GeneOntology

class openomics.database.ontology.GeneOntology(path='http://geneontology.org/gene-associations/', file_resources=None, col_rename={'DB_Object_ID': 'gene_id', 'DB_Object_Symbol': 'gene_name', 'GO_ID': 'go_id'}, npartitions=0, verbose=False)

Bases: openomics.database.ontology.Ontology

Attributes Summary

COLUMNS_RENAME_DICT

Methods Summary

add_predecessor_terms(annotation[, return_str])
filter_network(namespace)	Filter the subgraph node_list to only namespace terms.
get_predecessor_terms(annotation[, type])
info()
load_dataframe(file_resources[, npartitions])	Handles data preprocessing given the file_resources input, and returns a DataFrame.
load_network(file_resources)

Attributes Documentation

COLUMNS_RENAME_DICT = {'DB_Object_ID': 'gene_id', 'DB_Object_Symbol': 'gene_name', 'GO_ID': 'go_id'}

Methods Documentation

add_predecessor_terms(annotation, return_str=False)

filter_network(namespace)

Filter the subgraph node_list to only namespace terms. :param namespace: one of {“biological_process”, “cellular_component”, “molecular_function”}

get_predecessor_terms(annotation, type='is_a')

info()

load_dataframe(file_resources, npartitions=None)

Handles data preprocessing given the file_resources input, and returns a DataFrame.

Parameters

• file_resources (dict) – A dict with keys as filenames and values as full file path.

• npartitions (int) –

load_network(file_resources)