wiki:CuratorMeeting

Version 69 (modified by val_wood, 10 years ago) (diff)

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PomBase Curator Meetings

Meetings held

6 Sept. 2011

  • Annotation extensions (with Chris, Emily, Jane; morning)
    • relations
      • direct and indirect regulation - has_regulation_target, plus child term(s) to be added (see what Chris has put in file)
      • when to use has_substrate - with MF catalytic activity terms
      • upstream & downstream
      • negating annotation extensions
  • Gene expression controlled curation
    • current capture of expression (some needs to migrate to annotation_extension)
    • how should we do this in future?
  • Phenotype modelling (with Kim & Mark; afternoon)
  • WT phenotypes

3/4 October 2011

  • As part of planning meeting Midori went through phenotype model for Chad (link to planning meeting minutes)
  • As follow on from phenotype modelling we drew up a draft workflow for capturing data in the curation tool (We will all work through this when curating phenotypes)
  • Midori went over basics of using subversion, esp. resolving conflicts
  • Bio-Curator meeting abstracts (Nov 30).http://pir.georgetown.edu/biocuration2012.html/instructions.html hopefully Antonia can attend
  • General curation work

17/18 October 2011

  • Antonia's list

  • Regulation
    • Direct vs indirect
    • regulation of cell cycle and signal transduction
    • start and end of a process

3/4 November 2011

  • Identified and co-curated papers for undergraduate workshop

14 November 2011

  • round robin, next 2 weeks priorities etc

  • GO meeting debrief
  • Need a list of curation tool features, existing and proposed
  • Had a discussion about annotation extension When to pre-compose in ontology (during etc)
  • Also discussed phenotype curation, probably only need condition extension initially
  • Discussed how location required for process is equivalent to process dependent on localization to componet
  • Val will migrate all required_for attached to components to process terms and move all dependent on to children
  • PomBase? release pending, discussion about a few thing required for release, and revised release date to 28th

15 November 2011

2 December 2011

  • Midori OBO-Edit basics
    • loading viewing browsing searching etc (need to be able to view relations ontology)
  • Posters for biocuration
  • Antonia's questions
    • during ->happens_during migration
    • plasmid expression
  • How to capture dephosphorylated/dephosphorylation
  • Export formats for phenotype etc.
    • consider annotation_extension=condition -> condition=?
  • RT verses jira
  • pombelist FAQ proposal (putting pomblist "experimental items into Susan F's FAQ)
  • Val - short term priorities

  • Documentation plan (if time)
    • Dropbox/pombase/Documentation_and_help/FAQ_items.txt
  • [Pombase-chado] [ pombase-Chado-3440222 ] residue syntax to fix

NEXT MEETING DATE TDB

  • Val - long term priorities
    • review of SF items
    • what needs to be done before community curation launch
  • Discuss what we need for the curation tool interface wrt
    • i) annotation extensions
    • ii) annotation transfer of extensions and qualifier

Future Meeting Discussion Items, please move forward if more urgent

In rough order of priority:

  • Using OBO-Edit, part 2: editing & saving
    • make a "condition" ontology
  • cleavage and PRO usage for column 17
  • Follow up from phenotype workflow
    • We have only allowed condition as an annotation_extension, which others has Antonia used (i.e do we need to allow other extensions)... so far now

  • where does conjugation begin, (is signalling from pheromone part of conjugation, or regulation of conjugation? Juan says regulation)
  • Q Do people need more Artemis examples?
  • migrate extensions in the annotation tool to the non-deprecated terms
  • consistency checking exercises of curated papers (in pairs?)
  • controlled curation, still need to cover genome org/pathway/protein sequence feature/warning
  • Discuss "Splitting out complementation"
  • Discuss GO "response to"
  • Discuss GO "involved" in Vs. "during"
  • Discuss annotation consistency between complexes and process (should we suggest complex/process links?)
  • Precomposition, where to stop. Is this too much precomposition?
  • GO annotation redundancy (experimental Vs. non experimental)
  • direct binding
  • taxon restrictions
  • improving annotation for uncharacterised genes
  • updating products

Later

  • More on Pfam, false negatives, clans
  • localization dependencies
  • Gene naming and GNC
  • Broader annotation consistency checks, Matrix project, GO slim term comparison
  • Reference genomes
  • Regulation
    • Direct vs indirect
    • e.g autophagy example
    • regulation of cell cycle and signal transduction
    • start and end of a process
  • Function/process links
  • External sources of GO data
  • Updating EMBL
  • Updating GO
  • Updating ortholog table
  • Download data formats (gff etc)
  • editing sequence in Artemis
  • systematic reduction of the orphan set