Version 107 (modified by val_wood, 10 years ago) (diff)


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). 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) From Midori ( 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?
    • 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 plan (inline/context dependent help) for
    • curation tool help
    • Pombase Dropbox/pombase/Documentation_and_help/FAQ_items.txt
    • 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
    • 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?
  • 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)

To discuss with Mark

  • Query tool download options
    • 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 files
      • filenames .html confusing
      • can the files render in the browser, or as GeneDB separate options for viewing in browser and download?

  • tab delimited file options
    • can files be tab delimited rather than comma?
    • Gene names list default
    • Allow user to select additional column options, other names, product, GO annotations, orthologs (yeast, human-later), interaction
  • Sequence download option

  • 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:

  • 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


  • 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