get_hierarchy

get_hierarchy(prefix, *, extra_relations=None, properties=None, **kwargs)[source]

Get hierarchy of parents as a directed graph.

Parameters:

  • prefix (str) – The name of the namespace.

  • include_part_of – Add “part of” relations. Only works if the relations are properly defined using bfo:0000050 ! part of or bfo:0000051 ! has part

  • include_has_member – Add “has member” relations. These aren’t part of the BFO, but are hacked into PyOBO using pyobo.struct.typedef.has_member for relationships like from protein families to their actual proteins.

  • extra_relations (Iterable[ReferenceHint] | None) – Other relations that you want to include in the hierarchy. For example, it might be useful to include the positively_regulates

  • properties (Iterable[ReferenceHint] | None) – Properties to include in the data part of each node. For example, might want to include SMILES strings with the ChEBI tree.

  • force – should the resources be reloaded when extracting relations?

  • kwargs (Unpack[HierarchyKwargs])

Returns:

A directional graph representing the hierarchy

Return type:

nx.DiGraph[Reference]

This function thinly wraps _get_hierarchy_helper() to make it easier to work with the lru_cache mechanism.