Version 489 (modified by val_wood, 8 years ago) (diff)


PomBase Curator Meetings


Done 21st/22 Jan

  • Discussed BIoGRID issue reported by Kathy yesterday, and by Henry previously
    • see my response waiting e-mail folder
      • waiting to hear back from BioGRID
  • brainstormed mockup of graphical display of modifications and mutations in sequence context
    • Done a first pass, Val (or somebody) will mock up, see Ensembl variation image
  • look at these process annotations (compare function/ process, and consider in response to)
  • Val to document that annotations should be made preferentially on function with regulation targets and conditions.
  • Obsolete annotation in biological process can be removed AI Val tidy pap1 TF as discussed at curator meeting / promoter DNA binding, it has the promoter and tf regulated. Always represent on MF if possible


  • text, for whether a paper contains curatable gene or not (is this OK?) (YES, OK)
  • text, Add allele and evidence misleading "add more alleles using this term" (non issue)
  • text, do you want to transfer evidence or condition (
  • evaluating curtain tool, where do people expected to go (gene page or summary page) after annotation completion? - if I have annotated a single gene I expect to stay on that page. I f I have transferred annotations I feel as though I should go back to the summary page. Or is that odd? (non issue)


  • cut phenotype (DONE new ticket raised to correct existing term, will need to obsolete and reannotate)

Physical Interactions

  • Antonia - Should we add GO/protein binding terms for enzyme/substrate combinations?
    • Antonia should we use the BioGRID evidence code "biochemical activity" which we don't use at the moment.
      • No but can capture high confidence with GO protein binding
  • Discussed when to capture physical interactions in GO using 'protein binding' in general.
    • Only for direct, high confidence interactions. I.e within complex, or modification/target

PomBase gene page overhaul

  • Descided how we would like to display annotations to streamline/ hide redundancy
  • changes to data layout and sorting on gene page, user configuration Val to mock up and document

Next Items, in rough order of priority


  • plan roadshow dates/places
    • Val will get UK lab list
    • Midori will draft e-mail


Phenotypes for double mutants

  • display/
  • querying/enrichment etc (we can probably bump this to next meeting?)

Ontology questions

  • has_output between process and structure phenotypes, e.g. abolished actomyosin contractile ring assembly has_output contractile ring absent I am not sure what the question is, but I guess there must be one, so I think the first question is to guess the question.
  • Discuss has_part in relation to annotation propagation in Canto
    • SF 566 use has_part relationships for ontology term drill-down (related thread is 'using has_part for ontology drill down' and NTR: srebp catabolism for an illustration Q are phenotype has_parts visible in the curation tool?
  • Discuss the item about capturing phenotypic observations vs. Phenotypes thread PMID:19033384

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)

Curation issues syntax and ontologies

  • penetrance high/medium/low
    • see e-mail "extending penetrance extensions"

Curation issues biology

  • secretion vs. exocytosis "If proteins are secreted only by exocytosis in fission yeast, I can add synonyms to the FYPO terms, even though the corresponding synonyms wouldn't work for GO (nor for the generic cell phenotype uber-ontology)" (e-mail 'mug33 checks 2')
  • representing core stress response genes and "response to stress", specifically i) stress signalling ii) antioxidents etc (thread 'Annotation extension paper' this came up in AE pper egs)

  • Go through curation tracker, assign people, priorities
  • Tidy wiki, move obsolete pages

Lower priority

  • 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- Go through curation tracker high priority items (some are duplicated below)
  • 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.

  • Genetic interactions ontology
  • Discuss regulation of G1/S in relation to 6ff4c9edff12167b (look at annotation in context of all genes in this session)
  • discuss establishment of cell polarity and the signalling network (MOR) (see e-mail Created new session 31b82829d0c47e4d from PMID:23649273 )
  • Curating alternative transcripts
  • transcription related Sushils thesis and e-mail "2 MF transcription terms, sound the same"
  • regulation of histone modifications., GO or phenotype? /curs/97535c919f7436fe thread

Later/ In progress

  • check Biogrid data alignment progress with Antonia

  • In progress
  • how to represent the reintegration assays ? (see for example Alper/Partridege? and Shanker/PArtridge
    • decided for now just to represent the deletion phenotype , and then do a GO process for the 'reestablishment etc.