Obo

class pyobo.Obo(date=<factory>, data_version=None, force=False)[source]

Bases: object

An OBO document.

Attributes Summary

`auto_generated_by`	An annotation about how an ontology was generated
`bioversions_key`
`data_version`	The ontology version
`date_formatted`	Get the date as a formatted string.
`dynamic_version`	Set to true for resources that are unversioned/very dynamic, like HGNC
`force`	Should this ontology be reloaded?
`format_version`	The OBO format
`hierarchy`	A graph representing the parent/child relationships between the entities.
`idspaces`	The idspaces used in the document
`iter_only`	For super-sized datasets that shouldn't be read into memory
`name`	The name of the ontology.
`properties_header`	Property dataframe header.
`relations_header`	Header for the relations dataframe.
`static_version`	Set to a static version for the resource (i.e., the resource is not itself versioned)
`synonym_typedefs`	Synonym type definitions
`typedefs`	Type definitions
`xrefs_header`	The header for the xref dataframe.

Methods Summary

`ancestors`(identifier)	Return a set of identifiers for parents of the given identifier.
`cli`()	Run the CLI for this class.
`descendants`(identifier)	Return a set of identifiers for the children of the given identifier.
`get_cls_cli`()	Get the CLI for this class.
`get_filtered_multixrefs_mapping`(prefix, *[, ...])	Get filtered xrefs as a dictionary.
`get_filtered_properties_df`(prop, *[, use_tqdm])	Get a dataframe of terms' identifiers to the given property's values.
`get_filtered_properties_mapping`(prop, *[, ...])	Get a mapping from a term's identifier to the property.
`get_filtered_properties_multimapping`(prop, *)	Get a mapping from a term's identifier to the property values.
`get_filtered_relations_df`(relation, *[, ...])	Get a specific relation from OBO.
`get_filtered_xrefs_mapping`(prefix, *[, use_tqdm])	Get filtered xrefs as a dictionary.
`get_id_alts_mapping`()	Get a mapping from identifiers to a list of alternative identifiers.
`get_id_definition_mapping`(*[, use_tqdm])	Get a mapping from identifiers to definitions.
`get_id_multirelations_mapping`(typedef, *[, ...])	Get a mapping from identifiers to a list of all references for the given relation.
`get_id_name_mapping`(*[, use_tqdm])	Get a mapping from identifiers to names.
`get_id_species_mapping`(*[, prefix, use_tqdm])	Get a mapping from identifiers to species.
`get_id_synonyms_mapping`(*[, use_tqdm])	Get a mapping from identifiers to a list of sorted synonym strings.
`get_ids`(*[, use_tqdm])	Get the set of identifiers.
`get_metadata`()	Get metadata.
`get_properties_df`(*[, use_tqdm])	Get all properties as a dataframe.
`get_relation`(source_identifier, relation, ...)	Get the value for a bijective relation mapping between this resource and a target resource.
`get_relation_mapping`(relation, target_prefix, *)	Get a mapping from the term's identifier to the target's identifier.
`get_relation_multimapping`(relation, ...[, ...])	Get a mapping from the term's identifier to the target's identifiers.
`get_relations_df`(*[, use_tqdm])	Get all relations from the OBO.
`get_typedef_df`([use_tqdm])	Get a typedef dataframe.
`get_typedef_id_name_mapping`()	Get a mapping from typedefs' identifiers to names.
`get_xrefs_df`(*[, use_tqdm])	Get a dataframe of all xrefs extracted from the OBO document.
`is_descendant`(descendant, ancestor)	Return if the given identifier is a descendent of the ancestor.
`iter_property_rows`(*[, use_tqdm])	Iterate property rows.
`iter_relation_rows`([use_tqdm])	Iterate the relations' rows.
`iter_terms`([force])	Iterate over terms in this ontology.
`iter_typedef_id_name`()	Iterate over typedefs' identifiers and their respective names.
`iterate_alt_rows`()	Iterate over pairs of terms' primary identifiers and alternate identifiers.
`iterate_alts`()	Iterate over alternative identifiers.
`iterate_filtered_properties`(prop, *[, use_tqdm])	Iterate over tuples of terms and the values for the given property.
`iterate_filtered_relations`(relation, *[, ...])	Iterate over tuples of terms and ther targets for the given relation.
`iterate_filtered_relations_filtered_targets`(...)	Iterate over relationships between one identifier and another.
`iterate_filtered_xrefs`(prefix, *[, use_tqdm])	Iterate over xrefs to a given prefix.
`iterate_id_definition`(*[, use_tqdm])	Iterate over pairs of terms' identifiers and their respective definitions.
`iterate_id_name`(*[, use_tqdm])	Iterate identifier name pairs.
`iterate_id_species`(*[, prefix, use_tqdm])	Iterate over terms' identifiers and respective species (if available).
`iterate_ids`(*[, use_tqdm])	Iterate over identifiers.
`iterate_obo_lines`()	Iterate over the lines to write in an OBO file.
`iterate_properties`(*[, use_tqdm])	Iterate over tuples of terms, properties, and their values.
`iterate_relations`(*[, use_tqdm])	Iterate over tuples of terms, relations, and their targets.
`iterate_synonym_rows`(*[, use_tqdm])	Iterate over pairs of identifier and synonym text.
`iterate_synonyms`(*[, use_tqdm])	Iterate over pairs of term and synonym object.
`iterate_xref_rows`(*[, use_tqdm])	Iterate over terms' identifiers, xref prefixes, and xref identifiers.
`iterate_xrefs`(*[, use_tqdm])	Iterate over xrefs.
`to_obonet`(*[, use_tqdm])	Export as a :mod`obonet` style graph.
`write_default`([use_tqdm, force, write_obo, ...])	Write the OBO to the default path.
`write_obo`([file, use_tqdm])	Write the OBO to a file.
`write_obonet_gz`(path)	Write the OBO to a gzipped dump in Obonet JSON.

Attributes Documentation

auto_generated_by: ClassVar[Optional[str]] = None: An annotation about how an ontology was generated

bioversions_key: ClassVar[Optional[str]] = None

data_version: Optional[str] = None: The ontology version

date_formatted: Get the date as a formatted string.

dynamic_version: ClassVar[bool] = False: Set to true for resources that are unversioned/very dynamic, like HGNC

force: bool = False: Should this ontology be reloaded?

format_version: ClassVar[str] = '1.2': The OBO format

hierarchy

A graph representing the parent/child relationships between the entities.

To get all children of a given entity, do:

from pyobo import get_obo
obo = get_obo('go')

identifier = '1905571'  # interleukin-10 receptor complex
is_complex = '0032991' in  nx.descendants(obo.hierarchy, identifier)  # should be true

idspaces: ClassVar[Optional[Mapping[str, str]]] = None: The idspaces used in the document

iter_only: ClassVar[bool] = False: For super-sized datasets that shouldn’t be read into memory

name: ClassVar[Optional[str]] = None: The name of the ontology. If not given, tries looking up with the Bioregistry.

properties_header: Property dataframe header.

relations_header: Header for the relations dataframe.

static_version: ClassVar[Optional[str]] = None: Set to a static version for the resource (i.e., the resource is not itself versioned)

synonym_typedefs: ClassVar[Optional[List[SynonymTypeDef]]] = None: Synonym type definitions

typedefs: ClassVar[Optional[List[TypeDef]]] = None: Type definitions

xrefs_header: The header for the xref dataframe.

Methods Documentation

ancestors(identifier)[source]

Return a set of identifiers for parents of the given identifier.

Return type:: Set[str]

classmethod cli()[source]

Run the CLI for this class.

Return type:: None

descendants(identifier)[source]

Return a set of identifiers for the children of the given identifier.

Return type:: Set[str]

classmethod get_cls_cli()[source]

Get the CLI for this class.

Return type:: Command

get_filtered_multixrefs_mapping(prefix, *, use_tqdm=False)[source]

Get filtered xrefs as a dictionary.

Return type:: Mapping[str, List[str]]

get_filtered_properties_df(prop, *, use_tqdm=False)[source]

Get a dataframe of terms’ identifiers to the given property’s values.

Return type:: DataFrame

get_filtered_properties_mapping(prop, *, use_tqdm=False)[source]: Get a mapping from a term’s identifier to the property. :rtype: Mapping[str, str]

Warning

Assumes there’s only one version of the property for each term.

get_filtered_properties_multimapping(prop, *, use_tqdm=False)[source]

Get a mapping from a term’s identifier to the property values.

Return type:: Mapping[str, List[str]]

get_filtered_relations_df(relation, *, use_tqdm=False)[source]

Get a specific relation from OBO.

Return type:: DataFrame

get_filtered_xrefs_mapping(prefix, *, use_tqdm=False)[source]

Get filtered xrefs as a dictionary.

Return type:: Mapping[str, str]

get_id_alts_mapping()[source]

Get a mapping from identifiers to a list of alternative identifiers.

Return type:: Mapping[str, List[str]]

get_id_definition_mapping(*, use_tqdm=False)[source]

Get a mapping from identifiers to definitions.

Return type:: Mapping[str, str]

get_id_multirelations_mapping(typedef, *, use_tqdm=False)[source]

Get a mapping from identifiers to a list of all references for the given relation.

Return type:: Mapping[str, List[Reference]]

get_id_name_mapping(*, use_tqdm=False)[source]

Get a mapping from identifiers to names.

Return type:: Mapping[str, str]

get_id_species_mapping(*, prefix=None, use_tqdm=False)[source]

Get a mapping from identifiers to species.

Return type:: Mapping[str, str]

get_id_synonyms_mapping(*, use_tqdm=False)[source]

Get a mapping from identifiers to a list of sorted synonym strings.

Return type:: Mapping[str, List[str]]

get_ids(*, use_tqdm=False)[source]

Get the set of identifiers.

Return type:: Set[str]

get_metadata()[source]

Get metadata.

Return type:: Mapping[str, Any]

get_properties_df(*, use_tqdm=False)[source]

Get all properties as a dataframe.

Return type:: DataFrame

get_relation(source_identifier, relation, target_prefix, *, use_tqdm=False)[source]

Get the value for a bijective relation mapping between this resource and a target resource.

>>> from pyobo.sources.hgnc import get_obo
>>> obo = get_obo()
>>> human_mapt_hgnc_id = '6893'
:rtype: :py:data:`~typing.Optional`\[:py:class:`str`]

>>> mouse_mapt_mgi_id = '97180'
>>> assert mouse_mapt_mgi_id == obo.get_relation(human_mapt_hgnc_id, 'ro:HOM0000017', 'mgi')

get_relation_mapping(relation, target_prefix, *, use_tqdm=False)[source]

Get a mapping from the term’s identifier to the target’s identifier. :rtype: Mapping[str, str]

Warning

Assumes there’s only one version of the property for each term.

Example usage: get homology between HGNC and MGI:

>>> from pyobo.sources.hgnc import get_obo
>>> obo = get_obo()
>>> human_mapt_hgnc_id = '6893'
>>> mouse_mapt_mgi_id = '97180'
>>> hgnc_mgi_orthology_mapping = obo.get_relation_mapping('ro:HOM0000017', 'mgi')
>>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]

get_relation_multimapping(relation, target_prefix, *, use_tqdm=False)[source]

Get a mapping from the term’s identifier to the target’s identifiers.

Return type:: Mapping[str, List[str]]

get_relations_df(*, use_tqdm=False)[source]

Get all relations from the OBO.

Return type:: DataFrame

get_typedef_df(use_tqdm=False)[source]

Get a typedef dataframe.

Return type:: DataFrame

get_typedef_id_name_mapping()[source]

Get a mapping from typedefs’ identifiers to names.

Return type:: Mapping[str, str]

get_xrefs_df(*, use_tqdm=False)[source]

Get a dataframe of all xrefs extracted from the OBO document.

Return type:: DataFrame

is_descendant(descendant, ancestor)[source]

Return if the given identifier is a descendent of the ancestor.

from pyobo import get_obo
obo = get_obo('go')

interleukin_10_complex = '1905571'  # interleukin-10 receptor complex
all_complexes = '0032991'
assert obo.is_descendant('1905571', '0032991')