PyOBO 0.9.2 Documentation

pyobo Package

A python package for handling and generating OBO.


ensure_path(prefix, *parts, url[, version, ...])

Download a file if it doesn't exist.

from_obo_path(path[, prefix, strict])

Get the OBO graph from a path.

from_obonet(graph, *[, strict])

Get all of the terms from a OBO graph.

get_alts_to_id(prefix[, force])

Get alternative id to primary id mapping.

get_ancestors(prefix, identifier[, ...])

Get all of the ancestors (parents) of the term as CURIEs.

get_definition(prefix, identifier)

Get the definition for an entity.

get_descendants(prefix, identifier[, ...])

Get all of the descendants (children) of the term as CURIEs.

get_equivalent(curie[, cutoff])

Get equivalent CURIEs.

get_filtered_properties_df(prefix, prop, *)

Extract a single property for each term.

get_filtered_properties_mapping(prefix, prop, *)

Extract a single property for each term as a dictionary.

get_filtered_properties_multimapping(prefix, ...)

Extract multiple properties for each term as a dictionary.

get_filtered_relations_df(prefix, relation, *)

Get all of the given relation.

get_filtered_xrefs(prefix, xref_prefix[, ...])

Get xrefs to a given target.

get_hierarchy(prefix, *[, include_part_of, ...])

Get hierarchy of parents as a directed graph.

get_id_definition_mapping(prefix, *[, ...])

Get a mapping of descriptions.

get_id_multirelations_mapping(prefix, typedef, *)

Get the OBO file and output a synonym dictionary.

get_id_name_mapping(prefix, *[, force, ...])

Get an identifier to name mapping for the OBO file.

get_id_species_mapping(prefix[, force, ...])

Get an identifier to species mapping.

get_id_synonyms_mapping(prefix, *[, force, ...])

Get the OBO file and output a synonym dictionary.

get_id_to_alts(prefix[, force])

Get alternate identifiers.

get_ids(prefix[, force, strict, version])

Get the set of identifiers for this prefix.

get_name(prefix, identifier)

Get the name for an entity.


Get the name for a CURIE, if possible.

get_name_id_mapping(prefix[, force])

Get a name to identifier mapping for the OBO file.

get_ontology(prefix, *[, force, rewrite, ...])

Get the OBO for a given graph.


Get the primary curie for an entity.

get_primary_identifier(prefix, identifier)

Get the primary identifier for an entity.


Get the priority CURIE mapped to the best namespace.

get_properties(prefix, identifier, prop)

Extract a set of properties for the given entity.

get_properties_df(prefix, *[, force])

Extract properties.

get_property(prefix, identifier, prop)

Extract a single property for the given entity.

get_relation(prefix, source_identifier, ...)

Get the target identifier corresponding to the given relationship from the source prefix/identifier pair.

get_relation_mapping(prefix, relation, ...)

Get relations from identifiers in the source prefix to target prefix with the given relation.

get_relations_df(prefix, *[, use_tqdm, ...])

Get all relations from the OBO.

get_species(prefix, identifier)

Get the species.

get_sssom_df(prefix, *[, predicate_id, ...])

Get xrefs from a source as an SSSOM dataframe.

get_subhierarchy(prefix, identifier[, ...])

Get the subhierarchy for a given node.

get_synonyms(prefix, identifier)

Get the synonyms for an entity.

get_typedef_df(prefix[, force])

Get an identifier to name mapping for the typedefs in an OBO file.


Get the PyOBO version string, including a git hash.

get_xref(prefix, identifier, new_prefix[, flip])

Get the xref with the new prefix if a direct path exists.

get_xrefs(prefix, xref_prefix[, flip, ...])

Get xrefs to a given target.

get_xrefs_df(prefix, *[, use_tqdm, force, ...])

Get all xrefs.

ground(prefix, query)

Normalize a string given the prefix's labels and synonyms.

has_ancestor(prefix, identifier, ...)

Check that the first identifier has the second as an ancestor.


Check if there's a plugin for converting the prefix.


Check if there's a plugin for converting the prefix.

is_descendent(prefix, identifier, ...)

Check that the first identifier has the second as a descendent.


Get all modules in the PyOBO sources.

iter_xref_plugins([use_tqdm, skip_below])

Get all modules in the PyOBO sources.

normalize_curie(curie, *[, strict])

Parse a string that looks like a CURIE.


Get parse results from an OBO graph.

run_nomenclature_plugin(prefix[, version])

Get a converted PyOBO source.


Get a converted PyOBO source.


Canonicalizer(graph[, priority, cutoff])

Wraps a graph and priority list to allow getting the best identifier.

Obo([date, data_version, force])

An OBO document.


A utility for normalizing by names.


A namespace, identifier, and label.

Synonym(name[, specificity, type, provenance])

A synonym with optional specificity and references.

SynonymTypeDef(reference[, specificity])

A type definition for synonyms in OBO.

Term(reference[, definition, provenance, ...])

A term in OBO.

TypeDef(reference[, comment, namespace, ...])

A type definition in OBO.

Class Inheritance Diagram

Inheritance diagram of pyobo.xrefdb.canonicalizer.Canonicalizer, pyobo.struct.struct.Obo, pyobo.normalizer.OboNormalizer, pyobo.struct.reference.Reference, pyobo.struct.struct.Synonym, pyobo.struct.struct.SynonymTypeDef, pyobo.struct.struct.Term, pyobo.struct.typedef.TypeDef

Indices and Tables