Ontology

class openomics.database.ontology.Ontology(path, file_resources=None, blocksize=None, **kwargs)

Bases: openomics.database.base.Database

Attributes Summary

Methods Summary

filter_annotation(annotation)
filter_network(namespace)	Filter the subgraph node_list to only namespace terms.
get_child_nodes()
get_dfs_paths(root_nodes[, filter_duplicates])	Return all depth-first search paths from root node(s) to children node by traversing the ontology directed graph.
get_node_color([file])
get_root_nodes()
load_network(file_resources)	rtype Tuple[MultiDiGraph, List[str]]
remove_predecessor_terms(annotation[, sep])

Attributes Documentation

Methods Documentation

filter_annotation(annotation)

filter_network(namespace)

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

Return type

None

get_child_nodes()

get_dfs_paths(root_nodes, filter_duplicates=False)

Return all depth-first search paths from root node(s) to children node by traversing the ontology directed graph. :param root_nodes: [”GO:0008150”] if biological processes, [”GO:0003674”] if molecular_function, or [”GO:0005575”] if cellular_component :type root_nodes: list :param filter_duplicates: whether to remove duplicated paths that end up at the same leaf nodes :type filter_duplicates: bool

Returns: pd.DataFrame of all paths starting from the root nodes.

static get_node_color(file='~/Bioinformatics_ExternalData/GeneOntology/go_colors_biological.csv')

get_root_nodes()

load_network(file_resources)

Return type

Tuple[MultiDiGraph, List[str]]

remove_predecessor_terms(annotation, sep='\\\\||;')