WBConfCall 2014.09.18-Agenda and Minutes

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SAB Agenda - Topics, Time Slots, etc.

Brief summary from the Sequence Feature jamboree

I will give a short summary of the work done this week in Boston - Mary Ann

Disclaimer - am jet lagged!



SAB Agenda - Topics, Time Slots, etc.


Below is what was discussed at today’s site-wide conference call. Please also refer to the SAB 2014 wiki page.

  • [wiki.wormbase.org/index.php/2014_Advisory_Board_Meeting]

Paul S charged us with thinking about the following when creating our talks:

  • 1) What do we want from the advisors.
  • 2) To keep in mind that there are many new advisors so we also need to address the “back story” …What we do and why.
  • 3) Time division and schedule – we may need to adjust to make sure advisors will be able to attend topics of their expertise as not every advisors will be present for the whole meeting.

Talks Discussed


Paul will begin meeting with “ What is WormBase” and his talk will include an introduction to the following topics (not necessarily in order):

  • Personnel – who we are and what we are doing.
  • Curation status and effort.
  • Automation – Where we stand, what are the limits and scaling problems.He will highlight recent work on concise descriptions and how there may be community involvement.
  • Advances – mention website restructure.
  • More WormBase tools for users, WormMine and “outside” tools (e.g. ensembl).
  • Topic Curation – how we do this.


  • Overview of build and what we have done (including ncRNA and highthrouput variations and community annotation tools (e.g. WebApollo)(Kevin)
  • Nomenclature (Mary Ann)
  • Sequence curation update – other worms including parasitic nematodes/ How we prioritize with all the new sequence
  • Parasite


  • Introduction/overview of website/metrics…what’s used and not (todd)
  • Development summary/ move to cloud / time allocations

Possible Additional Talks? Topics to discuss?

  • Val Woods – CANTO (community annotation)
  • Talks by other advisors
    • J Ewbank – power user
    • R Sommer - Pristionchus
  •  ???Database migration – probably too technical and beyond the scope…probably wont get input from advisors.
  • Standard formats for journals - What they require authors to do to ease our curation.
  • Need to discuss more about tools for clustering and enrichment – what to develop and what is already developed by others to address questions like “given a set of genes, find commonalities in (for example) anatomy– Wen and/or Raymond will address this in their talks.
  • Wen will give a talk on microarrays and expression data/ expression clustering. How we use this data

Things to think about

Where to put size of the worm research field (user community) and its growth?

Sunday Afternoon Project meeting

  • We will NOT run through our talks, but can discuss slides with others in working groups.
  • Working Groups – ideas for groups include:
    • Database Migration
    • Website- Documentation and guides/user experience and displays.
    • Phenologs - orthologous phenotypes between organisms. How to curate worm phenotypes to make it easier to compare to human disease genes. Link changes in sequence and motifs to phenotypes.
      • Side discussions (not quite large enough for a work group)
        • Ranjana would like to talk about homology and orthology
        • Chris would like to discuss RNAi mapping of other species

Brief summary from the Sequence Feature jamboree

Recently Mary Ann, Gary W, Xiaodong and Daniela met in Boston, MA for a three day “Sequence Features Jamboree” in order to streamline curation of this data type. They found this forum to be extremely productive, and a report will be available soon. In spite if her jet lag Mary Ann gave a very nice “concise description” of the jamboree at the conference call today, a summary follows:

3 major themes addressed

1) Identification of papers -

Papers will move from Hinxton to Caltech, and Juancarlos and Daniela will set up a new OA for their curation. This will allow them to be curated and cataloged on the curation status form.

The group, working with textpresso, need to set up string matching to identify papers.

2) Streamline pipeline of curation between Hinxton and Caltech –

Prioritize which papers to do, for example if the paper also has expression data, the paper can be curated at the same time for sequence features.

Some small model changes are expected

3) Web display of sequence features –

  • They discussed the best way to display this information on the website, and creation or changes to the following were mentioned:
    • Sequence features summary page,
    • Widget,
    • CDS and transcript pages
    • Display in Jbrowse
      • (On call Chris suggested also having information on the protein pages)