wiki:CuratorMeeting

Version 422 (modified by val_wood, 8 years ago) (diff)

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PomBase Curator Meetings

PreviousCurationMeetings

Next Items, in rough order of priority

  • what we do about phenotypes for double mutants (display/query/enrichment etc)
  • PHAF/GPAD/GPI files for export/import etc.
  • It seems odd that sty1 will only be annotated to "response to oxidative stress" via 'regulation....it's almost as if we need a term "signalling in response to oxidative stress"
  • Discuss regulation of G1/S in relation to 6ff4c9edff12167b (look at annotation in context of all genes in this session)
  • If time go through curation tracker, and see what can be done quickly
  • Should we add GO/protein binding terms for enzyme/substrate combinations?
    • should we use the BioGrid? evidence code "biochemical activity" which we don't use at the moment.
  • discuss establishment of cell polarity and the signalling network (MOR) (see e-mail Created new session 31b82829d0c47e4d from PMID:23649273)

Tuesday 23rd April

Monday 6 May

Cancelled

Mon 13th May

Sort out what we're doing for pombe meeting - lunchtime demos/tutorials; anything else?

(continue on 14th if we don't finish on 13th)

Tue 22 May

Cancelled

Next plan dates, no room booked, will probably need a pre-pombe 2013 meeting between 10- 21 June

  • Galaxy demo, pombe specific example (would the bent cells work?) (POSTPONED UNTIL SOME GALAXY ISSUES FIXED< SUBMITTED TO GO HELP)

Next

  • Figure out what we need for meiosis, meiotic cell cycle, etc. in FYPO SF 709
  • Use of inhibited by...used for "biological inhibition" (i.e regulation) and exogenous inhibition...discuss?
  • discuss what should be the default text for searching terms etc (see e-mail with subject "default text")
  • GO regulation of process discuss, make guidelines
    • Signal transduction upstream of transcription (adenylate cyclase, git pathway)
    • regulation of transcription regulating process (gene specific transcription)
      • Martin's paper PMID:19101542
      • Charlie's 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?)
  • Discussion about has_part and how it affects curation
    • see e.g. in e-mail folder NTR: srebp catabolism
    • e.g wnt signalling has_part MAP kinase
    • e.g. primer synthesis
    • you can't infer annotations in either direction over a has_part relation, but if you want to see the "whole" for a gene that's annotated to the "part", that's ok ...
  • extension syntax e.g.

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

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

Data types/ Data descriptions

Specific Curation issues, biology

  • Trancription overhaul ....documentation etc (terms for sequence specific transcription factors)
  • cell wall assembly and biogenesis

https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3544811&group_id=36855

  • where does conjugation begin, (is signalling from pheromone part of conjugation, or regulation of conjugation? Juan says regulation)

Other

  • Are all things which can be migrated from the wiki to the curation tool?
  • 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?)

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
  • 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

  • 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

POSTPONED

  • pombe budding yeast and human orthologs (POSTPONED until new human orthologs appear in PomBase), updating orthologs, and ortholog tables
  • qualifier documentation for "controlled curations"
  • 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'?)).
  • Annotating sequence features
    • promoter features, ID? and syntax
    • we need a way to physically annotate the processed and unprocessed peptides and attach SO terms directly to them (we could do this now using misc_feature and a SO term, and we couldn't use them as objects to annotate to directly in Artemis/Chado?)
  • Implications of sequence changes for residues and alleles , checks curators need to take, also need to discuss this with Mark
  • 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.
  • Regulation rules (ongoing, will do when Val has done basic documentation/"rules") (POSTPONED)
  • Making IC annotations (in Artemis) (I don't know if there is still anything to discuss about this?)
  • Session approval (list of things to check), seems to be working OK, but we could do with a list of basic checks
  • systematic IDs for transposons (make SF item) ...postponed until needed
  • 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

POSTPONED, no changes required at present, qualifier is not used much

  • 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
  • Discuss if ISS should be filtered ISS isn't in the list. We have IEA, IEP, NAS, RCA, TAS and IC. POSTPONED< Still thinking about this
  • disease ontology (Postponed until we have disease ontology IDs)
  • consider name for species distribution (pending inspiration)
  • Discuss and look over NOTs (postponed)