QCQA next call: Difference between revisions

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== Ontology tracker ==
== Ontology tracker ==
*[https://github.com/geneontology/go-ontology/issues/16108 GO:0071554 cell wall organization and biogenesis taxon restrictions #16108]
*[https://github.com/geneontology/go-ontology/issues/16108 GO:0071554 cell wall organization and biogenesis taxon restrictions #16108]
=How to blacklist papers=
This would include retracted papers and predatory journals
https://github.com/geneontology/go-annotation/issues/2029
= 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]]

Revision as of 16:53, 30 August 2018

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

github tickets

Ontology tracker

How to blacklist papers

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


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.

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