Usage

bioontologies.robot Module

A wrapper around ROBOT functionality.

See also

https://robot.obolibrary.org

Functions

convert(input_path, output_path[, ...])	Convert an OBO file to an OWL file with ROBOT.
convert_to_obograph(input_path, *[, ...])	Convert a local OWL file to a JSON file.
convert_to_obograph_local(path, *[, ...])	Convert a local OWL/OBO file to an OBO Graph JSON object.
convert_to_obograph_remote(iri, *[, ...])	Convert a remote OWL/OBO file to an OBO Graph JSON object.
get_obograph_by_iri(iri[, timeout])	Get an ontology by its OBO Graph JSON iri.
get_obograph_by_path(path, *[, iri])	Get an ontology by its OBO Graph JSON file path.
get_obograph_by_prefix(prefix, *[, ...])	Get an ontology by its Bioregistry prefix.
is_available()	Check if ROBOT is available.

Classes

ParseResults(graph_document, messages, iri)

A dataclass containing an OBO Graph JSON and text output from ROBOT.

bioontologies.obograph Module

Data structures for representing OBO Graphs.

See also

https://github.com/geneontology/obographs

Classes

Definition(*[, val, xrefs, references, ...])	Represents a definition for a node.
Edge(*, sub, pred, obj[, meta, ...])	Represents an edge in an OBO Graph.
Graph(*, id, meta, nodes, edges, ...)	A graph corresponds to an ontology.
GraphDocument(*, graphs)	Represents a list of OBO graphs.
Meta(*[, definition, subsets, xrefs, ...])	Represents the metadata about a node or ontology.
Node(*, id[, lbl, meta, reference, standardized])	Represents a node in an OBO Graph.
Property(*, pred, val[, standardized, ...])	Represent a property inside a metadata element.
Synonym(*, val, pred, synonymType, xrefs, ...)	Represents a synonym inside an object meta.
Xref(*, val[, predicate_raw, predicate, ...])	Represents a cross-reference.