Annotation polishing

Annotation polishing focuses on making existing model annotations more consistent and MIRIAM-compliant. It is useful when a model already contains identifiers, but not if the URI patterns, qualifiers or annotation formatting are inconsistent.

The command-line entry point is:

refinegems curate annotations MODEL.xml --outdir polished_annotations

Internally, this uses polish_annotations(). The function checks the annotation resources attached to model entities, generates MIRIAM-compliant URI patterns and writes a table of invalid annotations, that could not be fixed, to the output directory.

The option --new-pattern controls whether the newer CURIE pattern database_prefix:local_identifier is used when creating identifiers:

refinegems curate annotations MODEL.xml --new-pattern True --outdir polished_annotations

When to use

Use annotation polishing before downstream workflows that depend on machine-readable identifiers, for example pathway addition, gap-filling or external quality checks. It can also be useful before comparing models, because normalised identifiers reduce the number of differences caused only by formatting.