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geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
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GO_REF:0000051 deprecated #2152

Open ValWood opened 1 year ago

ValWood commented 1 year ago

We use this for NAS, I can't find the memo about deprecation, but I have 641 errors in the GO checks file.

what reference should we use for NAS?

I usually use it when I am expecting the annotation to be over-ridden soon by PAINT, or another source but I can't make an ISO because the publication is new and hasn't been annotated. It seems odd to use the publication ID here because fission yeast is not mentioned.

My aim is to purge all NAS in the next couple of years, they are reduced from 1000 in 2017.

pgaudet commented 1 year ago

There is no ticket, I had emailed you.

I thought NAS's were still authors statements, ie they should cite a PMID.

GOREF_0000051 talks about Keywords:

S. pombe keyword mapping Active 2006-2012. Keywords derived from manually curated primary annotation, e.g. gene product descriptions, are mapped to GO terms. Annotations made by this method have the evidence code Non-traceable Author Statement (NAS), and are filtered from the PomBase annotation files wherever another annotation exists that is equally or more specific, and supported by experimental or manually evaluated comparative evidence (such as ISS and its subtypes). Formerly GOC:pombekw2GO.

This seems a bit different from what you are describing above.

ValWood commented 1 year ago

Ah right, i got confused. We do have some legacy NAS made from keywords too. Most of these are probably now covered by other annotations but some do still exist.

I suggest to reinstate for now, and when I get a new curator, hopefully in the NY (advertising soon), I'll put them on to this.

pgaudet commented 1 year ago

Reinstated.

I also remove the comment 'Active 2006-2012.', since it looks like this method is still valid (even though there may not be new annotations using that).