Annotation Conf. Call August 27, 2013: Difference between revisions
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====Paper 2: PMID 10882066 (Title: Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins.)==== | ====Paper 2: PMID 10882066 (Title: Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins.)==== | ||
[[File:PMID10882066.pdf]] | |||
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. |
Revision as of 18:52, 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) |
---|---|---|---|---|
SCC2, Q04002 | GO:71169 | IMP | PMID:10882066 | has_target: GO:0034990, happens_during: GO:6260/DNA replication |