QCQA next call: Difference between revisions
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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). | 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. | 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 | |||
[[Category:Quality Control]] | [[Category:Quality Control]] | ||
Revision as of 10:30, 13 August 2018
- What should the QC priorities be ?
- Which annotation validation rules are currently implemented ? https://github.com/geneontology/go-annotation/issues/1928
- 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?