graphkb.genes¶

Methods for retrieving gene annotation lists from GraphKB

ONCOKB_SOURCE_NAME¶

ONCOKB_SOURCE_NAME = 'oncokb'

ONCOGENE¶

ONCOGENE = 'oncogenic'

TUMOUR_SUPPRESSIVE¶

TUMOUR_SUPPRESSIVE = 'tumour suppressive'

FUSION_NAMES¶

FUSION_NAMES = ['structural variant', 'fusion']

GENE_RETURN_PROPERTIES¶

GENE_RETURN_PROPERTIES = [
    'name',
    '@rid',
    '@class',
    'sourceId',
    'sourceIdVersion',
    'source.name',
    'source.@rid',
    'displayName',
    'biotype',
    'deprecated',
]

get_oncokb_oncogenes()¶

Gets the list of oncogenes stored in GraphKB derived from OncoKB

def get_oncokb_oncogenes(conn: GraphKBConnection) -> List[Ontology]:

Args

conn (GraphKBConnection): the graphkb connection object

Returns

List[Ontology]: gene (Feature) records

get_oncokb_tumour_supressors()¶

Gets the list of tumour supressor genes stored in GraphKB derived from OncoKB

def get_oncokb_tumour_supressors(conn: GraphKBConnection) -> List[Ontology]:

Args

conn (GraphKBConnection): the graphkb connection object

Returns

List[Ontology]: gene (Feature) records

get_genes_from_variant_types()¶

Retrieve a list of Genes which are found in variants on the given types

def get_genes_from_variant_types(
    conn: GraphKBConnection,
    types: List[str],
    source_record_ids: List[str] = [],
    ignore_cache: bool = False,
) -> List[Ontology]:

Args

conn (GraphKBConnection): the graphkb connection object
types (List[str]): list of names of variant types
source_record_ids (List[str]): list of sources ids to filter genes by
ignore_cache (bool)

Returns

List[Ontology]: gene (Feature) records