Improve HGNC export

src/pyobo/resources/so.py

@@ -21,6 +21,12 @@
 
 def get_so_name(so_id: str) -> str | None:
     """Get the name from the identifier."""
+    if so_id == "0003002":
+        # see https://github.com/The-Sequence-Ontology/SO-Ontologies/pull/668
+        return "viral integration site"
+    if so_id == "0003001":
+        # see https://github.com/The-Sequence-Ontology/SO-Ontologies/pull/667
+        return "cluster RNA gene"
     return load_so().get(so_id)
 
 

src/pyobo/sources/hgnc/hgnc.py

@@ -14,27 +14,25 @@
 
 from pyobo.api.utils import get_version
 from pyobo.resources.so import get_so_name
-from pyobo.struct import (
-    Annotation,
-    Obo,
-    OBOLiteral,
-    Reference,
-    Term,
-    from_species,
-    has_gene_product,
-    is_mentioned_by,
-    member_of,
-    orthologous,
-    transcribes_to,
-)
+from pyobo.sources.hgnc.hgncgenefamily import GENE_GROUP_PREFIX, get_gene_family_terms
+from pyobo.struct import Annotation, Obo, OBOLiteral, Reference, Term
 from pyobo.struct.struct import gene_symbol_synonym, previous_gene_symbol, previous_name
 from pyobo.struct.typedef import (
     comment,
+    enables,
     ends,
     exact_match,
+    from_species,
     gene_product_enables,
+    gene_product_of,
+    has_gene_product,
+    has_member,
+    is_mentioned_by,
     located_in,
+    member_of,
+    orthologous,
     starts,
+    transcribes_to,
 )
 from pyobo.utils.path import ensure_path
 
@@ -137,6 +135,7 @@
     "homeodb",  # TODO add to bioregistry, though this is defunct
     "mamit-trnadb",  # TODO add to bioregistry, though this is defunct
     "mane_select",  # TODO
+    "gene_group",  # gene_group_id is needed, but this just has label
 }
 
 #: A mapping from HGNC's locus_type annotations to sequence ontology identifiers
@@ -195,8 +194,10 @@ class HGNCGetter(Obo):
     typedefs = [
         from_species,
         has_gene_product,
+        gene_product_of,
         gene_product_enables,
         transcribes_to,
+        has_member,
         orthologous,
         member_of,
         exact_match,
@@ -205,6 +206,7 @@ class HGNCGetter(Obo):
         starts,
         ends,
         comment,
+        enables,
     ]
     synonym_typedefs = [
         previous_name,
@@ -262,6 +264,8 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
         for so_id in sorted(_so_ids)
     ]
 
+    yield from get_gene_family_terms(version=version, force=force)
+
     statuses = set()
     for entry in tqdm(entries, desc=f"Mapping {PREFIX}", unit="gene", unit_scale=True):
         name, symbol, identifier = (
@@ -393,15 +397,10 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
             term.append_mentioned_by(Reference(prefix="pubmed", identifier=str(pubmed_id)))
 
         gene_group_ids = entry.pop("gene_group_id", [])
-        gene_groups = entry.pop("gene_group", [])
-        for gene_group_id, gene_group_label in zip(gene_group_ids, gene_groups, strict=False):
+        for gene_group_id in gene_group_ids:
             term.append_relationship(
                 member_of,
-                Reference(
-                    prefix="hgnc.genegroup",
-                    identifier=str(gene_group_id),
-                    name=gene_group_label,
-                ),
+                Reference(prefix=GENE_GROUP_PREFIX, identifier=str(gene_group_id)),
             )
 
         for alias_symbol in entry.pop("alias_symbol", []):

src/pyobo/sources/hgnc/hgncgenefamily.py

@@ -5,16 +5,20 @@
 
 import pandas as pd
 
-from ...struct import Obo, Reference, Term, is_mentioned_by
+from ...api.utils import get_version
+from ...struct.struct import Obo, Reference, Term
 from ...struct.struct import abbreviation as symbol_type
-from ...struct.typedef import enables, exact_match, from_species
+from ...struct.typedef import enables, exact_match, from_species, is_mentioned_by
 from ...utils.path import ensure_df
 
 __all__ = [
+    "GENE_GROUP_REFERENCE",
+    "GENE_GROUP_TERM",
     "HGNCGroupGetter",
+    "get_gene_family_terms",
 ]
 
-PREFIX = "hgnc.genegroup"
+GENE_GROUP_PREFIX = "hgnc.genegroup"
 FAMILIES_URL = "https://storage.googleapis.com/public-download-files/hgnc/csv/csv/genefamily_db_tables/family.csv"
 FAMILIES_ALIAS_URL = "https://storage.googleapis.com/public-download-files/hgnc/csv/csv/genefamily_db_tables/family_alias.csv"
 HIERARCHY_URL = "https://storage.googleapis.com/public-download-files/hgnc/csv/csv/genefamily_db_tables/hierarchy.csv"
@@ -23,19 +27,21 @@
 class HGNCGroupGetter(Obo):
     """An ontology representation of HGNC's gene group nomenclature."""
 
-    ontology = PREFIX
+    ontology = GENE_GROUP_PREFIX
     bioversions_key = "hgnc"
     synonym_typedefs = [symbol_type]
     typedefs = [from_species, enables, exact_match, is_mentioned_by]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        return get_terms(force=force)
+        return get_gene_family_terms(force=force)
 
 
-def get_hierarchy(force: bool = False) -> Mapping[str, list[str]]:
+def get_hierarchy(*, version: str | None = None, force: bool = False) -> Mapping[str, list[str]]:
     """Get the HGNC Gene Families hierarchy as a dictionary."""
-    df = ensure_df(PREFIX, url=HIERARCHY_URL, force=force, sep=",")
+    if version is None:
+        version = get_version("hgnc")
+    df = ensure_df(GENE_GROUP_PREFIX, url=HIERARCHY_URL, force=force, sep=",", version=version)
     d = defaultdict(list)
     for parent_id, child_id in df.values:
         d[child_id].append(parent_id)
@@ -44,51 +50,51 @@ def get_hierarchy(force: bool = False) -> Mapping[str, list[str]]:
 
 COLUMNS = ["id", "abbreviation", "name", "pubmed_ids", "desc_comment", "desc_go"]
 
+GENE_GROUP_REFERENCE = Reference(prefix="SO", identifier="0005855", name="gene group")
+GENE_GROUP_TERM = Term(reference=GENE_GROUP_REFERENCE)
 
-def get_terms(force: bool = False) -> Iterable[Term]:
+
+def get_gene_family_terms(*, version: str | None = None, force: bool = False) -> Iterable[Term]:
     """Get the HGNC Gene Group terms."""
-    terms = list(_get_terms_helper(force=force))
-    hierarchy = get_hierarchy(force=force)
+    if version is None:
+        version = get_version("hgnc")
+
+    terms = list(_get_terms_helper(force=force, version=version))
+    hierarchy = get_hierarchy(force=force, version=version)
 
-    id_to_term = {term.reference.identifier: term for term in terms}
+    id_to_term = {term.identifier: term for term in terms}
     for child_id, parent_ids in hierarchy.items():
         child: Term = id_to_term[child_id]
         for parent_id in parent_ids:
-            parent: Term = id_to_term[parent_id]
-            child.append_parent(
-                Reference(
-                    prefix=PREFIX,
-                    identifier=parent_id,
-                    name=parent.name,
-                )
-            )
-    gene_group = Reference(prefix="SO", identifier="0005855", name="gene group")
-    yield Term(reference=gene_group)
+            child.append_parent(id_to_term[parent_id])
+    yield GENE_GROUP_TERM
     for term in terms:
         if not term.parents:
-            term.append_parent(gene_group)
+            term.append_parent(GENE_GROUP_REFERENCE)
     yield from terms
 
 
-def _get_terms_helper(force: bool = False) -> Iterable[Term]:
-    alias_df = ensure_df(PREFIX, url=FAMILIES_ALIAS_URL, force=force, sep=",")
+def _get_terms_helper(version: str, force: bool = False) -> Iterable[Term]:
+    alias_df = ensure_df(
+        GENE_GROUP_PREFIX, url=FAMILIES_ALIAS_URL, force=force, sep=",", version=version
+    )
     aliases = defaultdict(set)
     for _id, family_id, alias in alias_df.values:
         aliases[family_id].add(alias)
 
-    df = ensure_df(PREFIX, url=FAMILIES_URL, force=force, sep=",")
+    df = ensure_df(GENE_GROUP_PREFIX, url=FAMILIES_URL, force=force, sep=",", version=version)
     for gene_group_id, symbol, name, pubmed_ids, definition, desc_go in df[COLUMNS].values:
         if not definition or pd.isna(definition):
             definition = None
         term = Term(
-            reference=Reference(prefix=PREFIX, identifier=gene_group_id, name=name),
+            reference=Reference(prefix=GENE_GROUP_PREFIX, identifier=gene_group_id, name=name),
             definition=definition,
         )
         if pubmed_ids and pd.notna(pubmed_ids):
-            for s in pubmed_ids.replace(" ", ",").split(","):
-                s = s.strip()
-                if s:
-                    term.append_mentioned_by(Reference(prefix="pubmed", identifier=s))
+            for pubmed_id in pubmed_ids.replace(" ", ",").split(","):
+                pubmed_id = pubmed_id.strip()
+                if pubmed_id:
+                    term.append_mentioned_by(Reference(prefix="pubmed", identifier=pubmed_id))
         if desc_go and pd.notna(desc_go):
             go_id = desc_go[len("http://purl.uniprot.org/go/") :]
             term.append_relationship(enables, Reference(prefix="GO", identifier=go_id))

src/pyobo/struct/typedef.py

@@ -55,6 +55,7 @@
     "is_antagonist_of",
     "is_defined_by",
     "is_inverse_agonist_of",
+    "is_mentioned_by",
     "located_in",
     "mapping_has_confidence",
     "mapping_has_justification",