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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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Review NOT annotations with an extension #2109

Open pgaudet opened 5 years ago

pgaudet commented 5 years ago

Hello,

There is a new rule that would forbid NOT annotations with extensions. Most annotations are from MGI @ukemi

https://docs.google.com/spreadsheets/d/172dNbAfDDGa11-inan_yQQPt6hONDPtwtigFxmPHra4/edit#gid=0

Can you have a look and see if that new rule is OK for you ?

Thanks, Pascale

ukemi commented 5 years ago

Why is this rule in place? Annotation extensions add specificity to GO terms themselves, so it is no different than creating a specific GO term and then adding a NOT annotation to it.

RLovering commented 5 years ago

I thought this rule had always been in place. the problem is if the extension is not applied then 'NOT' is just to the term, and sometimes people want to say "NOT" only with the extended term and not to the basic term.

ukemi commented 5 years ago

Hmm. If the extension is in place, then the NOT should only be applied to the extended term. There are other cases where a NOT is in pace for one gene product of a given gene, but not another. If the gene products are not specified in enough detail, then it can look like a gene has both a NOT annotation and a 'positive' annotation to the same gene.

hdrabkin commented 5 years ago

If something is found to be involved in a process in the liver but not in the kidney (was looked at), I would certainly use the "NOT" for the annotation to the kidney.