Version 648 (modified by vw253, 6 years ago) (diff)


PomBase Curator Meetings


Next Items, in rough order of priority

Curation priorities

  • Processing phenotype screens
    • Down to one assigned to Jurg (community) and one where I have a couple of questions to discuss (midori 2015-03-25)
  • General curation priorities based on biology
  • make podcasts to demo curation tool (announce on pombelist)
  • return papers to submitters if we think they haven't done some data-types (still thinking about this)

  • conflicting extensions used for 'binding of promoter' 'binds' and 'at', see cdc10 and res2

Ontology questions

  • Q when we say ‘arrest’ what do we mean?, should all 'arrest' phenotypes distinguish between normal and abnormal (should cell cycle arrest phenotype, and some children, be not for direct annotation)

Annotation issues, syntax, procedures, extensions etc

  • protein domain specific binding, see example in e-mail
  • discuss Rama's question about "response to" extensions
    • also discuss what is being regulated here .....I don't think it is -ve reg of the transition (this acts through cdc2 and not through trancription)
  • PENDING Val will look into this during G1/S cell cycle updates (not to self, background thread is in curation meeting folder)
  • longer term: decide what IDs we actually want to enter at curation time (and whether Canto or Chado should do any fancy mapping taking ontology term and extension relation into account)

Curation issues biology (by 'slim' or broad annotation topic)

Cell Cycle

Chromatin Organization

  • regulation of histone modifications., GO or phenotype? /curs/97535c919f7436fe thread

Establishment and/or maintenance of Cell Polarity

  • discuss establishment of cell polarity and the signalling network (MOR)

(see e-mail Created new session 31b82829d0c47e4d from PMID:23649273 )


  • Canto documentation required
    • From Scott: provide even one paper and walk the user through entering the paper, the genes and a sample entry. Then you could also walk through an administrative approval and saving the data to Chado (Kim suggested we start with just a list of bullet points)
    • and

Community curation paper

  • Community curation spreadsheet: Community Curation errors spreadsheet replace
  • Talk about spreadsheets. We should be able to use Canto to report differences between curator and community now all annotations have recorded person. The only thing we won't be able to capture is when a curation is wrong an d is deleted and replaces so we will need to continue to monitor this?
  • Discuss paper outline (contents)

Lower priority

  • Discuss the item about capturing phenotypic observations vs. Phenotypes thread PMID:19033384 (postponed, needs more thinking, we don't completely know what to do about it)
  • Val- update on phenotype mapping, where it is, what to do with removed annotations
  • advanced search, better to have just query management ?
  • how to represent the reintegration assays ? (see for example Alper/Partridge and Shanker/Partridge
    • decided for now just to represent the deletion phenotype, and then do a GO process for the 'reestablishment etc.