Obo

class 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`
`check_bioregistry_prefix`	Should the prefix be validated against the Bioregistry?
`data_version`	The ontology version
`date`	The date the ontology was generated
`date_formatted`	Get the date as a formatted string.
`dynamic_version`	Set to true for resources that are unversioned/very dynamic, like MGI
`edges_header`	Header for the edges dataframe.
`force`	Should this ontology be reloaded?
`hierarchy`	A graph representing the parent/child relationships between the entities.
`idspaces`	The idspaces used in the document
`imports`
`iter_only`	For super-sized datasets that shouldn't be read into memory
`literal_properties_header`	Property dataframe header.
`name`	The name of the ontology.
`nodes_header`	Get the header for nodes.
`object_properties_header`	Property dataframe header.
`ontology`	The prefix for the ontology
`ontology_iri`
`ontology_version_iri`
`properties_header`	Property dataframe header.
`property_values`
`relations_header`	Header for the relations dataframe.
`root_terms`	Root terms to use for the ontology
`skip_maintainers`	Allow skipping adding maintainers annotations, in case the resource maintainers don't want their names associated with the OWL exports that e.g. end up on EBI OLS.
`static_version`	Set to a static version for the resource (i.e., the resource is not itself versioned)
`subsetdefs`
`synonym_typedefs`	Synonym type definitions
`typedefs`	Type definitions

Methods Summary

`ancestors`(identifier)	Return a set of identifiers for parents of the given identifier.
`cli`(*args)	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_edges_df`(*[, use_tqdm])	Get an edges dataframe.
`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_grounder`()	Get a grounder from this ontology.
`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_literal_mappings`()	Get literal mappings in a standard data model.
`get_literal_mappings_df`()	Get a literal mappings dataframe.
`get_literal_properties_df`(*[, use_tqdm])	Get all properties as a dataframe.
`get_mappings_df`(*[, use_tqdm])	Get a dataframe with SSSOM extracted from the OBO document.
`get_metadata`()	Get metadata.
`get_object_properties_df`(*[, use_tqdm])	Get all properties as a dataframe.
`get_obsolete`(*[, use_tqdm])	Get the set of obsolete identifiers.
`get_properties_df`(*[, use_tqdm, drop_na])	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_semantic_mappings`(*[, progress])	Iterate over semantic mappings.
`get_typedef_df`([use_tqdm])	Get a typedef dataframe.
`get_typedef_id_name_mapping`()	Get a mapping from typedefs' identifiers to names.
`is_descendant`(descendant, ancestor)	Return if the given identifier is a descendant of the ancestor.
`iter_literal_properties`(*[, use_tqdm])	Iterate over literal properties quads.
`iter_object_properties`(*[, use_tqdm])	Iterate over object property triples.
`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_edge_rows`([use_tqdm])	Iterate the edge rows.
`iterate_edges`(*[, use_tqdm, include_xrefs])	Iterate over triples of terms, relations, and their targets.
`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_literal_mapping_rows`()	Iterate over literal mapping rows.
`iterate_node_rows`([sep])	Get a nodes iterator appropriate for serialization.
`iterate_obo_lines`([emit_object_properties, ...])	Iterate over the lines to write in an OBO file.
`iterate_properties`(*[, use_tqdm])	Iterate over tuples of terms, properties, and their values.
`iterate_references`(*[, use_tqdm])	Iterate over identifiers.
`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_xrefs`(*[, use_tqdm])	Iterate over xrefs.
`to_obonet`(*[, use_tqdm])	Export as a :mod`obonet` style graph.
`write_cache`(*[, force])	Write cache parts.
`write_default`([use_tqdm, force, write_obo, ...])	Write the OBO to the default path.
`write_edges`(path)	Write a edges TSV file.
`write_metadata`()	Write the metadata JSON file.
`write_nodes`(path)	Write a nodes TSV file.
`write_obo`([file, use_tqdm, ...])	Write the OBO to a file.
`write_obograph`(path, *[, converter])	Write OBO Graph JSON.
`write_obonet_gz`(path)	Write the OBO to a gzipped dump in Obonet JSON.
`write_ofn`(path)	Write as Functional OWL (OFN).
`write_owl`(path)	Write OWL, by first outputting OFN then converting with ROBOT.
`write_prefix_map`()	Write a prefix map file that includes all prefixes used in this ontology.
`write_rdf`(path)	Write as Turtle RDF.

Attributes Documentation

Parameters:

date (datetime | None)
data_version (str | None)
force (bool)

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

bioversions_key: ClassVar[str | None] = None

check_bioregistry_prefix: ClassVar[bool] = True: Should the prefix be validated against the Bioregistry?

data_version: str | None = None: The ontology version

date: datetime | None = <dataclasses._MISSING_TYPE object>: The date the ontology was generated

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 MGI

edges_header: Header for the edges dataframe.

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

hierarchy

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

To get all children of a given entity, do:

from pyobo import get_ontology

obo = get_ontology("go")

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

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

imports: ClassVar[list[str] | None] = None

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

literal_properties_header: Property dataframe header.

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

nodes_header: Get the header for nodes.

object_properties_header: Property dataframe header.

ontology: ClassVar[str] = <dataclasses._MISSING_TYPE object>: The prefix for the ontology

ontology_iri: ClassVar[str | None] = None

ontology_version_iri: ClassVar[str | None] = None

properties_header: Property dataframe header.

property_values: ClassVar[list[Annotation] | None] = None

relations_header: Header for the relations dataframe.

root_terms: ClassVar[list[NormalizedNamableReference] | None] = None: Root terms to use for the ontology

skip_maintainers: ClassVar[bool] = False: Allow skipping adding maintainers annotations, in case the resource maintainers don’t want their names associated with the OWL exports that e.g. end up on EBI OLS

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

subsetdefs: ClassVar[dict[NormalizedNamableReference, str] | None] = None

synonym_typedefs: ClassVar[list[SynonymTypeDef] | None] = None: Synonym type definitions

typedefs: ClassVar[list[TypeDef] | None] = None: Type definitions

Methods Documentation

ancestors(identifier)[source]

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

Parameters:: identifier (str)
Return type:: set[str]

classmethod cli(*args)[source]

Run the CLI for this class.

Parameters:: args (Any)
Return type:: Any

descendants(identifier)[source]

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

Parameters:: identifier (str)
Return type:: set[str]

classmethod get_cls_cli()[source]

Get the CLI for this class.

Return type:: Command

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

Get an edges dataframe.

Parameters:: use_tqdm (bool)
Return type:: DataFrame

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

Get filtered xrefs as a dictionary.

Parameters:

prefix (str)
use_tqdm (bool)

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.

Parameters:

prop (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
use_tqdm (bool)

Return type:

DataFrame

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

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

Warning

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

Parameters:

prop (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
use_tqdm (bool)

Return type:

Mapping[str, str]

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

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

Parameters:

prop (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
use_tqdm (bool)

Return type:

Mapping[str, list[str]]

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

Get a specific relation from OBO.

Parameters:

relation (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
use_tqdm (bool)

Return type:

DataFrame

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

Get filtered xrefs as a dictionary.

Parameters:

prefix (str)
use_tqdm (bool)

Return type:

Mapping[str, str]

get_grounder()[source]

Get a grounder from this ontology.

Returns:: An object that can be used for named entity recognition and named entity normalization
Return type:: Grounder

Here’s example usage for a built-in ontology:

import pyobo
import ssslm

ontology = pyobo.get_ontology("taxrank")
grounder: ssslm.Grounder = ontology.get_grounder()
matches: list[ssslm.Match] = grounder.ground("species")

Here’s example usage for a custom ontology:

import pyobo
import ssslm
from urllib.request import urlretrieve

url = "http://purl.obolibrary.org/obo/taxrank.obo"
path = "taxrank.obo"
urlretrieve(url, path)

ontology = pyobo.from_obo_path(path, prefix="taxrank")
grounder: ssslm.Grounder = ontology.get_grounder()
matches: list[ssslm.Match] = grounder.get_matches("species")

Warning

It’s required to tell PyOBO the prefix for a custom ontology when using pyobo.from_obo_path(), and it must be registered in the Bioregistry

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.

Parameters:: use_tqdm (bool)
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.

Parameters:

typedef (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
use_tqdm (bool)

Return type:

Mapping[str, list[NormalizedNamableReference]]

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

Get a mapping from identifiers to names.

Parameters:: use_tqdm (bool)
Return type:: Mapping[str, str]

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

Get a mapping from identifiers to species.

Parameters:

prefix (str | None)
use_tqdm (bool)

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.

Parameters:: use_tqdm (bool)
Return type:: Mapping[str, list[str]]

get_ids(*, use_tqdm=False)[source]

Get the set of identifiers.

Parameters:: use_tqdm (bool)
Return type:: set[str]

get_literal_mappings()[source]

Get literal mappings in a standard data model.

Return type:: Iterable[LiteralMapping]

get_literal_mappings_df()[source]

Get a literal mappings dataframe.

Return type:: DataFrame

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

Get all properties as a dataframe.

Parameters:: use_tqdm (bool)
Return type:: DataFrame

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

Get a dataframe with SSSOM extracted from the OBO document.

Parameters:: use_tqdm (bool) – Should a progres bar be shown
Returns:: A pandas dataframe representing SSSOM records
Return type:: DataFrame

get_metadata()[source]

Get metadata.

Return type:: dict[str, Any]

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

Get all properties as a dataframe.

Parameters:: use_tqdm (bool)
Return type:: DataFrame

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

Get the set of obsolete identifiers.

Parameters:: use_tqdm (bool)
Return type:: set[str]

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

Get all properties as a dataframe.

Parameters:

use_tqdm (bool)
drop_na (bool)

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 HGNCGetter
>>> obo = HGNCGetter()
>>> human_mapt_hgnc_id = "6893"
>>> mouse_mapt_mgi_id = "97180"
>>> assert mouse_mapt_mgi_id == obo.get_relation(human_mapt_hgnc_id, "ro:HOM0000017", "mgi")

Parameters:

source_identifier (str)
relation (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
target_prefix (str)
use_tqdm (bool)

Return type:

str | None

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

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

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 HGNCGetter
>>> obo = HGNCGetter()
>>> 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]

Parameters:

relation (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
target_prefix (str)
use_tqdm (bool)

Return type:

Mapping[str, str]

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

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

Parameters:

relation (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
target_prefix (str)
use_tqdm (bool)

Return type:

Mapping[str, list[str]]

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

Get all relations from the OBO.

Parameters:: use_tqdm (bool)
Return type:: DataFrame

get_semantic_mappings(*, progress=False)[source]

Iterate over semantic mappings.

Parameters:: progress (bool)
Return type:: Iterable[SemanticMapping]

get_typedef_df(use_tqdm=False)[source]

Get a typedef dataframe.

Parameters:: use_tqdm (bool)
Return type:: DataFrame

get_typedef_id_name_mapping()[source]

Get a mapping from typedefs’ identifiers to names.

Return type:: Mapping[str, str]

is_descendant(descendant, ancestor)[source]

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

from pyobo import get_ontology

obo = get_ontology("go")

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

Parameters:

descendant (str)
ancestor (str)

Return type:

bool

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

Iterate over literal properties quads.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[str, str, str, str, str]]

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

Iterate over object property triples.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[str, str, str]]

iter_relation_rows(use_tqdm=False)[source]

Iterate the relations’ rows.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[str, str, str, str, str]]

iter_terms(force=False)[source]

Iterate over terms in this ontology.

Parameters:: force (bool)
Return type:: Iterable[Term]

iter_typedef_id_name()[source]

Iterate over typedefs’ identifiers and their respective names.

Return type:: Iterable[tuple[str, str | None]]

iterate_alt_rows()[source]

Iterate over pairs of terms’ primary identifiers and alternate identifiers.

Return type:: Iterable[tuple[str, str]]

iterate_alts()[source]

Iterate over alternative identifiers.

Return type:: Iterable[tuple[Stanza, NormalizedNamableReference]]

iterate_edge_rows(use_tqdm=False)[source]

Iterate the edge rows.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[str, str, str]]

iterate_edges(*, use_tqdm=False, include_xrefs=True)[source]

Iterate over triples of terms, relations, and their targets.

Parameters:

use_tqdm (bool)
include_xrefs (bool)

Return type:

Iterable[tuple[Stanza, TypeDef, NormalizedNamableReference]]

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

Iterate over tuples of terms and the values for the given property.

Parameters:

prop (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
use_tqdm (bool)

Return type:

Iterable[tuple[Stanza, str]]

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

Iterate over tuples of terms and ther targets for the given relation.

Parameters:

relation (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
use_tqdm (bool)

Return type:

Iterable[tuple[Stanza, NormalizedNamableReference]]

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

Iterate over relationships between one identifier and another.

Parameters:

relation (NormalizedNamableReference | Referenced | Reference | NamedReference | tuple[str, str] | str)
target_prefix (str)
use_tqdm (bool)

Return type:

Iterable[tuple[Stanza, NormalizedNamableReference]]

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

Iterate over xrefs to a given prefix.

Parameters:

prefix (str)
use_tqdm (bool)

Return type:

Iterable[tuple[Stanza, NormalizedNamableReference]]

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

Iterate over pairs of terms’ identifiers and their respective definitions.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[str, str]]

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

Iterate identifier name pairs.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[str, str]]

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

Iterate over terms’ identifiers and respective species (if available).

Parameters:

prefix (str | None)
use_tqdm (bool)

Return type:

Iterable[tuple[str, str]]

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

Iterate over identifiers.

Parameters:: use_tqdm (bool)
Return type:: Iterable[str]

iterate_literal_mapping_rows()[source]

Iterate over literal mapping rows.

Return type:: Iterable[LiteralMappingTuple]

iterate_node_rows(sep=';')[source]

Get a nodes iterator appropriate for serialization.

Parameters:: sep (str)
Return type:: Iterable[Sequence[str]]

iterate_obo_lines(emit_object_properties=True, emit_annotation_properties=True)[source]

Iterate over the lines to write in an OBO file.

Here’s the order:

format-version (technically, this is the only required field)
data-version
date
saved-by
auto-generated-by
import
subsetdef
synonymtypedef
default-namespace
namespace-id-rule
idspace
treat-xrefs-as-equivalent
treat-xrefs-as-genus-differentia
treat-xrefs-as-relationship
treat-xrefs-as-is_a
remark
ontology

Parameters:

emit_object_properties (bool)
emit_annotation_properties (bool)

Return type:

Iterable[str]

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

Iterate over tuples of terms, properties, and their values.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[Stanza, Annotation]]

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

Iterate over identifiers.

Parameters:: use_tqdm (bool)
Return type:: Iterable[NormalizedNamableReference]

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

Iterate over tuples of terms, relations, and their targets.

This only outputs stuff from the relationship: tag, not all possible triples. For that, see iterate_edges().

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[Stanza, TypeDef, NormalizedNamableReference]]

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

Iterate over pairs of identifier and synonym text.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[str, str]]

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

Iterate over pairs of term and synonym object.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[Stanza, Synonym]]

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

Iterate over xrefs.

Parameters:: use_tqdm (bool)
Return type:: Iterable[tuple[Stanza, NormalizedNamableReference]]

to_obonet(*, use_tqdm=False)[source]

Export as a :mod`obonet` style graph.

Parameters:

self (Obo)
use_tqdm (bool)

Return type:

MultiDiGraph

write_cache(*, force=False)[source]

Write cache parts.

Parameters:: force (bool)
Return type:: None

write_default(use_tqdm=False, force=False, write_obo=False, write_obonet=False, write_obograph=False, write_owl=False, write_ofn=False, write_ttl=False, write_nodes=False, obograph_use_internal=False, write_cache=True)[source]

Write the OBO to the default path.

Parameters:

use_tqdm (bool)
force (bool)
write_obo (bool)
write_obonet (bool)
write_obograph (bool)
write_owl (bool)
write_ofn (bool)
write_ttl (bool)
write_nodes (bool)
obograph_use_internal (bool)
write_cache (bool)

Return type:

None

write_edges(path)[source]

Write a edges TSV file.

Parameters:: path (str | Path)
Return type:: None

write_metadata()[source]

Write the metadata JSON file.

Return type:: None

write_nodes(path)[source]

Write a nodes TSV file.

Parameters:: path (str | Path)
Return type:: None

write_obo(file=None, *, use_tqdm=False, emit_object_properties=True, emit_annotation_properties=True)[source]

Write the OBO to a file.

Parameters:

file (None | str | TextIO | Path)
use_tqdm (bool)
emit_object_properties (bool)
emit_annotation_properties (bool)

Return type:

None

write_obograph(path, *, converter=None)[source]

Write OBO Graph JSON.

Parameters:

path (str | Path)
converter (Converter | None)

Return type:

None

write_obonet_gz(path)[source]

Write the OBO to a gzipped dump in Obonet JSON.

Parameters:: path (str | Path)
Return type:: None

write_ofn(path)[source]

Write as Functional OWL (OFN).

Parameters:: path (str | Path)
Return type:: None

write_owl(path)[source]

Write OWL, by first outputting OFN then converting with ROBOT.

Parameters:: path (str | Path)
Return type:: None

write_prefix_map()[source]

Write a prefix map file that includes all prefixes used in this ontology.

Return type:: None

write_rdf(path)[source]

Write as Turtle RDF.

Parameters:: path (str | Path)
Return type:: None