pypath.inputs.go.go_annotations_goose§

pypath.inputs.go.go_annotations_goose(organism=9606, aspects=('C', 'F', 'P'), uniprots=None)[source]§

Queries GO annotations by AmiGO goose.

IMPORTANT: This is not the preferred method any more to get terms and annotations. Recently the preferred method to access GO annotations is pypath.inputs.go.go_annotations_solr. The data in GO MySQL instances has not been updated since Dec 2016. Unfortunately the providers ceased to support MySQL, the most flexible and highest performance access to GO data. The replacement is Solr which is far from providing the same features as MySQL.

Returns terms in dict of dicts and annotations in dict of dicts of sets. In both dicts the keys are aspects by their one letter codes. In the term dicts keys are GO accessions and values are their names. In the annotation dicts keys are UniProt IDs and values are sets of GO accessions.

Parameters:

organism (int) – NCBI Taxonomy ID of one organism. Default is human (9606).
aspects (tuple) – GO aspects: C, F and P for cellular_component, molecular_function and biological_process, respectively.
uniprots (list) – Optionally a list of UniProt IDs. If None, results for all proteins returned.