Ontology databases

openomics.database.ontology Module

Functions

dfs_path(graph, path)
filter_dfs_paths(paths_df)
flatten(lst)
flatten_list(list_in)
slice_adj(adj, node_list, nodes_A[, nodes_B])	param adj
traverse_predecessors(network, seed_node[, type])	Returns all successor terms from seed_node by traversing the ontology network with edges == type.
write_taxonomy(network, root_nodes, file_path)	param network A network with edge(i, j) where i is a node and j is a child of i.

Classes

Database(path[, file_resources, col_rename, …])	This is a base class used to instantiate an external Database given a a set of files from either local files or URLs.
GeneOntology([path, file_resources, …])
HumanPhenotypeOntology(path[, …])
Ontology(path[, file_resources, col_rename, …])

Class Inheritance Diagram