Version 246 (modified by val_wood, 9 years ago) (diff)


PomBase Curator Meetings


Next Items, in rough order of priority

  • extension syntax e.g.

annotation_extension=requires_modification(MOD:00046),​ residue=S462​ or annotation_extension=requires_modification(MOD:00046,​ residue=S462​)

  • Reminder flagging HTP papers
  • postponed until Kim gets further, low priority revisit complementation

  • Regulation rules (ongoing, will do when Val has done basic documentation/"rules")
  • Session approval (list of things to check), Val in progress
  • qualifier documentation for "controlled curations"
  • budding yeast and human orthologs
  • protein binding
    • direct /indirect see e-mail thread "protein-protein interaction phenotype"
  • disease ontology

OBO edit (below moved from other meeting page - Antonia

  • Sort out definitions

Phenotype ontology (Midori 2012-02-29)

  • We've decided to make some phenotype terms obsolete and use conditions to capture temperature, carbon source, nitrogen source, etc. Last call to review the affected terms -- are there any that we should keep after all?
    • normal growth at high temperature FYPO:0000674
    • viable at high temperature FYPO:0000282
    • sensitive to cold FYPO:0000080
    • sensitive to high osmolarity FYPO:0000081
    • sensitive to high temperature FYPO:0000082
    • slow growth at high temperature FYPO:0000247
    • normal cell growth on ammonia nitrogen source FYPO:0000242
    • normal cell growth on proline nitrogen source FYPO:0000243
    • slow cell growth on ammonia nitrogen source FYPO:0000249
    • slow cell growth on proline nitrogen source FYPO:0000250
    • slow cell growth on galactose carbon source FYPO:0000251
    • slow cell growth on glycerol/ethanol carbon source FYPO:0000442
    • increased cell growth rate on glucose carbon source FYPO:0000637
    • slow cell growth on glycerol carbon source FYPO:0000684
  • update 2012-03-09: I'm now thinking of keeping just heat sensitive (FYPO:82) and cold sensitive (FYPO:80) as a practical matter -- lots of community curators/users will search for them! The rest could probably still go, converted to parent + condition(s).

  • Curation tool related, progress towards launch
  • SF related
  • Making IC annotations (in Artemis)

Help/ Documentation plan

  • FAQ update
  • Ensembl Help update
  • Curation tool help update

Data types/ Data descriptions


  • Need a list of curation tool features, existing and proposed
  • need to document allele descriptions
  • Implications of sequence change for residues and alleles , checks curators need to take, also need to discuss this with Mark
  • Trancription overhaul ....documentation etc (terms for sequence specific transcription factors)
  • contributes_to qualifier


  • 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)
  • controlled curation, still need to cover genome org/pathway/protein sequence feature/warning

  • Discuss annotation consistency between complexes and process (should we suggest complex/process links?)

HAve been liasing with Emily and . Emiliy's documentation on this should be available shortly, so we will revisit when this is available...

Future tasks to discuss with Mark

  • User configuration of gene pages (discuss in detail in future)
    • Ability to collapse/open sections by default
    • Ability to configure order of sections on gene pages
    • Some sections may become so long that we need to rethink how redundant data is presented (Antonia's examples)
  • Discuss column 17 display (this might result in a new jira item)
  • Where did the annotation_extension data preview go (It was nearly right....)

Future Meeting Discussion Items, please move forward if more urgent

Low Priority

Quality Control and consistency checks

  • Compare to existing curation
  • Compare to orthologs
  • look at domain data
  • other complex subunits
  • Matrix (interseciton of processes)
  • MAking annotation inferences using existing annotations
    • carbohydrate metabolism and cell surface -> extracellular polysaccharide metabolic process???
    • transcription related (appropriate TF and DNA binding terms)
    • vesicel mediated transport / intracellualr protein transport
    • telomeric DNA binding -> telomeric region
    • GTPase -> GTP binding


  • Orthology
  • Discuss GO "response to"
  • Discuss GO "involved" in vs. "during"
  • More on Pfam, false negatives, clans
  • localization dependencies
  • Gene naming and GNC
  • Broader annotation consistency checks, Matrix project, GO slim term comparison
  • Reference genomes
  • taxon restrictions
  • improving annotation for uncharacterised genes
  • updating products
  • 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
  • explain filtering GO annotation redundancy (experimental vs. non experimental)