Version 525 (modified by val_wood, 7 years ago) (diff)


PomBase Curator Meetings


Next Items, in rough order of priority

  • Elenor Hidalgos feeedback,
    • We should go through this feedback and work out if the is a way to improve the capture of the "restored growth"

Ontology questions

  • Merge 'inviable spore' (or inviable spore population?) and 'abolished sporulation' - almost certainly a good idea, since there isn't really any practical way to gauge spore viability than to see if it sporulates. But which name and logical definition should we keep? (SFs 592, 785 and any linked)
    • also consider cell vs. population angle for sporulation occurrence/frequency terms (SF 1319)
    • obsolete FYPO:0000279 because azygotic sporulation isn't abnormal; it happens under specific growth/nutrient conditions (some info in SF 1431)
  • 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
  • Discuss "when to request a new GO term"

Annotation issues, syntax, procedures etc

  • A heads up meiosis (mieotic nuclear division) vs meiosis (meiotic cell cycle)
    • please note the difference, especially in extensions during (meiotic cell cycle)

  • How many has_direct_input do we have on processes

What are we saying here and could it be represented more specifically as a molecular function (more specific)

  • Update on this. It isn't necessarily wrong, but it isn't the most specific possible annotation if its has_direct_input and it isn't on the MF term
  • Query from Antonia Subject d384a52dcc0dc8a1 about Should the substrate be the domain or the gene product?
  • Do not annotate subset...Keep an eye out for terms which could be included (not in logs yet)

Curation issues biology

  • Issues related to branching and T-shaped phenotype
  • 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) antioxidants etc (thread 'Annotation extension paper' this came up in AE pper egs)
  • localization vs transport vs targeting

also, all protein localization GO terms should have annotation extensions

  • I was trying to work out if we were resolved with all of the "cut" remapping, but ran into something more hazardous...if the jira ticket is fixed we can follow up on this..I think what needs to happen is to compare the new cuts to the old cuts to see which ones need to be migrated to the more specific term


  • Canto documentation required


  • 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


  • 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

Consistent labels for track displays

Alternative transcripts

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)

Annotation extensions

  • Discuss use of has_direct_input (a.k.a. has_substrate) v.s. has_indirect_input v. the parent has_input
  • At its simplest I can't think of an example where we would not use has_direct _input with a MF term. I would use has_input or has_indirect input for upstream regulators (i.e BP regulation of enzyme or process terms).
  • revisit

Curation issues syntax and ontologies

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

  • annotating cleavage sites

Curation management

  • Go through curation tracker, assign people, priorities

  • Tidy wiki, move obsolete pages

Lower priority

  • 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- 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
  • advanced search, better to have just query management ?

Later/ In progress

  • check Biogrid data alignment progress with Antonia

  • 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.