Version 28 (modified by val_wood, 10 years ago) (diff)


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

Next meeting, date TBA

In rough order of priority:

  • Midori to go over basics of using subversion, esp. resolving conflicts
  • Midori OBO-Edit basics (I'd like to be able to view the relations ontology as a graph!)
    • loading, viewing, browsing & searching
  • Go through curated examples on wiki and check syntax

Future Meeting Discussion Items, please move forward if more urgent

  • WT phenotypes
  • Arrange dates for next meeting
  • Q Do people need more Artemis examples?
  • Phenotype specificity
  • migrate their extensions in the  annotation tool to the non-deprecrated terms
  • consistency checking exercises of curated papers (in pairs?)
  • controlled curation, still need to cover genome org/pathway/protein sequence feature/warning
  • Curation Tool discussions
    • need to decide how best to present curation of annotation_extensions/ and ability to transfer of info from extensions

  • Go through Source Forge Tracker tasks
  • 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 restictions
  • improving annotation for uncharacterised genes
  • updating products


  • 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
  • Using OBO-Edit, part 2: editing & saving

Later, after migration to new system

  • Updating EMBL
  • Updating GO
  • Updating ortholog table
  • Download data formats (gff etc)
  • editing sequence in Artemis
  • systematic reduction of the orphan set