypeDef(reference=default_reference(PREFIX, "nonvaccine"), predicate_type="annotation")
 
 ACRONYM_RE = re.compile("^[A-Z]+$")
 

src/pyobo/sources/geonames/utils.py

@@ -33,7 +33,8 @@
 
 # Type definitions
 CODE_TYPEDEF = TypeDef(
-    reference=default_reference(PREFIX, "code", name="GeoNames code"), is_metadata_tag=True
+    reference=default_reference(PREFIX, "code", name="GeoNames code"),
+    predicate_type="annotation",
 )
 
 SYNONYMS_DF_COLUMNS = [

src/pyobo/sources/goldbook.py

@@ -18,7 +18,7 @@
 URL = "https://goldbook.iupac.org/terms/index/all/json/download"
 TERM_URL_FORMAT = "https://goldbook.iupac.org/terms/view/{}/json"
 
-HAS_STATUS = TypeDef(reference=default_reference(PREFIX, "hasStatus"), is_metadata_tag=True)
+HAS_STATUS = TypeDef(reference=default_reference(PREFIX, "hasStatus"), predicate_type="annotation")
 
 
 class GoldBookGetter(Obo):

src/pyobo/sources/iana_media_type.py

@@ -66,7 +66,7 @@ def _get_mimetypes() -> dict[str, dict[str, Any]]:
     domain=ROOT_MEDIA_TYPE.reference,
     range=ROOT_FILE_FORMAT.reference,
     definition="Connects a media type with a file format that has been observed to encode it",
-    is_metadata_tag=True,
+    predicate_type="annotation",
 )
 
 

src/pyobo/sources/icd/icd11.py

@@ -34,7 +34,9 @@
 PREFIX = "icd11"
 CODE_PREFIX = "icd11.code"
 
-CODE_PROP = TypeDef(reference=default_reference(PREFIX, "icd_mms_code"), is_metadata_tag=True)
+CODE_PROP = TypeDef(
+    reference=default_reference(PREFIX, "icd_mms_code"), predicate_type="annotation"
+)
 
 
 class ICD11Getter(Obo):

src/pyobo/sources/msigdb.py

@@ -20,14 +20,20 @@
 PREFIX = "msigdb"
 BASE_URL = "https://data.broadinstitute.org/gsea-msigdb/msigdb/release"
 
-CATEGORY_CODE = TypeDef.default(PREFIX, "category_code", name="category code", is_metadata_tag=True)
+CATEGORY_CODE = TypeDef.default(
+    PREFIX, "category_code", name="category code", predicate_type="annotation"
+)
 SUB_CATEGORY_CODE = TypeDef.default(
-    PREFIX, "sub_category_code", name="sub-category code", is_metadata_tag=True
+    PREFIX, "sub_category_code", name="sub-category code", predicate_type="annotation"
+)
+CONTRIBUTOR = TypeDef.default(
+    PREFIX, "contributor", name="contributor", predicate_type="annotation"
+)
+EXACT_SOURCE = TypeDef.default(
+    PREFIX, "exact_source", name="exact source", predicate_type="annotation"
 )
-CONTRIBUTOR = TypeDef.default(PREFIX, "contributor", name="contributor", is_metadata_tag=True)
-EXACT_SOURCE = TypeDef.default(PREFIX, "exact_source", name="exact source", is_metadata_tag=True)
 EXTERNAL_DETAILS_URL = TypeDef.default(
-    PREFIX, "external_details_url", name="external details URL", is_metadata_tag=True
+    PREFIX, "external_details_url", name="external details URL", predicate_type="annotation"
 )
 
 PROPERTIES = [

src/pyobo/sources/pharmgkb/pharmgkb_variant.py

@@ -16,7 +16,7 @@
 
 
 HAS_GENE_ASSOCIATION = TypeDef.default(
-    PREFIX, "hasGeneAssociation", name="has gene association", is_metadata_tag=True
+    PREFIX, "hasGeneAssociation", name="has gene association", predicate_type="annotation"
 )