Annotation Conf. Call November 26, 2013: Difference between revisions

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* RAD51 has increased strand exchange activity in the presence of RPA complex. How do we capture this in col-16?
* RAD51 has increased strand exchange activity in the presence of RPA complex or RPA promotes this activity. For the RPA "promoted" part, we can't use "activated_by" relationship in col 16, because this relationship is only appropriate for chemicals. We could capture this is an forward annotation for RPA: create a new term for positive regulation of strand invasion and annotate RPA to this term with target rad51 - the problem: the subunits will have to be annotated to this term and not the complex as a whole. Can activated_by relationship be relaxed for use in these situations or do we have to wait to annotate to complexes as objects.


{| class="wikitable" border="1"
{| class="wikitable" border="1"
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|IDA
|IDA
|PMID:8066464
|PMID:8066464
|? (Replication protein A complex serves as an accessory factor or regulator, but RPA is a complex)
|? (Replication protein A complex serves as an accessory factor or activated_by, 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?
* 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?

Revision as of 20:17, 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

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 or RPA promotes this activity. For the RPA "promoted" part, we can't use "activated_by" relationship in col 16, because this relationship is only appropriate for chemicals. We could capture this is an forward annotation for RPA: create a new term for positive regulation of strand invasion and annotate RPA to this term with target rad51 - the problem: the subunits will have to be annotated to this term and not the complex as a whole. Can activated_by relationship be relaxed for use in these situations or do we have to wait to annotate to complexes as objects.
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 activated_by, 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?