Reference

biomappings.gilda_utils Module

Utilities for generating predictions with pyobo/gilda.

Functions

`append_gilda_predictions`(prefix, ...[, ...])	Add gilda predictions to the Biomappings predictions.tsv file.
`iter_prediction_tuples`(prefix, provenance, *)	Iterate over prediction tuples for a given prefix.
`filter_custom`(predictions, custom_filter)	Filter out custom mappings.
`filter_existing_xrefs`(predictions, prefixes)	Filter predictions that match xrefs already loaded through PyOBO.
`has_mapping`(prefix, identifier, target_prefix)	Check if there's already a mapping available for this entity in a target namespace.

biomappings.utils Module

Utilities.

Functions

`get_git_hash`()	Get the git hash.
`get_script_url`(fname)	Get the source path for this script.
`get_canonical_tuple`(mapping)	Get the canonical tuple from a mapping entry.
`check_valid_prefix_id`(prefix, identifier)	Check the prefix/identifier pair is valid.
`get_curie`(prefix, identifier, *[, preferred])	Get a normalized curie from a pre-parsed prefix/identifier pair.

Classes

`UnregisteredPrefix`	Raised for an invalid prefix.
`UnstandardizedPrefix`(prefix, norm_prefix)	Raised for an unstandardized prefix.
`InvalidIdentifier`(prefix, identifier)	Raised for an invalid identifier.
`InvalidNormIdentifier`(prefix, identifier, ...)	Raised for an invalid normalized identifier.
`InvalidIdentifierPattern`(prefix, identifier, ...)	Raised for an identifier that doesn't match the pattern.

Class Inheritance Diagram

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biomappings.testing Module

Validation tests for biomappings.

Classes

`IntegrityTestCase`([methodName])	Data integrity tests.
`PathIntegrityTestCase`([methodName])	A test case that can be configured with paths.

Class Inheritance Diagram

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