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SDEV-4155 - switch to source.displayName for Pharmacogenomic filterin… #116

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SDEV-4155 - switch to source.displayName for Pharmacogenomic filterin… #116

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13ee76a
SDEV-4155 - switch to source.displayName for Pharmacogenomic filterin…
dustinbleile Feb 16, 2024
4594200
SDEV-4155 - PR - add get_pharmacogenomic_info GSC_PHARMACOGENOMIC_SOU…
dustinbleile Feb 16, 2024
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2 changes: 1 addition & 1 deletion graphkb/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@
CANCER_GENE = "cancer gene"
FUSION_NAMES = ["structural variant", "fusion"]

PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST = ["cancer genome interpreter", "civic"]
GSC_PHARMACOGENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST = ["CGI", "CIViC"]

BASE_THERAPEUTIC_TERMS = ["therapeutic efficacy", "eligibility"]
# the order here is the order these are applied, the first category matched is returned
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14 changes: 11 additions & 3 deletions graphkb/genes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
GENE_RETURN_PROPERTIES,
ONCOGENE,
ONCOKB_SOURCE_NAME,
PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST,
GSC_PHARMACOGENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST,
PREFERRED_GENE_SOURCE,
RELEVANCE_BASE_TERMS,
TSO500_SOURCE_NAME,
Expand Down Expand Up @@ -309,7 +309,9 @@ def get_cancer_predisposition_info(


def get_pharmacogenomic_info(
conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
conn: GraphKBConnection,
source: str = PREFERRED_GENE_SOURCE,
excluded_statement_sources: List[str]=GSC_PHARMACOGENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST
) -> Tuple[List[str], Dict[str, str]]:
"""
Return two lists from GraphKB, one of pharmacogenomic genes and one of associated variants.
Expand All @@ -323,6 +325,11 @@ def get_pharmacogenomic_info(

Example: https://graphkb.bcgsc.ca/view/Statement/154:9574

Args:
conn (GraphKBConnection): GraphKB connection object
source (str): Gene name source id - for form of gene name symbols used
excluded_statement_sources (List): List of displayNames for statement sources to exclude

Returns:
genes: list of pharmacogenomic genes
variants: dictionary mapping pharmacogenomic variant IDs to variant display names
Expand All @@ -349,12 +356,13 @@ def get_pharmacogenomic_info(
"conditions.reference2.biotype",
"conditions.reference2.displayName",
"source.name",
"source.displayName",
],
},
ignore_cache=False,
):
if record["source"]: # type: ignore
if record["source"]["name"].lower() in PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST: # type: ignore
if record["source"]["displayName"] in excluded_statement_sources: # type: ignore
continue

for condition in record["conditions"]: # type: ignore
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