Version 644 (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


  • Sushil Tripathi's thesis and e-mail "2 MF transcription terms, sound the same"

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
  • Tidy wiki, move obsolete pages


  • plan roadshow dates/places
    • Val will get UK lab list (done)
    • Midori will draft e-mail (done)
    • after BYG and Toronto, will begin to pin down dates. Antonia will try to set up some whilst at BYG

  • Newsletter?
  • Gene naming 3578 genes primary name assigned (now 3671)
  • annotation complete genes
  • annotation amnesty
  • solicit more HTP datasets
  • unknowns
  • curation progress (numbers),
    • community, new tool, focussed efforts, areas, networks, resources allocation, reduced staffing numbers

PomBase website

  • Future Gene page changes
    • column sorting (click header etc.)
    • user configuration (page section order/ compact vs. expanded/show/hide page sections)
    • mock something up for so M will understand what V wants on the HTP submission form

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)

  • collection of phenotype images
  • Low penetrance check (I think this is about population phenotype-> fully penetrant?)

  • Idea for accessing completed curation sessions add review links to paper section for community curated papers
  • Future Pombelist posts
    • physical interaction Biogrid vs GO
    • phenotypes vs. processes
    • Did you know's
    • Adding gene names
    • preparing HTP datasets
    • community curation demo etc
    • alignments Draw attention too specifically, Update re improved alignments and Schizos new 'did you knows'
    • CommunityAlerts etc
  • gene name descriptions to phenotypes, add to phenotype ontology for searching?

  • Val- update on phenotype mapping, where it is, what to do with removed annotations
  • Antonia- Summarize community curation session quality/ ommissions
  • Val- viability exercise results (query intersection)
  • PHAF/GPAD/GPI files for export/import etc.
  • advanced search, better to have just query management ?
  • Genetic interactions ontology
  • 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.