Version 599 (modified by vw253, 7 years ago) (diff)


PomBase Curator Meetings


Next Items, in rough order of priority

Curation priorities

Other tasks

  • which other releations need to be included in Canto?
  • Discussion about search behavior for phenotypes (alleles, conditions, multigene, and GO extensions Decided:
    • For now we will only provide allele type filter (ignore conditions, penetance, expressivity) for phenotype, Midiri will do a mock up (null expression/overexpression)
  • Discussion for how to handle searches on GO extensions was postponed, and will be addressed when we go through the relations list and decide what type of queries might be useful
  • For multi gene phenotypes so far decided
    • will need to be able to search on a phenotype and then filter on one of i) single gene phenotype. Single gene phenotype only will allow the allele filter option. II) single or multi gene phenotype iii) multi gene phenotype only
  • we are not currently sure what the results page should show. Two types of output, geneotype list and genes. A summary of the geneotype list and the gene list? discuss this next.
    • The gene list will populate the current query history table. but the query history will need an additional table for geneotypes (what do we want to be able to do with geneotype lists in the history?)
    • need the ability to filter results to present genotypes with a specific gene
  • How the landing pages from ontology terms should be handled


  • logs, val 49, antoni 50, midori 51
    • reminder, include the GO terms we don't annotate (canto only)

Things to do after multi-gene phenotypes available

  • update curation tool documentation
  • get some example multigene phenotypes visible on pomBase pages ( where is display mock-up )
  • update pombase web documentation to reflect new in
  • announce multi gene phenotype availability
    • make podcasts to demo curation tool (announce on pombelist)
    • send out session reminders, and new sessions
    • target individual groups who have not participated, or who have stalled sessions

Ontology questions

Annotation issues, syntax, procedures, extensions etc

  • annotate to protein complex ID (can get from PRO)?
    • example: PMID:18723846 has direct assays showing ORC binding to origin DNA, but doesn't distinguish subunits; from other work, it's known that some but not all ORC subunits actually make contact with DNA. Annotate all to DNA binding anyway, with or without contributes_to, or annotate to a complex ID? (I'd prefer the latter but will it break anything?)
    • same paper: similar issue for annotation extension - cdt1 or cdc18 increase ORC origin binding - put complex ID in has_regulation_target ext?
  • 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)
  • How to capture phenotypes from PMID:15941470? Cdc23S424::Tcs allele has TEV cleavage site introduced after Ser424; TEV protease removes C-terminal 170 amino acids, so when TEV protease is expressed, you see what happens to the cell when Cdc23 is truncated. I've thought of three bad ways to annotate, and no good ways (details stashed in note-to-self file; some also in (mah)
  • 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 BYGa and Toronto, will begin to pin down dates. Antonia will try to set up some whilst at BYG

PomBase website

  • Phenotypes for double mutants
    • Jira tickets for display changes: PB-1836 and sub-tasks
    • querying/enrichment etc (postponed, discuss in context of querying alleles, conditions etc plan for 2 days, 2nd day with Mark)
  • GO display
  • Gene page changes to do through with Mark in person
    • compact GO & FYPO displays as in Jira tickets above
    • column sorting (click header etc.)
    • clever ways to group ontology terms by some sort of similarity measure
    • redundancy filtering, esp. for GO
    • user configuration
      • page section order
      • compact vs. expanded view (where relevant)
      • show/hide page sections

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 penetracne 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
  • 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.