wiki:CuratorMeeting

Version 481 (modified by val_wood, 8 years ago) (diff)

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PomBase Curator Meetings

PreviousCurationMeetings

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

Canto

  • text, for whether a paper contains curatable gene or not https://sourceforge.net/p/pombase/curation-tool/624/ (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 (open ticket)
  • 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)

FYPO

  • 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

Outreach

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

PomBase

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

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)

Lower priority

  • 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 etc
  • 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

https://sourceforge.net/p/pombase/curation-tasks/258/

  • 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.