Annotation Conf. Call November 26, 2013: Difference between revisions
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Any questions on Jenkins email alerts about your GAF files? | Any questions on Jenkins email alerts about your GAF files? | ||
===Curation question=== | |||
* We noticed that there are some histone kinase terms that include the name of the residue that is being phosphorylated in the term name itself | |||
(http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0035174#lineage). Although histones are very well conserved, there are still some differences in the sequence and the serine is always not in the same position in all organisms, but often the context is the same (i.e it is +/- one or two residues). | |||
**should we requesting a new term for each specific residue | |||
**should there be a taxon constraint (because for example, position 14 in H2B may not have serine in all organisms) | |||
===Column-16 curation questions=== | ===Column-16 curation questions=== | ||
Revision as of 14:57, 25 November 2013
Agenda
Jenkins email alerts
Any questions on Jenkins email alerts about your GAF files?
Curation question
- We noticed that there are some histone kinase terms that include the name of the residue that is being phosphorylated in the term name itself
(http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0035174#lineage). Although histones are very well conserved, there are still some differences in the sequence and the serine is always not in the same position in all organisms, but often the context is the same (i.e it is +/- one or two residues).
- should we requesting a new term for each specific residue
- should there be a taxon constraint (because for example, position 14 in H2B may not have serine in all organisms)
Column-16 curation questions
- Forward annotation example: In yeast, CNB1 is the regulatory subunit and CNA1 and CMP2 are the catalytic subunits of the Calcineurin complex (http://www.yeastgenome.org/cgi-bin/GO/goTerm.pl?goid=5955, phosphatase complex).
| DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
|---|---|---|---|---|
| CNB1 | GO:8597 (calcium-dependent protein S/T phosphatase regulator activity) | IDA | PMID:1321337 | has_regulation_target: CNA1, CMP2 |
| CNA1 | GO:4723 (calcium-dependent protein S/T phosphatase) | IDA | PMID:1321337 | requires_regulator: CNB1 |
| CMP2 | GO:4723 (calcium-dependent protein S/T phosphatase) | IDA | PMID:1321337 | requires_regulator: CNB1 |
- RAD51 has increased strand exchange activity in the presence of RPA complex. How do we capture this in col-16?
| DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
|---|---|---|---|---|
| RAD51 | GO:recombinase activity | IDA | PMID:8066464 | ? (Replication protein A complex serves as an accessory factor or regulator, but RPA is a complex) |
- Would you add the substrate information in col-16 for phosphorylation BP annotation if we have already captured the substrate for the Kinase activity, MF annotation?