PyOBO 0.11.2 Documentation

pyobo Package

A python package for handling and generating OBO.

Functions

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, version])	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, version])	Get the definition for an entity.
get_descendants(prefix[, identifier, ...])	Get all 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 the given relation.
get_filtered_xrefs(prefix, xref_prefix, *[, ...])	Get xrefs to a given target.
get_graph(prefix, **kwargs)	Get the relation graph.
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, version])	Get alternate identifiers.
get_ids(prefix, *[, force, strict, version])	Get the set of identifiers for this prefix.
get_name(prefix[, identifier, version])	Get the name for an entity.
get_name_by_curie(curie, *[, version])	Get the name for a CURIE, if possible.
get_name_id_mapping(prefix, *[, force, version])	Get a name to identifier mapping for the OBO file.
get_obsolete(prefix, *[, force, strict, version])	Get the set of obsolete local unique identifiers.
get_ontology(prefix, *[, force, rewrite, ...])	Get the OBO for a given graph.
get_primary_curie(curie, *[, version])	Get the primary curie for an entity.
get_primary_identifier(prefix, identifier, *)	Get the primary identifier for an entity.
get_priority_curie(curie)	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, version])	Extract properties.
get_property(prefix, identifier, prop, **kwargs)	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, *[, version])	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, version])	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, *[, use_tqdm, force, ...])	Get all xrefs.
ground(prefix, query)	Normalize a string given the prefix's labels and synonyms.
has_ancestor(prefix, identifier, ...[, version])	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.
has_xref_plugin(prefix)	Check if there's a plugin for converting the prefix.
is_descendent(prefix, identifier, ...[, version])	Check that the first identifier has the second as a descendent.
iter_nomenclature_plugins()	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.
parse_results_from_obo(obo)	Get parse results from an OBO graph.
run_nomenclature_plugin(prefix[, version])	Get a converted PyOBO source.
run_xref_plugin(prefix)	Get a converted PyOBO source.

Classes

Canonicalizer(graph[, priority, cutoff])	Wraps a graph and priority list to allow getting the best identifier.
Obo(date, data_version, force)	An OBO document.
OboNormalizer(prefix)	A utility for normalizing by names.
Reference(*, prefix, identifier[, name])	A namespace, identifier, and label.
Synonym(name, specificity, , , ] =, type, ...)	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

Table of Contents

Getting Started

• Installation
• Command Line Interface
  • pyobo

Indices and Tables

• Index

• Module Index

• Search Page