Version 208 (modified by val_wood, 10 years ago) (diff)


PomBase Curator Meetings


Next Meeting

Priorities for next few weeks

  • GO through Antonia extensions (kim generated file with links to sessions)


  • Curation tool related, progress towards launch
  • SF related
  • publications
  • extensions on phenotypes generally
  • Questions, should annotation extension (gene products) be stored in duplicate on phenotypes and GO annotations?)
    • making links between phenotypes and GO terms, when should a GO annotation be made
  • Making IC annotations (in Artemis)
  • capturing or inferring recessivity/dominence (and capturing heterozygosity or homozygosity in a diploid)
    • Will discuss when we have real life examples
  • has Antonia got any outstanding questions about relations (e-mail thread on Thursday)
    • if we have the list of relations we have used we can go through this. required_for came up....
  • Localization questions, use PMID:20298435 egs.
    • should the localization only be direct transport, anchoring, chaperoning? what about complex assembly, or part of a complex


  • User testing discussion


Antonia's Questions

Small/ongoing projects

  • Using OBO-Edit, part 2: editing & saving
    • make a "condition" ontology

Help/ Documentation plan

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

Data types/ Data descriptions

  • revisit expression syntax
    • final decision so far was expression_type= detail=relevent annotation extension level=increased/decreased
    • should be able to retrofit them into the data model later.....
    • maybe should migrate to Artemis?
    • also need to retrofit existing gene expression annotation
    • discuss curation tool options
    • discuss all with Kim


  • Need a list of curation tool features, existing and proposed
  • need to thrash out 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)
  • controlled curation type -pathway
  • contributes_to qualifier


  • Follow up from phenotype workflow

  • 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)
  • Q Do people need more Artemis examples?
  • controlled curation, still need to cover genome org/pathway/protein sequence feature/warning

  • direct binding

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)