WBConfCall 2012.12.06-Agenda and Minutes

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Proposed Model changes

Link to the model changes proposed for WS236 WS236_Models.wrm

Link to human disease model changes Model_changes_to_capture_and_consolidate_human_disease_data

Proposed for inclusion in WS236

    1 * General housekeeping - ?Accession class
    2 * Transposon gene reactivation - Paul
        2.1 Poor nomenclature in ?Gene history and Event
        2.2 Gene::Transposon
        2.3 #Gene_history_action
    3 * Sequence collection - Kevin
    4 * Strain modifications
        4.1 ?Strain - Michael
        4.2 ?Strain - Mary Ann
        4.3 ?Strain - Mary Ann
    5 * ?Drug_resistance
    6 * ?Variation and ?Feature mapping changes
        6.1 Mapping
        6.2 Gary W.
    7 * ?Gene and Disease Ontology - Ranjana
    8 * Condition Class - Wen

There is no major reason to discuss the minor models proposals at this call, but if anyone has anything that they wish to contribute on some of the consequences of policy change/new classes, please feel free.

Possible discussion areas

Transposon gene re-classification

This has come about by user feedback and Jonathan H. remarking on at least twice when visiting Hinxton.

  • Historically as CDSs were identified as encoding a Transposable element related protein the CDS was re-classified as a "Transposon CDS" and the corresponding WBGene killed off (removing lots of standard data as is done with "Dead Genes").
  • This causes the desired effect of removing the proteins from the C. elegans protein dataset but also gives a very poor display for these objects on the website.
  • I have proposed model changes to better reflect the reality of the situation and allow better display
  • I have also proposed a policy change that re-populates a lot of the data that is removed from the ?Gene object as well as re-classifying them as Suppressed rather than Dead.

Comments from the Call

  • the transposon genes should get a concise description, and Kimberley would work together with Paul D on this

?Gene and Disease Ontology

Discussion on wiki.

This model has had considerable discussion and rearrangement and looks almost polished. If others could take a look at the model in the linked Models WS236 document that would be good.

Outstanding issue:

  1. Index and Parent::Child associations - Is this redundant?
  2. Need to remove UNIQUE from synonym line in ?DO_term

comments from the call

  • Ranjana will send some data to Paul for testing
  • OICR will coordinate with CalTech about the links/references (and create a GitHub ticket)

Advisory Board Meeting

Updates from the WormBase Groups [A-Z]


  • Juancarlos has a prototype curation status tracker, including statistics. Currently used for SVM curation, could be useful for other things too.
  • there was work to temporarily resurrect a sequence-extraction tool from Igor, which might be replaced by intermine in the future


  • there will be a hackathon for the WS235 website release
  • there is a protoype ace->intermine importer to supplement the GFF->intermine (with the usual XML intermediate)
  • will try to get a working InterMine prototype up for the ABM
  • are exploring alternatives to CouchDB to store highly connected graphs (form ACeDB)

B.malayi (Hinxton/WashU)

  • pre-release curation of Brugia is finished
  • Nameserver is updated
  • B.malayi is in the process of being submitted to INSDC
    • WormBase took ownership of the Sequencing/Genome Project
    • we moved the entries from GenBank to ENA
    • we submitted the clones
    • pending: AGP/annotation submission
    • pending: synchronisation of Uniprot with ENA and WormBase (so we don't kill all Brugia proteins from Uniprot)
  • in WS235 B.malayi will appear as alternative assembly on the WormBase GBrowse
  • B.malayi will go into WS236 as core species (including a set of predicted operons)
  • we added remarks to specify groups of genes:
    • drug targets
    • vaccination targets
    • parasite specific genes
    • ...

COmments from the Call

Will show CalTech which curation categories we currently have for Brugia malayi, as some might work very well as description / GO / DO / etc. and come from mixed sources (Publications, Analysis, Pathway mappings, etc).


  • next one is Gary Williams from WormBase-Hinxton

open tickets

from: https://github.com/WormBase/website/issues?labels=HelpDesk&state=open

notable ones: