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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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Review guidelines for manual annotations (ISA/ISM/ISS) using protein familes resources in 'with' #2295

Open pgaudet opened 5 years ago

pgaudet commented 5 years ago

Should they be subject to the 1-year expiration date rule?

We probably want to remove old 'ISM-like' annotation: TIGR_TIGRFAMS identifier in their with/from. The type of the entities supplied by these two databases is not compatible - according to the rules in eco-usage-constraints.yaml - with the ISS evidence code (strictly, not compatible with ECO:0000250); however, it is compatible with ECO:0000247 (ISA).

Should we change the rule?

ValWood commented 5 years ago

I would prefer not, we have 1555 ISM applied carefully over ti,e with the same criteria as ISM/ISS. Eventually they will hopefully be replaced by EXP or PAINT, but I don't want to lose them as they are not currently available from any other source. They are mainly used for large families (like fungal transcription factor families), where is not possible to infer orthology, but the entire family is known to be involved in a specific process.

A suggestion for the TIGRFAMS, these should all be possible to supersede by InterPRO mapping if they were valid (many may not even be correct, a LOT of protein family mappings get refined).

It might be worth to get a list of the "term/TIGRFAM ID pair" and check the current InterPRo mappings include these annotation. This would not take to long and would bring everything up to date. Perhaps InterPRo could help with this once we know the size of the list. It makes sense to mintain these annotation in the non-maintained sets as IEA this way they will become subject to natural QC as families are updated and refined, so they would no longer become stagnent. Once we know the valid mappings are covered this annotation set could be discontinued.