Version 189 (modified by val_wood, 10 years ago) (diff)


PomBase Curator Meetings


Next meeting

January 23rd- 27th

Monday 23rd a.m.


  • RT versus jira (For a while we will probably stick with RT)
    • RT is now be configured so we see all responses.
    • Val demo how to configure dash to show all open/ closed items / assign itmes DONE
    • Val will encourage people to submit to helpdesk, or will summarize and post queries later
    • Note make sure any feedback received is appended to closed items as comments.
  • Proposed system:
    • Antonia monitors the helpdesk
    • 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 website queries (including queries which will raise new jira tracker issues or feature requests), Antonia for requests to curate papers), but we can always reassign if they go to the wrong person...)
    • Once a query is answered Antonia will 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

  • Getting feedback from authors on completed papers Val will write an email to send out with curation sessions We should keep a file of people who have been sent completed sessions as the next paper they should curate themselves
  • Need a list of curation tool features, existing and proposed

Tuesday 24rd a.m.

To discuss with Kim

  • Next things for Kim to work on (rough order) Curation tool

  • need to thrash out allele descriptions
  • Val needs to check that the proposal to change the tool fits with the phenotype format/model
  • 4. Annotation extensions
    • I.e which extensions need to be available for i) each ontology ii) each term
    • ii) annotation transfer of extensions and qualifier
  • 5. New datatypes, expression (dependent on outcome of discussion below), complementation (probably we will split out complementation as a curation type in the tool), protein sequence features (subset of SO)
    • GO through high priority SF items (1 & 2 above)

  • New features
    • See SF tracker

Tuesday 24rd p.m.

To discuss with Mark

All items from discussion with mark added to relelvant jira tracker Other Action items

  • Usage stats, updates for planning meeting
  • Download file options (val to document)
  • replacing current ftp site and download files (val to document)
  • Update planning meeting agenda based on discussions with Mark and any newly completed jira items

4 p.m.

  • GO Annotation Conference call

Wednesday 25th a.m.

Miscellaneous curation issues

  • How to capture dephosphorylated/dephosphorylation DONE

  • Trancription overhaul ....documentation etc (terms for sequence specific transcription factors)
  • in vitro (Val, I have existing qualifiers and I wonder if these should be converted to evidence, sub-type of IDA, check)

Wednesday 25th p.m.

Thursday 26th a.m.

Thursday 26th p.m.

PomBase planning meeting

Friday 27th a.m.

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)

Next Meeting

Antonia's Questions

Help/ Documentation plan

  • FAQ update
  • Ensembl Help update
  • Curation tool help update

Data types/ Data descriptions

  • revisit expression syntax
    • final decision so far was expression_type= detail=relevent annotation extension level=increased/decreased
    • 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


  • Using OBO-Edit, part 2: editing & saving
    • make a "condition" ontology
  • Follow up from phenotype workflow

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

  • 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?
  • controlled curation, still need to cover genome org/pathway/protein sequence feature/warning

  • GO annotation redundancy (experimental vs. non experimental)
  • direct binding

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

  • Discuss GO "response to"
  • Discuss GO "involved" in vs. "during"
  • More on Pfam, false negatives, clans
  • localization dependencies
  • Gene naming and GNC
  • Broader annotation consistency checks, Matrix project, GO slim term comparison
  • Reference genomes
  • 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
  • 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