Update exact matches

biopragmatics · Oct 30, 2023 · 81d971f · 81d971f
1 parent f34041d
commit 81d971f
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Showing 4 changed files with 10 additions and 8 deletions.
diff --git a/src/pyobo/sources/depmap.py b/src/pyobo/sources/depmap.py
@@ -84,9 +84,9 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
                     continue
                 term.append_synonym(alias)
         if pd.notna(cosmic_id):
-            term.append_xref(Reference(prefix="cosmic.cell", identifier=cosmic_id))
+            term.append_exact_match(Reference(prefix="cosmic.cell", identifier=cosmic_id))
         if pd.notna(cellosaurus_id):
-            term.append_xref(Reference(prefix="cellosaurus", identifier=cellosaurus_id))
+            term.append_exact_match(Reference(prefix="cellosaurus", identifier=cellosaurus_id))
 
         # WTSI stands for welcome trust sanger institute
         # Not sure where this prefix goes

diff --git a/src/pyobo/sources/mgi.py b/src/pyobo/sources/mgi.py
@@ -161,7 +161,9 @@ def get_terms(force: bool = False) -> Iterable[Term]:
             for synonym in mgi_to_synonyms[identifier]:
                 term.append_synonym(Synonym(name=synonym))
         if identifier in mgi_to_entrez_id:
-            term.append_xref(Reference(prefix="ncbigene", identifier=mgi_to_entrez_id[identifier]))
+            term.append_exact_match(
+                Reference(prefix="ncbigene", identifier=mgi_to_entrez_id[identifier])
+            )
         for ensembl_id in mgi_to_ensemble_accession_ids[identifier]:
             term.append_xref(Reference(prefix="ensembl", identifier=ensembl_id))
         for ensembl_id in mgi_to_ensemble_transcript_ids[identifier]:

diff --git a/src/pyobo/sources/slm.py b/src/pyobo/sources/slm.py
@@ -107,13 +107,13 @@ def iter_terms(version: str, force: bool = False):
         if pd.notna(inchikey):
             if inchikey.startswith("InChIKey="):
                 inchikey = inchikey[len("InChIKey=") :]
-            term.append_xref(Reference(prefix="inchikey", identifier=inchikey))
+            term.append_exact_match(Reference(prefix="inchikey", identifier=inchikey))
         if pd.notna(chebi_id):
-            term.append_xref(("chebi", chebi_id))
+            term.append_exact_match(("chebi", chebi_id))
         if pd.notna(lipidmaps_id):
-            term.append_xref(("lipidmaps", lipidmaps_id))
+            term.append_exact_match(("lipidmaps", lipidmaps_id))
         if pd.notna(hmdb_id):
-            term.append_xref(("hmdb", hmdb_id))
+            term.append_exact_match(("hmdb", hmdb_id))
         if pd.notna(pmids):
             for pmid in pmids.split("|"):
                 term.append_provenance(("pubmed", pmid))

diff --git a/src/pyobo/sources/zfin.py b/src/pyobo/sources/zfin.py
@@ -135,7 +135,7 @@ def get_terms(force: bool = False, version: Optional[str] = None) -> Iterable[Te
             term.append_alt(alt_id)
         entrez_id = entrez_mappings.get(identifier)
         if entrez_id:
-            term.append_xref(Reference(prefix="ncbigene", identifier=entrez_id))
+            term.append_exact_match(Reference(prefix="ncbigene", identifier=entrez_id))
         for uniprot_id in uniprot_mappings.get(identifier, []):
             term.append_relationship(has_gene_product, Reference.auto("uniprot", uniprot_id))
         for hgnc_id in human_orthologs.get(identifier, []):