QCQA next call

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Preparing for GOC meeting

Annotation redundancy - non-experimental annotations

Discussion: Annotation redundancy - non-experimental annotations

Different types of redundancy

There is no use case for users of MODs and AMiGO to see automated annotations when EXP annotations are present. If somebody wants a complete set of annotations from a mapping resource these could be made available separately.

New error reports - status

http://snapshot.geneontology.org/reports/gorule-report.html https://github.com/geneontology/go-site/issues/709

How to blacklist papers

Pascale

  • List/form template of excluded papers or combinations of PMID/Gene/GO

Update: Unmaintained annotation sets

https://github.com/geneontology/go-annotation/issues/1724#issuecomment-390136730

  • AI: check status with Tony - Unmaintained annotation sets

TIGR, JCVI, PAMGO ISS annotations: Michelle: The ISS annotations from at least TIGR (and should be also JCVI and PAMGO) were all manual. They were either matches to HMMs or based on pairwise alignments. We used IEA for any annotations that were automatic from our pipeline and not reviewed. I assume JCVI continued that process after I left - at least until they stopped using their pipeline and shifted completely to using the NCBI PGAP tool (prokaryotic genome annotation pipeline). I think we (and hopefully PAMGO) were pretty good about using the GO_REFs to indicate whether it was HMM or pairwise. The problem with replacing our HMM annotations with InterPro2GO mappings is that we made much more specific annotations based on HMMs than what the InterPro mappings often do. I'd hate to lose those but I understand your desire to keep the annotations current.

Reported from the previous meeting

  • GO-CAM QC plan
    • including SynGO, > 90 % of the production models


To revisit later

SPKW hierarchy - at odds with transitivity as found in GO ontology?

    • https://github.com/geneontology/go-annotation/issues/2036
    • emailed Chris, Seth about help with querying the GO database for non-redundant SPKW-based annotations (2018-08-16)
    • Kimberly: WB looking into the information added by SPKW in WormBase. From that evaluation we can perhaps decide whether we want to keep them.