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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Parse manually curated file and map YeastPathway IDs to BPs #260

Closed dustine32 closed 1 year ago

dustine32 commented 1 year ago

For #255.

This adds the new lookup file (yeast_pathway_ids_to_process_gos.tsv). If not found in this file it will fall back to checking MetaCyc xrefs in the GO ontology already implemented in #159.

Includes a standard test checking that a pathway's main process node is of type GO:0006696.

kltm commented 1 year ago

Naturally, merge with freedom.

A did want to ask about the origin of this mapping file. As this is a one-off ingest, it doesn't really matter, but where did it come from?

dustine32 commented 1 year ago

@kltm Right, thank you! I forgot to say how I created the lookup file.

Originally from the YeastPathways2BP spreadsheet @suzialeksander and Stacia manually filled in. Available here: https://docs.google.com/spreadsheets/d/1TklacC5v_kFgA-iXLMjZ0-RZTnoGDgv3/edit#gid=422325565 I just copy-pasted columns 1 (Pathway ID) and 3 (BP GO term) into a TSV to make yeast_pathway_ids_to_process_gos.tsv.