GeneOntology#
- class openomics.database.ontology.GeneOntology(path='http://geneontology.org/gene-associations/', species='human', file_resources=None, index_col='DB_Object_Symbol', keys=None, col_rename={'DB_Object_ID': 'gene_id', 'DB_Object_Symbol': 'gene_name', 'GO_ID': 'go_id', 'Taxon_ID': 'species_id'}, blocksize=None, **kwargs)[source][source]#
Bases:
openomics.database.ontology.Ontology
Loads the GeneOntology database from http://geneontology.org .
Default path: “http://geneontology.org/gene-associations/”.
- Default file_resources: {
“go-basic.obo”: “http://purl.obolibrary.org/obo/go/go-basic.obo”, “goa_human.gaf”: “goa_human.gaf.gz”, “goa_human_rna.gaf”: “goa_human_rna.gaf.gz”, “goa_human_isoform.gaf”: “goa_human_isoform.gaf.gz”,
}
Attributes Summary
Methods Summary
add_predecessor_terms
(anns[, edge_type, sep])filter_network
(namespace)Filter the subgraph node_list to only namespace terms.
info
()load_dataframe
(file_resources[, blocksize])Handles data preprocessing given the file_resources input, and returns a DataFrame.
load_network
(file_resources)- rtype
Tuple
[Graph
,ndarray
]
Attributes Documentation
- COLUMNS_RENAME_DICT = {'DB_Object_ID': 'gene_id', 'DB_Object_Symbol': 'gene_name', 'GO_ID': 'go_id', 'Taxon_ID': 'species_id'}[source]#
Methods Documentation
- filter_network(namespace)[source]#
Filter the subgraph node_list to only namespace terms. :param namespace: one of {“biological_process”, “cellular_component”, “molecular_function”}
- Return type
None