wiki:CuratorMeeting

Version 87 (modified by antonialock, 10 years ago) (diff)

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PomBase Curator Meetings

Meetings held

6 Sept. 2011

  • Annotation extensions (with Chris, Emily, Jane; morning)
    • relations
      • direct and indirect regulation - has_regulation_target, plus child term(s) to be added (see what Chris has put in file)
      • when to use has_substrate - with MF catalytic activity terms
      • upstream & downstream
      • negating annotation extensions
  • Gene expression controlled curation
    • current capture of expression (some needs to migrate to annotation_extension)
    • how should we do this in future?
  • Phenotype modelling (with Kim & Mark; afternoon)
  • WT phenotypes

3/4 October 2011

  • As part of planning meeting Midori went through phenotype model for Chad (link to planning meeting minutes)
  • As follow on from phenotype modelling we drew up a draft workflow for capturing data in the curation tool (We will all work through this when curating phenotypes)
  • Midori went over basics of using subversion, esp. resolving conflicts
  • Bio-Curator meeting abstracts (Nov 30).http://pir.georgetown.edu/biocuration2012.html/instructions.html hopefully Antonia can attend
  • General curation work

17/18 October 2011

  • Antonia's list

  • Regulation
    • Direct vs indirect
    • regulation of cell cycle and signal transduction
    • start and end of a process

3/4 November 2011

  • Identified and co-curated papers for undergraduate workshop

14 November 2011

  • round robin, next 2 weeks priorities etc

  • GO meeting debrief
  • Had a discussion about annotation extension When to pre-compose in ontology (during etc)
  • Also discussed phenotype curation, probably only need condition extension initially
  • Discussed how location required for process is equivalent to process dependent on localization to componet
  • need to migrate all required_for attached to components to process terms and move all dependent on to children
  • PomBase? release pending, discussion about a few thing required for release, and revised release date to 28th

15 November 2011

Future meetings

2 December 2011

  • round robin, next 2 weeks priorities etc
  • Midori OBO-Edit basics
    • loading viewing browsing searching etc (need to be able to view relations ontology)
  • Posters for biocuration

January 23rd/ 24th

  • RT versus jira
    • For a while we will probably stick with RT
      • who gets RT tracker e-mails?
      • Need to figure out how to get the closed items to display be default to everyone (i.e. Midori's saved search)
      • Need to figure out why the automatic CC back to helpdesk does not work ( gives e-mail with no content, but if you type helpdesk@… explicitly you do get the response?
    • I'd like to propose a system something along the lines of:
      • Antonia monitors the helpdesk (so will go thorough some basic instruction on how to assign RT items to others)
      • Antonia decides if she can't answer the query who would be able to best answer (probably me at first for most legacy or data related questions, and Mark for inclusion of HTP datasets, Midori for PomBase? site specific use or requests which will raise new jira tracker issues/features), but we can always reassign if they go to the wrong person...)
      • Once a query is answered Antonia can draft an FAQ item (if relevant) from the response, and send to Midori for editing and including in the PomBase? FAQ
      • Hopefully after a year or so we will have answered most of the common queries and so increasing Antonia can increasingly point users directly to the FAQ.
  • Help Documentation (inline/context dependent help) for
    • curation tool
    • Pombase
    • query builder
  • Val - short term priorities
    • curation tool related

  • Val - long term priorities
    • review of SF items
    • what needs to be done before community curation launch
  • Need a list of curation tool features, existing and proposed
    • Discuss what we need for the curation tool interface wrt
      • i) annotation extensions
      • ii) annotation transfer of extensions and qualifier
  • Antonia's questions
    • during ->happens_during migration
    • plasmid expression
  • How to capture dephosphorylated/dephosphorylation
  • Export formats for phenotype etc.
    • consider annotation_extension=condition -> condition=?
  • pombelist FAQ proposal (putting pombelist "experimental" items into Susan F's FAQ)
  • Documentation plan
    • Dropbox/pombase/Documentation_and_help/FAQ_items.txt
    • curation tool help
  • Arrange dates for next meeting(s)
  • discuss Antonia's example for "repression as opposite of overexpression"
    • did we make a decision here? knockdown? is it documented?
  • To discuss with Mark
    • UTRs on gene pages/ in Ensembl (access to db_xref & sequence) see http://www.ebi.ac.uk/panda/jira/browse/PB-471
    • Query tool download options
      • Gene names list default
      • UTRs or upstream downstream regions as a sequence download option
    • replacing current ftp site and download files (currently links to Sanger and matches GeneDB datasets)
    • EG release cycle, advance warning for deadline for changes (procedures in place to let us know as soon as you know the dates)

Future Meeting Discussion Items, please move forward if more urgent

In rough order of priority:

  • Identifying test vs. empty curation sessions
  • Using OBO-Edit, part 2: editing & saving
    • make a "condition" ontology
  • cleavage and PRO usage for column 17
  • Follow up from phenotype workflow
    • We have only allowed condition as an annotation_extension, which others has Antonia used (i.e do we need to allow other extensions)... so far now

  • 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?
  • migrate extensions in the annotation tool to the non-deprecated terms
  • consistency checking exercises of curated papers (in pairs?)
  • controlled curation, still need to cover genome org/pathway/protein sequence feature/warning
  • Discuss "Splitting out complementation"
  • Discuss GO "response to"
  • Discuss GO "involved" in Vs. "during"
  • Discuss annotation consistency between complexes and process (should we suggest complex/process links?)
  • Precomposition, where to stop. Is this too much precomposition?
  • GO annotation redundancy (experimental Vs. non experimental)
  • direct binding
  • taxon restrictions
  • improving annotation for uncharacterised genes
  • updating products

Later

  • More on Pfam, false negatives, clans
  • localization dependencies
  • Gene naming and GNC
  • Broader annotation consistency checks, Matrix project, GO slim term comparison
  • Reference genomes
  • 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