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

Paper 1: PMID 8384702 (Title: MAP kinase-related FUS3 from S. cerevisiae is activated by STE7 in vitro)

File:PMID8384702.pdf

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.)

File:PMID10882066.pdf

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