wiki:CuratorMeeting

Version 298 (modified by val_wood, 9 years ago) (diff)

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PomBase Curator Meetings

PreviousCurationMeetings

Next Items, in rough order of priority

  • Annotating tRNA's: what did we decide about this? (can't add genes to tool, what ontology to use..). SO says that they can give us SOM terms.
  • Decreased transcr vs inviable.
  • sort out the reference pombe strain h90. Currently the taxon ID is used (briefly discussed - keep as is or change ref strain to h90 (and if so make a 'pretend sequence'?)).
  • GO regulation of process discuss, make guidelines
    • Signal transduction upstream of transcription (adenylate cyclase, git pathway)
    • regulation of transcription regulating process (gene specific transcription)
      • Martins paper PMID:19101542
      • Charlies gits
        • consider git1 barrier septum assembly annotation
    • Protein modification and regulation
      • see email exchange with David/SGD
      • curs/97535c919f7436fe (Winston lab paper)
    • relationship of chromatin silencing to transcription, see mcl1 (upstream effect?)
  • Make a mapping of relations to display on pages
    • Draft now in Dropbox/pombase/PomBase_website/extension_relation_display_text.txt (2012-09-17)
  • Discussion about has_part and how it affects curation
  • Dealing with diploids
    • how to specify a diploid genotype, and capture the info in curation tool
    • what to do when haploid spore phenotype depends on genotype of the parent diploid

  • extension syntax e.g.

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

  • Postponed workflow for curation tool, requesting terms (is OK for now need to check term requests)
  • postponed dephosphorylation etc (see Chado load error logs)
  • postponed GO through enrichment and slimming and update FAQ
  • postponed until Kim gets further, low priority revisit complementation

  • postponed 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"
  • pombase budding yeast and human orthologs (postponed until new human orthologs appear in PomBase?), updating orthologs, and ortholog tables
  • disease ontology
  • Sort out definitions

Phenotype ontology (Midori 2012-02-29)

  • Annotations: how to represent when alleles of interest are studied with another (non-null) allele of the same gene present
    • email sent 2012-06-27
    • example: mcm2 alleles in PMID:9383050
      • several different mcm2-x alleles assayed on plasmids, with mcm2+, mcm2delta, or mcm2 allele cdc19-P1 on chromosome
  • Pre- vs post-composing terms
    • background (older comments):
      • 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).
    • update 2012-06-12 (based on discussion in May): actually still thinking about this. It's a "when to pre- or post-compose terms" question, analogous to GO terms + extensions. Thoughts in progress noted here.

  • 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

General

  • 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

Other

  • 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

General

  • Discuss GO "response to"
  • More on Pfam, false negatives, clans
  • localization dependencies
  • Gene naming and GNC
  • Broader annotation consistency checks, Matrix project, GO slim term comparison
  • 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
  • Updating EMBL
  • Download data formats (gff etc)
  • editing sequence in Artemis
  • systematic reduction of the orphan set