QCQA call 2018-10-02

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New error reports

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

  • Discuss - feedback and priorities

Discussion: New error reports

Feature requests:

  • GO rule info (hover)
  • Copy original GAF header to the top of the report
  • Rewrite owlchecks rules
  • Display SPARQL results

-> Emailed Eric

github tickets

Ontology tracker: x catabolism in other species

Discussion: x catabolism in other species

Keep for now; it's ok to annotate 'x catabolic process' if a cell is degrading x, even if it doesn't produce it.


How to blacklist papers

This would include retracted papers and predatory journals https://github.com/geneontology/go-annotation/issues/2029

Discussion: How to blacklist papers

  • For now, we'll do an exclusion list of papers that we dont want to annotate, or papers/Gene/GOID
  • Discuss the idea of creating a 'paper skipped' list (Google form ? Other more sophisticated mechanism?)
  • AI: Add to Annotation documentation: List of predatory journals

New QC check?

Discussion: New QC check?

  • AI: Add new rule proposal

DONE: https://github.com/geneontology/go-site/issues/838

Reported from the previous meeting

  • Should Taxon checks be a hard check:

https://github.com/geneontology/go-site/issues/660 https://github.com/geneontology/go-site/issues/758

  • 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.

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

Discussion: SPKW

Kimberly: WB looking into the information added by SPKW in WormBase. From that evaluation we can perhaps decide whether we want to keep them.


Annotation redundancy - non-experimental annotations

Discussion: Annotation redundancy - non-experimental annotations

On the Montreal agenda - we will document then (or before)

To discuss at future meeting

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