Add get_cancer_genes

graphkb/genes.py

@@ -4,6 +4,7 @@
 from . import GraphKBConnection
 from .constants import (
     BASE_THERAPEUTIC_TERMS,
+    CANCER_GENE,
     CHROMOSOMES,
     FAILED_REVIEW_STATUS,
     GENE_RETURN_PROPERTIES,
@@ -12,6 +13,7 @@
     PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST,
     PREFERRED_GENE_SOURCE,
     RELEVANCE_BASE_TERMS,
+    TSO500_SOURCE_NAME,
     TUMOUR_SUPPRESSIVE,
 )
 from .match import get_equivalent_features
@@ -78,6 +80,18 @@ def get_oncokb_tumour_supressors(conn: GraphKBConnection) -> List[Ontology]:
     return _get_tumourigenesis_genes_list(conn, TUMOUR_SUPPRESSIVE, [ONCOKB_SOURCE_NAME])
 
 
+def get_cancer_genes(conn: GraphKBConnection) -> List[Ontology]:
+    """Get the list of cancer genes stored in GraphKB derived from OncoKB & TSO500.
+
+    Args:
+        conn: the graphkb connection object
+
+    Returns:
+        gene (Feature) records
+    """
+    return _get_tumourigenesis_genes_list(conn, CANCER_GENE, [ONCOKB_SOURCE_NAME, TSO500_SOURCE_NAME])
+
+
 def get_therapeutic_associated_genes(graphkb_conn: GraphKBConnection) -> List[Ontology]:
     """Genes related to a cancer-associated statement in Graphkb."""
     therapeutic_relevance = get_terms_set(graphkb_conn, BASE_THERAPEUTIC_TERMS)