Reference

A python package for handling and generating OBO.

Functions

build_ontology(prefix, *[, terms, ...])	Build an ontology from parts.
default_reference(prefix, identifier[, name])	Create a CURIE for an "unqualified" reference.
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, version, ...])	Get all the terms from a OBO graph.
get_alts_to_id(prefix, **kwargs)	Get alternative id to primary id mapping.
get_ancestors(prefix[, identifier])	Get all the ancestors (parents) of the term as CURIEs.
get_children(prefix[, identifier])	Get all the descendants (children) of the term as CURIEs.
get_definition(prefix[, identifier])	Get the definition for an entity.
get_descendants(prefix[, identifier])	Get all the descendants (children) of the term as CURIEs.
get_edges(prefix, **kwargs)	Get a list of edge triples.
get_edges_df(prefix, **kwargs)	Get a dataframe of edges triples.
get_filtered_properties_df(prefix, prop, ...)	Extract a single property for each term.
get_filtered_properties_mapping(prefix, ...)	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 the given relation.
get_filtered_xrefs(prefix, xref_prefix, *[, ...])	Get xrefs to a given target.
get_graph(prefix, **kwargs)	Get the relation graph.
get_graph_embeddings_df(prefix, *[, method, ...])	Get graph machine learning embeddings.
get_grounder(prefixes, *[, grounder_cls, ...])	Get a grounder for the given prefix(es).
get_hierarchy(prefix, *[, extra_relations, ...])	Get hierarchy of parents as a directed graph.
get_id_definition_mapping(prefix, **kwargs)	Get a mapping of descriptions.
get_id_multirelations_mapping(prefix, ...)	Get the OBO file and output a synonym dictionary.
get_id_name_mapping(prefix, **kwargs)	Get an identifier to name mapping for the OBO file.
get_id_species_mapping(prefix, **kwargs)	Get an identifier to species mapping.
get_id_synonyms_mapping(prefix, **kwargs)	Get the OBO file and output a synonym dictionary.
get_id_to_alts(prefix, **kwargs)	Get alternate identifiers.
get_ids(prefix, **kwargs)	Get the set of identifiers for this prefix.
get_literal_mappings(prefix, *[, skip_obsolete])	Get literal mappings.
get_literal_mappings_df(prefix, **kwargs)	Get a literal mappings dataframe.
get_literal_mappings_subset(prefix, ancestors, *)	Get a subset of literal mappings under the given ancestors.
get_literal_properties(prefix, **kwargs)	Get a list of literal property triples.
get_literal_properties_df(prefix, **kwargs)	Get a dataframe of literal property quads.
get_mappings_df(prefix, **kwargs)	Get semantic mappings from a source as an SSSOM dataframe.
get_metadata(prefix, **kwargs)	Get metadata for the ontology.
get_name(prefix[, identifier, ...])	Get the name for an entity.
get_name_by_curie(curie, /, *[, ...])	Get the name for a CURIE, if possible.
get_name_id_mapping(prefix, **kwargs)	Get a name to identifier mapping for the OBO file.
get_object_properties(prefix, **kwargs)	Get a list of object property triples.
get_object_properties_df(prefix, **kwargs)	Get a dataframe of object property triples.
get_obsolete(prefix, **kwargs)	Get the set of obsolete local unique identifiers.
get_ontology(prefix, *[, force, ...])	Get the OBO for a given graph.
get_primary_curie(prefix[, identifier])	Get the primary curie for an entity.
get_primary_identifier(prefix[, identifier])	Get the primary identifier for an entity.
get_primary_reference(prefix[, identifier])	Get the primary reference for an entity.
get_properties(prefix, identifier, prop, ...)	Extract a set of properties for the given entity.
get_properties_df(prefix, **kwargs)	Extract properties.
get_property(prefix, identifier, prop, **kwargs)	Extract a single property for the given entity.
get_references(prefix, **kwargs)	Get the set of identifiers for this prefix.
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, *[, wide])	Get all relations from the OBO.
get_scispacy_entities(prefix, **kwargs)	Iterate over entities in a given ontology via pyobo.
get_scispacy_entity_linker(prefix, *[, ...])	Get an entity linker for usage with scispacy.
get_scispacy_knowledgebase(prefix, **kwargs)	Get a lexical index for usage with scispacy.
get_semantic_mapping_metadata(prefix, *[, ...])	Get metadata for a resource.
get_semantic_mappings(prefix[, names])	Get semantic mappings.
get_species(prefix[, identifier])	Get the species.
get_sssom_df(prefix, **kwargs)	Get an SSSOM dataframe, replaced by get_mappings_df().
get_subhierarchy(prefix[, identifier])	Get the subhierarchy for a given node.
get_synonyms(prefix[, identifier])	Get the synonyms for an entity.
get_text_embedding(reference, *[, model])	Get a text embedding for an entity, or return none if no text is available.
get_text_embedding_similarity(reference_1, ...)	Get the pairwise similarity.
get_text_embeddings_df(prefix, *[, model])	Get embeddings for all entities in the resource.
get_typedef_df(prefix, **kwargs)	Get an identifier to name mapping for the typedefs in an OBO file.
get_version([with_git_hash])	Get the PyOBO version string, including a git hash.
get_xref(prefix, identifier, new_prefix, *)	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, **kwargs)	Get all xrefs.
ground()	Normalize a string given the prefix's labels and synonyms.
has_ancestor(reference, ancestor, /[, direction])	Check that the first identifier has the second as an ancestor.
has_nomenclature_plugin(prefix)	Check if there's a plugin for converting the prefix.
is_descendent(reference, ancestor, /, **kwargs)	Check if the refeference is a descendant of the ancestor.
iter_nomenclature_plugins()	Get all modules in the PyOBO sources.
run_nomenclature_plugin(prefix[, version])	Get a converted PyOBO source.

Classes

Annotation(predicate, value)	A tuple representing a predicate-object pair.
Obo([date, data_version, force])	An OBO document.
Reference	alias of NormalizedNamableReference
Synonym(name[, specificity, type, ...])	A synonym with optional specificity and references.
SynonymTypeDef(reference[, specificity])	A type definition for synonyms in OBO.
Term(reference[, definition, relationships, ...])	A term in OBO.
TypeDef(reference[, is_anonymous, ...])	A type definition in OBO.

Class Inheritance Diagram

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Constants for PyOBO.

Functions

check_should_cache(data)	Determine whether caching should be done based on generic keyword arguments.
check_should_force(data)	Determine whether caching should be forced based on generic keyword arguments.
check_should_use_tqdm(data)	Determine whether caching should be done based on generic keyword arguments.
get_semantic_mapping_metadata(prefix, *[, ...])	Get metadata for a resource.

Classes

DatabaseKwargs	Keyword arguments for database CLI functions.
GetOntologyKwargs	Represents the optional keyword arguments passed to pyobo.get_ontology().
IterHelperHelperDict	Represents arguments needed when iterating over all ontologies.
OntologyPathPack(format, path, rdf_format)	A format and path tuple.
SlimGetOntologyKwargs	Keyword arguments for database CLI functions.

Class Inheritance Diagram

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