Annotation Conf. Call 2016-04-26: Difference between revisions
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==Annotation Consistency Exercise== | ==Annotation Consistency Exercise== | ||
From PomBase | |||
PMID: 11493649 | |||
Fission yeast mfr1 activates APC and coordinates meiotic nuclear division with sporulation. | |||
Related Github tickets (These are quite long so I'll attempt to summarize): | |||
https://github.com/geneontology/go-ontology/issues/11977 | |||
The question here, was whether we needed a term for the APC complexed with its various inhibitors (researchers usually refer to these complexes as APC-(inhibitor/activator superscript) ). This gets quite complicated, because there are different activators and activators for different substrates at different cell cycle transitions, and for mitotic and meiotic cell cycles. | |||
I believe that the consensus from the GO meeting is that we don't need these terms, and we use "x complex binding" to represent these specific inhibitor/activator-complex interactions (the logic being that only the functional complex is represented in GO)? | |||
The second issue, was that we were following a precedent, and requesting these specific "APC-activator activity" terms. | |||
https://github.com/geneontology/go-ontology/issues/11757 | |||
The solution here was simple. The terms will all be merged back to the "function" term (i.e ubiquitin ligase activity, ubiquitin ligase inhibitor activity, and ubiquitin ligase activator activity). So, although these terms still exist they will be merged very soon. | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] | ||
Revision as of 09:04, 21 April 2016
Conference call Format
Standard Bluejeans link from meting home page
Agenda
IDA or IEP for an isoform annotation
Recently Karen was annotating a paper where an isoform-agnostic antibody was used to detect the presence of a protein in a cell. Subsequent experiments showed that an RNA coding for a specific isoform had the same localization, supporting that the protein isoform was localized to that component. The question came up as to whether we should use IDA or IEP for evidence to support this. Since the experiment did not address the protein isoform itself, is it an IDA?
Also worth noting that if we decide that this is IEP, we will need to change the rules on the validation script that checks GAFs since IEP is currently only allowed for Process annotations.
Switching over automated pipelines
How difficult would it be for groups to switch over their automated pipelines to allow us to give accurate attribution to groups who make the annotations?
Annotation Consistency Exercise
From PomBase
PMID: 11493649 Fission yeast mfr1 activates APC and coordinates meiotic nuclear division with sporulation.
Related Github tickets (These are quite long so I'll attempt to summarize):
https://github.com/geneontology/go-ontology/issues/11977 The question here, was whether we needed a term for the APC complexed with its various inhibitors (researchers usually refer to these complexes as APC-(inhibitor/activator superscript) ). This gets quite complicated, because there are different activators and activators for different substrates at different cell cycle transitions, and for mitotic and meiotic cell cycles. I believe that the consensus from the GO meeting is that we don't need these terms, and we use "x complex binding" to represent these specific inhibitor/activator-complex interactions (the logic being that only the functional complex is represented in GO)?
The second issue, was that we were following a precedent, and requesting these specific "APC-activator activity" terms. https://github.com/geneontology/go-ontology/issues/11757 The solution here was simple. The terms will all be merged back to the "function" term (i.e ubiquitin ligase activity, ubiquitin ligase inhibitor activity, and ubiquitin ligase activator activity). So, although these terms still exist they will be merged very soon.