Version 166 (modified by val_wood, 10 years ago) (diff)


PomBase Curator Meetings


Future meetings

January 23rd- 27th

Monday 23rd a.m.


  • RT versus jira (For a while we will probably stick with RT)
    • RT should now be configured so we see all responses.
    • Val demo how to configure dash to show all open/ closed items

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

  • 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)
  • Q Do we want the "do not respond to" message on closure?
  • Note make sure any feedback received is appended to closed items.
  • Proposed system:
    • 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, Antonia for requests to curate papers), 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.

Monday 23rd p.m.

Curation Tool

(Do this on Monday because it would be good to get up to speed before Kim joins us by Skype on Tuesday morning)

  • 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:
      • Triage options and refinement of,
      • Annotation extensions
        • I.e which extensions need to be available for i) each ontology ii) each term
        • ii) annotation transfer of extensions and qualifier

Tuesday 24rd a.m.

To discuss with Kim

Curation tool

  • Identifying test vs. empty curation sessions
    • Remove test sessions
    • Note that some sessions are empty (nothing to annotate)
    • Reactivating completed sessions
    • Are any sessions we need not in the wiki list?
    • sending out completed sessions to only link with no edit options, discuss?
  • New Data types
    • Complementation Discuss "Splitting out complementation"
    • Expression (see outcome of discussion above)
    • multi gene knockouts and phenotypes
      • Schema changes
      • Curation tool changes

  • New features
    • See SF tracker

While Kim and Mark chat curators can get on with some of Antonia's questions below

Tuesday 24rd p.m.

To discuss with Mark

  • val questions for Mark
    • see folder, includes GO slim/ convergent genes query (user queries generally)/ chado version/ usage stats
  • Usage stats, updates for planning meeting
  • Announcements for updated things/ new features
  • Query tool (add relevant 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 manipulation can be done here
      • If we need the interface, how will it be obvious 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 upload user defined list send user defined list to query/ query download options
    • 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?
    • 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)
  • Future user configuration of gene pages,
    • 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)
  • Brief discussion about future suppression of redundancy on the gene pages (may depend on avaiability of user configuration)
  • Brief discussion about column 17 display (this might result in a new jira item)
  • Where did the annotation_extension data preview go (It was nearly right....)
  • Compiling new features and sending to the mailing list
  • Demo "assembly re-mapper" to us

4 p.m.

  • GO Annotation Conference call

Wednesday 25th a.m.

Check through agenda for tomorrows meeting

Miscellaneous curation issues

  • How to capture dephosphorylated/dephosphorylation

and we should be able to retrofit them into the data model later.....

  • maybe should migrate to Artemis?
  • also need to retrofit existing gene expression annotation
  • discuss curation tool options
  • discuss all with Kim
  • Trancription overhaul ....documentation etc (terms for sequence specific transcription factors)
  • Make a page of commonly used lab strains
    • make a list of commonly used h90 derivatives with their mutations
      • 972 h- is h90 with mat2-p deleted
  • in vitro (Val, I have existing qualifiers and I wonder if these should be converted to evidence, sub-type of IDA, check)
  • Annotation extensiosn used with phenotypes, are these required?
    • hopefully will have a list from Kim, one which we know of is for 'has color' for pigmentation
    • Outcome, if we need extensions will need to extend phenotype import/export format

Wednesday 25th p.m.

Antonia's Questions

  • during ->happens_during migration
    • plasmid expression
      • Is this resolved? if so Antonia can you summarize allele/phenotype term/ condition/evidence combination you used, then we can record in the curator the documentation
    • 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:
    • potential 6 week student projects
  • Upadte planning meeting agenda based on discussions with Mark and nay newly completed jira items

Thursday 26th a.m.

Thursday 26th p.m.

PomBase? planning meeting

Friday 27th a.m.

Help/ Documentation plan

If we don't have time, can bump this to later in the week

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

Friday 27th p.m.


  • 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)

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 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