wiki:CuratorMeeting

Version 127 (modified by val_wood, 10 years ago) (diff)

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PomBase Curator Meetings

PreviousCurationMeetings

Future meetings

January 23rd/ 27th

Helpdesk

  • 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) From Midori ( https://rt.sanger.ac.uk/Search/Build.html?NewQuery=1 and look in the "Saved searches" box on the right. If it's worked, there will be an item in the "Load saved search" pulldown for "all resolved tickets". Select it, click the Load button, and then click either the "Add these terms and Search" button or the "Update format and Search" one.)
      • 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?
      • It is possible that CCing the tracker in response to an item which wasn't sent directly to the helpdesk does not open an item, only doing TO: (need to check this)
      • How do we view ALL open tickets (i.e once they are "taken" they only seem to be visible to the assignee?
  • Proposed system 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 plan

Need inline/context dependent help for:

  • curation tool help
  • Pombase
  • query builder
  • Simple search
  • Features on genepages
  • FAQ Dropbox/pombase/Documentation_and_help/FAQ_items.txt

Antonia's Questions

  • during ->happens_during migration
    • plasmid expression
    • Sort visitor pass (val added)
    • Is svn and artemis sorted? (val added)
    • discuss Antonia's example for "repression as opposite of overexpression"
      • did we make a decision here? knockdown? is it documented?
    • Possibly L-leucine removal was used here for cleavage:

Curation Tool

  • Getting feedback from authors on completed papers
  • Need a list of curation tool features, existing and proposed
    • Discuss what we need for the curation tool interface wrt
      • i) annotation extensions
        • I.e which extenstions need to be available for i) each ontology ii) each term
      • ii) annotation transfer of extensions and qualifier

Miscellaneous curation issues

  • How to capture dephosphorylated/dephosphorylation

General

  • Val - short term priorities
    • curation tool related
  • Val - long term priorities
    • review of SF items
    • what needs to be done before community curation launch
  • Export formats for phenotype etc.
    • consider annotation_extension=condition -> condition=?
  • pombelist FAQ proposal (putting pombelist "experimental" items into Susan F's FAQ)

To discuss with Kim

Curation tool

  • Identifying test vs. empty curation sessions
    • need to get rid of test sessions
    • Note that some test sessions are empty (nothing to annotate)

  • Curation tool/Chado

  • Are any sessions we need not in the wiki list?
  • New Data types
    • Complementation
    • Expression (see outcome of discussion abouve)
    • multi gene knockouts and phenotypes
      • Schema changes
      • Curation tool changes

  • New features
    • See SF tracker

To discuss with Mark

  • Query tool (add relevent SF items)
    • Discuss exactly what options can be done in the interface vs history
      • do we need the interface? or just the history if it was clear that query manipualtion can be done here
      • If we need the interface, how will it be obvius how nesting is done?
    • Discuss use of i) Add ii) AND?OR vs. Intersect/union
    • What is being searched by the query tool keyword search?
    • Ability to send user defined list to query/ query download
    • ability to send lists from Genedb to query history/download
      • Discuss Is evidence required in GO gene list? what happens if more than one evidence? (consistency?) see Genes annotated with GO:2000045 - regulation of G1/S transition of mitotic cell cycle (biological_process)
      • lists look different in different places, make gene list look more similar to query builder results list
    • Download file options
      • filenames .html confusing
      • can the files render in the browser, or as GeneDB separate options for viewing in browser and download?

  • replacing current ftp site and download files (currently links to Sanger and matches GeneDB datasets)
    • migration of Sanger ftp site
  • EG release cycle, advance warning for deadline for changes (procedures in place to let us know as soon as you know the dates)
  • Spacing on gene page

Future Meeting Discussion Items, please move forward if more urgent

In rough order of priority:

  • 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