Add new sources for CiVIC Gene and OMIM Phenotypic series (#176)

src/pyobo/getters.py

@@ -117,7 +117,7 @@ def get_ontology(
 
     ontology_format, path = _ensure_ontology_path(prefix, force=force, version=version)
     if path is None:
-        raise NoBuild
+        raise NoBuild(prefix)
     elif ontology_format == "obo":
         pass  # all gucci
     elif ontology_format == "owl":

src/pyobo/sources/__init__.py

@@ -8,6 +8,7 @@
 from .ccle import CCLEGetter
 from .cgnc import CGNCGetter
 from .chembl import ChEMBLCompoundGetter
+from .civic_gene import CIVICGeneGetter
 from .complexportal import ComplexPortalGetter
 from .conso import CONSOGetter
 from .cpt import CPTGetter
@@ -38,6 +39,7 @@
 from .msigdb import MSigDBGetter
 from .ncbigene import NCBIGeneGetter
 from .npass import NPASSGetter
+from .omim_ps import OMIMPSGetter
 from .pathbank import PathBankGetter
 from .pfam import PfamGetter
 from .pfam_clan import PfamClanGetter
@@ -61,6 +63,7 @@
     "AntibodyRegistryGetter",
     "CCLEGetter",
     "CGNCGetter",
+    "CIVICGeneGetter",
     "CONSOGetter",
     "CPTGetter",
     "CVXGetter",
@@ -94,6 +97,7 @@
     "MiRBaseMatureGetter",
     "NCBIGeneGetter",
     "NPASSGetter",
+    "OMIMPSGetter",
     "PIDGetter",
     "PathBankGetter",
     "PfamClanGetter",

src/pyobo/sources/civic_gene.py

@@ -0,0 +1,55 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for CiVIC Genes."""
+
+from typing import Iterable, Optional
+
+import pandas as pd
+
+from pyobo.struct import Obo, Reference, Term
+from pyobo.utils.path import ensure_df
+
+__all__ = [
+    "CIVICGeneGetter",
+]
+
+PREFIX = "civic.gid"
+URL = "https://civicdb.org/downloads/nightly/nightly-GeneSummaries.tsv"
+
+
+def _sort(_o, t):
+    return int(t.identifier)
+
+
+class CIVICGeneGetter(Obo):
+    """An ontology representation of CiVIC's gene nomenclature."""
+
+    bioversions_key = ontology = PREFIX
+    term_sort_key = _sort
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over gene terms for CiVIC."""
+        yield from get_terms(self.data_version, force=force)
+
+
+def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Term]:
+    """Get CIVIC terms."""
+    # if version is not None:
+    #     version_dt: datetime.date = dateutil.parser.parse(version)
+    # else:
+    #     version_dt: datetime.date = datetime.today()
+    # version = version_dt.strftime("01-%b-%Y")
+    # version is like 01-Feb-2024
+    url = f"https://civicdb.org/downloads/{version}/{version}-GeneSummaries.tsv"
+    df = ensure_df(prefix=PREFIX, url=url, sep="\t", force=force, dtype=str, version=version)
+    for identifier, _, name, entrez_id, description, _last_review, _flag in df.values:
+        term = Term(
+            reference=Reference(prefix=PREFIX, identifier=identifier, name=name),
+            definition=description if pd.notna(description) else None,
+        )
+        term.append_exact_match(Reference(prefix="ncbigene", identifier=entrez_id))
+        yield term
+
+
+if __name__ == "__main__":
+    CIVICGeneGetter.cli()

src/pyobo/sources/omim_ps.py

@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for OMIM Phenotypic Series."""
+
+import logging
+from typing import Iterable
+
+from bioversions.utils import get_soup
+
+from pyobo.struct import Obo, Term
+
+__all__ = [
+    "OMIMPSGetter",
+]
+
+
+logger = logging.getLogger(__name__)
+PREFIX = "omim.ps"
+URL = "https://omim.org/phenotypicSeriesTitles/all"
+
+
+class OMIMPSGetter(Obo):
+    """An ontology representation of OMIM Phenotypic Series."""
+
+    ontology = bioversions_key = PREFIX
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        soup = get_soup(URL, user_agent="Mozilla/5.0")
+        rows = soup.find(id="mimContent").find("table").find("tbody").find_all("tr")
+        for row in rows:
+            anchor = row.find("td").find("a")
+            name = anchor.text.strip()
+            identifier = anchor.attrs["href"][len("/phenotypicSeries/") :]
+            yield Term.from_triple(PREFIX, identifier, name)
+
+
+if __name__ == "__main__":
+    OMIMPSGetter.cli()

src/pyobo/xrefdb/sources/wikidata.py

@@ -24,7 +24,7 @@
 #: WikiData SPARQL endpoint. See https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service#Interfacing
 URL = "https://query.wikidata.org/bigdata/namespace/wdq/sparql"
 
-WIKIDATA_MAPPING_DIRECTORY = RAW_MODULE.submodule("wikidata", "mappings")
+WIKIDATA_MAPPING_DIRECTORY = RAW_MODULE.module("wikidata", "mappings")
 
 
 def get_wikidata_xrefs_df(*, use_tqdm: bool = True) -> pd.DataFrame: