WBConfCall 2021.06.03-Agenda and Minutes

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Help Desk

Open tickets:

Agenda and Minutes

WS281 New data for the release letter


Hinxton (follow on):

  • Expanded collection of C. elegans comparator genomes by adding a chromosome-scale draft C. bovis assembly {PMID:32109387}, and nine further draft assemblies of newly described Caenorhabditis species {PMID:1007946} and replaced two C. remanei strains (PX356 and PX439) with animproved chromosome-scale assembly of C. remanei PX506 {PMID:32111628}.
  • Magda: Tell users about new data and new genome analysis. Species in compara are different. New orthologies, homologies.
  • Paul: Major section in Genetics article, or microPublication.
  • Ranjana: Where is the data to point to users to it ?
  • Magda: In Species tab. Will edit and spruce it up. Gene Tree is slightly different. New files in FTP site.
  • Kevin: Produce trees in the background, but don't show on the website. Is an Alliance deliverable. To display trees may want to add to Alliance. More orthologs in gene pages and files.
  • Todd: Users probably won't notice, second microPublishing this.
  • Paul: Focus on Caenorhabditis statistics, so people don't have to make own trees for each family.
  • Kevin: Provide OrthoXML dumps of the trees ? Would make dumps available. Easy to figure out Compara pipeline. Not using part of the pipeline because requires molecular clock, nematodes don't have that because divergence in the phylum.
  • Paul: Might be able to for Caenorhabditis. Why does clock matter ?
  • Lincoln: Order, topology are important.
  • Kevin: https://hahnlab.github.io/CAFE/src_docs/html/index.html
  • Paul: Action item is to blog about it, Kevin generates data, Todd get display in Alliance, someone may microPublish it.

GSoC student to work on genomic locations of Variants

  • Hinxton has a GSoC student (Rishab) who will be working on extracting the genomic location of variations from full-text papers
  • Magda: Rishab will be around for a couple of months. Getting papers from Textpresso. Tiny extension of Variant pipeline. See if can automate labour-intensive pipeline, curate genomic location of Variants.
  • Ranjana: Are there plans to collect gain-of-function ?
  • Magda: A few other things are being considered, Valerio has some thoughts too.
  • Chris: Alliance Allele subgroup is discussing allowing option of Phenotype, but not requiring it. Other MODs do it without Phenotype.
  • Paul: Karen, what would we need for a curator/author template for a Nature of Allele microPublication ?

IWM coordination

  • Do we need to plan anything together for the upcoming IWM?

IWM 2021 WB Workshop

  • Scheduled for June 22, 2021
  • Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
  • Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
  • Here is the submitted workshop schedule:
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
  • Magda: Anything we still need to do ?
  • Chris: We're all set. People should coordinate with Magda about what should be covered in their data. 10-12 minute talks with time for questions.
  • Ranjana: Questions in chat ? Will need someone to collect questions like the webinars.
  • Magda: Paul D and Stavros will be at the meeting, will ask them to help with questions.
  • Raymond: One person from each site should be there to cover any WormBase knowledge.
  • Paul: Remind people about the Alliance, microPublication, what else ?
  • Chris: Community curation, highlight prolific contributors, awards ?
  • Paul: We could double the number of publications through microPublications. Forms are getting better.

WS280 WormBase ftp resync

  • There are still some issues with the C. elegans GAF and GPI files on the WormBase ftp site that are causing the GO release to fail
  • Corrected files are available on the EBI ftp site
  • If we haven't already, can we resync the ftp server?
  • GitHub ticket: https://github.com/WormBase/website/issues/8185
  • Kimberly: Need another resync from EBI to WB because of fixes to GAF and EBI files, they're holding up GO release.
  • Todd: Should be resynced, please check.

Github tickets having more info from Help Desk emails

  • Raymond: Help desk github ticket was removing contact information. Now that github is private, can we add the user email back, so we can find them more easily ?
  • Todd: We can do that.
  • Sibyl: Do our policies allow sharing contact info with external vendors (github) ?
  • Magda: Email address is not necessarily personal information, since anyone can make a dummy email.
  • Sibyl: Do we want name along with email address ?
  • Raymond: Would like whatever we get in the email, so we don't lose information.