WormBase-Caltech Weekly Calls July 2018

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July 5, 2018

Community Curation Mass Email update

  • Emails (1 per paper) sent (most batches 75 at a time): 3,227 total
    • June 11: 5
    • June 20: 15
    • June 21: 82
    • June 22: 6
    • June 25: 75
    • June 26: 80
    • June 28: 363
    • June 29: 600
    • June 30: 300
    • July 1: 450
    • July 2: 1,251
    • Email success rate:
      • 482 emails bounced (15%)
        • 74 bounced emails had a backup email (2%)
        • 292 bounced emails had no backup (12%)
        • 88% of emails were successfully sent
      • 52 out of office replies (2%)
  • Total community annotations received since June 11: 718 (115 papers)
    • June 13: 24 (3 papers)
    • June 14: 8 (3 papers)
    • June 17: 1 (1 paper)
    • June 20: 13 (3 papers)
    • June 21: 13 (4 papers)
    • June 25: 13 (4 papers)
    • June 26: 20 (7 papers)
    • June 28: 17 (8 papers)
    • June 29: 131 (8 papers)
    • June 30: 4 (2 papers)
    • July 1: 24 (5 papers)
    • July 2: 184 (36 papers)
    • July 3: 179 (20 papers)
    • July 4: 27 (9 papers)
    • July 5: 62 (pre-meeting) (4 papers)
  • We may want to give people the option to "opt-out" either for a paper or for all emails or both
  • May be good to ask SAB and users at meetings how they feel about these email requests
  • Is it worthwhile to send requests about same paper to same people after a wait period?

SAB Literature Curation overview

WS267 Citace upload

  • July 20th, upload to Hinxton
  • July 17th, local CIT upload

Model changes

  • Some minor tag name changes
  • Changes to GO_annotation to accommodate RO terms

Curation Status Form: flagged vs. validated papers

  • Papers validated by curators are not necessarily considered flagged
  • Author first pass forms: prepopulated with SVM, string-matches
  • Curation First Pass: are forms still used?
  • TFP (Textpresso first pass) not currently used?

July 19, 2018

PomBase SObA

  • Val Wood would be interested in using SObA for PomBase
  • Some immediate action items to deal with for expanding SObA to other ontologies and databases
  • Maybe highlight leaf nodes with more granular information? Already available in unweighted view


  • SAB suggested continuing site visits for WormBase tutorials
  • SAB suggested host institution provide funds; we can at least ask

July 26th, 2018

Temporarily Withdrawn Paper (WBPaper00054672)

  • A recently epublished Genetics paper (2018 Jun 26) "...has been temporarily removed at the authors' request, to allow review of a companion article. The article 301078 will appear in a future issue of GENETICS."
  • We already have the PDF in postgres (as of 2018-07-10), but I don't see the paper in TPC or the curation status form.
  • Is there anything we should do here? Temporarily remove the PDF from postgres?
    • Remove entirely and get new paper from scratch? OK

Expression display on the anatomy page

  • Suggested last week to have a way to display genes and associated evidences on the anatomy page. Rank order by number of evidences.
  • Mock here: https://docs.google.com/presentation/d/1HE_QhJrs5oScmORdiAAdTxfavAnF6NUQhtJGWvcC7EQ/edit#slide=id.p2
  • Consider grouping evidence per gene (Expr_pattern objects)
  • Should we apply a weight to each piece of evidence, type of evidence?
    • Apply less weight to large scale, e.g. RNAseq data?
  • Users likely want to know confidence of presence/absence call as well as degree of specificity
  • Need to consider methods used: Single-cell RNAseq of pool of cell types IDed by sequencing may not be as reliable an annotation to a specific cell, cell type or tissue; but single-cell RNAseq from physically isolated cells based on marker/reporter expression may be more reliable
  • We will first rank-order the list based on genes with a higher number of Expr_pattern objects

SAB Follow Up

  • SAB Report (Paul sent around a Word doc)


  • Can import annotations, but can't edit them and resubmit them; essentially read-only
  • Possibility of micropublishing a Noctua model

Picture curation

  • Marie-Claire started picture curation with Daniela
  • Jae reported that Simon James at Florey Institute of Neuroscience and Mental Health, Australia wants to submit many images (some published, some not)

Asian-Pacific Worm Meeting

  • 200+ attendees, mostly grad students, post docs, PIs
  • Complaining about connection speed; wondering when is the busiest time/highest traffic time, so they can avoid traffic? Will talk to Todd
    • Is this mostly users from China? Could it be a firewall issue? Seems to be all people from China, Japan, Korea, Australia, etc.
    • Can we set up a VPN to do remote response testing?
    • Can we login to a remote network (with permission) and test the WB site?
  • Some widgets, e.g. Location or Interactions, often throwing time-out errors; possibly due to too much data
    • What pages in particular? How frequently?
  • Some people feel that JBrowse is slower than GBrowse
  • People asking about essential genes in N2? Other strains? Other species? Junho Lee asked
    • Have a Postgres query to get a table of most considerations, but have to perform locally and send out table to users
    • Long term solution is implementation of ?Phenotype_experiment/?Phenotype_annotation class to query out a table
  • Gene descriptions sometimes inaccurate and/or public gene names in description inconsistent with current website display of public name
  • GO terms seem confusing or possibly redundant with other terms; good to get this feedback to GO
  • Micropublications:
    • What is the minimum requirement for micropublication? Each submission reviewed manually now; range of submission types
    • Can the data be reusable in other publications? Can be cited, but not republished as novel finding
    • Index by PubMed; working on it now; have ISSN from Library of Congress; working towards PubMed indexing
    • Impact factor? Cannot know until it's in PubMed and citations are accumulated
    • Plan is to expand to other species; store data in a repository, especially for species without an existing repository; could create a generic repository at AGR
    • People in other fields/working in other species, encourage reaching out to micropub team
  • Questions about WB/AGR interactions:
    • Will WormBase still be around after AGR? Yes, but perhaps integrated into the AGR portal/site eventually
  • Will WB be free forever? People know that FlyBase is asking for donations
    • Current funding mechanism does not allow WB to charge
  • Suggestions:
    • People find WormMine difficult to use; would like step-by-step tutorial, possibly video tutorials
      • Pointed users to WormBase YouTube channel
    • Data submission:
      • Junho Lee: de-novo genome assembly of Hawaiian strain; found interesting data, would like to submit (should discuss with Kevin Howe)
      • Image set to submit (Simon James, see above)
  • People were happy to see a WormBase curator at the meeting; would like to see WB curator at next meeting again
    • Next Asia meeting in Hong Kong in 2 years