Version 51 (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

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). 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 Novovember 2011 =

  • Identified and co-curated papers for undergraduate workshop

14/15 Novovember 2011 =

  • GO meeting debrief
    • When to pre-compose in ontology, when to use annotation extensions

see thread in Fwd: Re: sensitive ... (Re: hyphal growth)/ when to use annotation extensions

  • On a related note, phenotype extensions
    • Export formats for other data types
  • Curation practical, checking, need annotation notes, check set up.
  • RT verses jira
  • Arrange dates for next meeting(s)

Future Meeting Discussion Items, please move forward if more urgent

In rough order of priority:

  • cleavage and PRO usage for column 17
  • Midori OBO-Edit basics (I'd like to be able to view the relations ontology as a graph!)
    • loading, viewing, browsing & searching
  • 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)
  • Go through curated examples on wiki and check syntax
  • Are all things which can be migrated from the wiki to the curation tool?

  • where does conjugation begin, (is signalling from pheromone part of conjugation, or regulation of conjugation? Juan says regulation)
  • Discuss what we need for the curation tool interface wrt
    • i) annotation extensions
    • ii) annotation transfer of extensions and qualifier
  • 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
  • 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