Annotation Conf. Call August 27, 2013: Difference between revisions
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** Do we capture targets or substrates if it is an invitro assay | ** Do we capture targets or substrates if it is an invitro assay | ||
** FUS3 has to be phosphorylated by STE7 for it to phosphorylate FAR1. Should the relationship be dependent_on or requires_regulator? | ** FUS3 has to be phosphorylated by STE7 for it to phosphorylate FAR1. Should the relationship be dependent_on or requires_regulator? | ||
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Annotation extension to be discussed for the term establishment of protein localization to chromatin (BP) for SCC2 gene. | Annotation extension to be discussed for the term establishment of protein localization to chromatin (BP) for SCC2 gene. | ||
http://www.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?locus=scc2 | http://www.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?locus=scc2 | ||
{| class="wikitable" border="1" | |||
!DB (Col 2) | |||
!GO ID (Col 5) | |||
!ev.code | |||
!Reference (Col 6) | |||
!Extension (Col 16) | |||
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|GO: | |||
|IDA | |||
|PMID:10882066 | |||
|has_direct_input: | |||
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Revision as of 18:42, 23 August 2013
Agenda
Mailing lists, SF tracker etc
Val asked me (Rama) to give a refresher on where one should post what messages/questions. The following is what I have so far.
- SourceForge- for ontology term requests, annotation issues (mappings mostly)
- GO Help desk- when you dont know how to get some data, report something is not working (like AmiGO or the website)
- Mailing lists- make announcements, ask annotation related questions (which evidence code etc)
- Seth et al are using github to collect AmiGO2 bugs (https://github.com/kltm/amigo/issues), but if you can't find this URL, feel free to send email to go-help or post a message on go-consortium mailing list
Annotation Extension exercise
Annotation Extension to be discussed for the MAP kinase activity annotation for FUS3. GO annotations for FUS3- http://www.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?dbid=S000000112
DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
---|---|---|---|---|
FUS3, P16892 | GO:4707 (MAP kinase activity) | IDA | PMID:8384702 | has_direct_input: FAR1, requires_regulator:STE7 |
STE7, P06784 | GO:4708 (MAP kinase kinase activity) | IDA | PMID:8384702 | has_direct_input: FUS2, has_input: MF(ALPHA)1 (pheromone) |
- Questions for paper1:
- Do we capture autophosphorylation?
- Do we capture targets or substrates if it is an invitro assay
- FUS3 has to be phosphorylated by STE7 for it to phosphorylate FAR1. Should the relationship be dependent_on or requires_regulator?
- Paper 2: PMID 10882066 (Title: Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins.)
Annotation extension to be discussed for the term establishment of protein localization to chromatin (BP) for SCC2 gene. http://www.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?locus=scc2
DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
---|---|---|---|---|
GO: | IDA | PMID:10882066 | has_direct_input: |