QCQA next call: Difference between revisions

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http://wiki.geneontology.org/index.php/QCQA_call_2018-08-21


=New error reports=
Action points from GOC meeting
http://snapshot.geneontology.org/reports/gorule-report.html
* Using Matrix more widely for QC
Discuss - feedback and priorities
* See whether FlyBase Annotation Saturation strategy can be used at a larger scale


= github tickets =
* Remove all PINC annotations?
== Ontology tracker ==
*[https://github.com/geneontology/go-ontology/issues/16108 GO:0071554 cell wall organization and biogenesis taxon restrictions #16108]


=How to blacklist papers=
=UniProt annotation issues=
This would include retracted papers and predatory journals
* Figure out a way to export users from UniProt annotations
https://github.com/geneontology/go-annotation/issues/2029
* Could we have the ORCID for everyone ?


= New QC check? =
*Check for genes annotated to an MF as well as BP 'regulation of that same MF'?
*Would that ever make sense?
*See https://www.uniprot.org/uniprot/Q7Z7L7 as an example
= 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
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?
**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)
*Annotation redundancy - non-experimental annotations
**Can we come up with a proposal for the Montreal meeting?
**http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda#Handling_redundant_information
* GO-CAM QC plan
** including SynGO, > 90 % of the production models




[[Category:Quality Control]]
[[Category:Quality Control]]

Latest revision as of 07:06, 28 June 2019

Action points from GOC meeting

  • Using Matrix more widely for QC
  • See whether FlyBase Annotation Saturation strategy can be used at a larger scale
  • Remove all PINC annotations?

UniProt annotation issues

  • Figure out a way to export users from UniProt annotations
  • Could we have the ORCID for everyone ?