wiki:CuratorMeeting

Version 265 (modified by val_wood, 9 years ago) (diff)

--

PomBase Curator Meetings

PreviousCurationMeetings

Next Items, in rough order of priority

  • Phenotype assumptions: do we want some 'default' conditions that are true for most experiments, unless otherwise stated? See for instance the terms decreased aerobic cell growth on glucose carbon source / slow cell growth / etc

DONE (in part) Decided to make some assumptions for "standard" conditionss, and request terms for non standard conditions (if standard condition terms are requested, they can be added as synonymns and liberally commented) https://sourceforge.net/tracker/?func=detail&aid=3547584&group_id=65526&atid=2096431

  • Decide workflow for annotation transfer for phenotypes in the curation tool

DONE https://sourceforge.net/tracker/?func=detail&aid=3547608&group_id=65526&atid=2525791

  • Postponed workflow for curation tool, requesting terms (is OK for now need to check term requests)
  • Discussion about has_part and how it affects curation
  • Discussion about annotation specificity
    • curators collect examples of where they wondered whether they were going "too specific"
    • Curators to co-curate Espenshade papers to get a feel what degree of specificity we want to capture

  • extension syntax e.g.

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

  • 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"
  • 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)

  • 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

  • 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

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

  • 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)