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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Add do-not-annotate to cell wall #21669

Closed cmungall closed 3 years ago

cmungall commented 3 years ago

Rationale:

This creates ragged annotation whereby some things are are annotated to cell wall and sometimes to more specific such as plant cell wall, e.g.

image

This in turn leads to issues with enrichment (1) [minor] testing more hypotheses than is necessary, increasing the p-value (2) confusing duplicative results as in the enrichment here:

https://github.com/geneontology/helpdesk/issues/322

Surely in all cases it should be possible to make a more specific annotation. Presumably I know if I am making a plant vs fungal cell wall

image

Note: for cases like this where the differentia is a taxon we could auto-infer deeper placement via gaferencer. But it seems simpler just to put this back on the annotation provider.

pgaudet commented 3 years ago

So, we'd recommend:
bacteria: annotate to GO:0009274 peptidoglycan-based cell wall plants: annotate to GO:0009505 plant-type cell wall fungi: GO:0009277 fungal-type cell wall archae = ??? GO:0030115 S-layer ? (see PMID:31214995)