WormBase-Caltech Weekly Calls

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July 6, 2017


  • Use for all literature curation in future?
  • We would need to see how it could be used for all data types
  • We would also want a full-time developer working on Noctua; maybe bring Juancarlos into the project


  • SPELL related data - how to deal with?
    • Data: recalculated, mapping, results dependent on SPELL
    • Analysis (clustering tool): clunky, freezes w/limited resources
  • Wen will work with Juancarlos to generate a SimpleMine-like tool for downloading data sets
  • Wen has to remove log files to make space on machine
  • ~360 data sets
  • Current virtual machine has 10G memory; is becoming limiting
  • SPELL has lots of dependencies; difficult to account for them all when building SPELL
  • Would be good if we could setup a new (larger) virtual machine to run SPELL; how much time/resources do we want to spend on it?


  • Poster at Zebrafish meeting pointing to micropublications
  • Microarray micropublications? Unpublished results
  • Can make links to GEO submissions
  • Daniela and Karen can draw up a mock publication to look at as a template

Community Curation

  • Considering sending requests to only one person, first author when have info
  • This should allow for more emails to be sent out per week, and more submissions, even if we maintain the 16% response rate
  • Chris will work with Juancarlos once he's back from vacation
  • What's next data type? Interactions? Site of action? Anatomy?
  • What's required for site of action? Phenotype, gene, cell/tissue where gene is introduced or removed
  • Can send requests to lab heads to fill in phenotype info for alleles from their lab


  • Will human genes link to AGR human gene pages? Gene Cards? HGNC?

July 13, 2017

Allele attribute assignment

  • Some attributes of alleles are currently only assigned in the context of a phenotype annotation
  • Many times these attributes are reported independently of a phenotype experiment
  • It would be good to have a mechanism to curate these attributes to alleles independent of phenotype curation
  • As far as modeling goes I (Chris) had intended to do dump these attributes directly into the ?Variation object like this:
Null  ?Phenotype_experiment
  • This would allow us to always point to a ?Phenotype_experiment object as a container of evidence, but if we don't always have a ?Phenotype_experiment object to point to then maybe a better approach is just to reference the paper like this:
Null  ?Paper
  • This would require a separate curation pipeline from phenotype to capture these attributes; will discuss more with Mary Ann when she's back from vacation
  • We discussed and came up with a couple of potential solutions:
  • First:
Variation_effect  Null  ?Text  #Evidence
  • Second:
Variation_effect  Null  ?Paper  #Evidence
  • The first solution allows to put in a free text remark, potentially referencing a phenotype or some detail, with the #Evidence hash allowing reference to a paper or a person_evidence
  • The second solution requires reference to a ?Paper object, which would require a reworking of all person evidence/personal communication to become ?Paper objects, with an #Evidence hash to capture remarks

Phenotype form submission requests

  • Originally we sent email requests independently of Author First Pass pipeline emails
  • Now a link to phenotype form is being included in Author First Pass emails, and we're putting a hold on all new email requests to corresponding author for one month
  • I (Chris) am considering returning to original approach of sending requests independently of AFP (and focusing on first authors), to see if we can get response rate up at all

New WormBase Caltech server

  • We're getting a new server, to consolidate different computers and their services
  • Let Raymond know if you have an idea for another (extra) use of the server
  • Will likely re-use altair.caltech.edu
  • 96 GB memory, ~6 TB hard drive


  • SPELL could go on new server
  • Moved from current virtual machine to KVM
  • Could expand memory and CPU

July 20, 2017

Variation effect assignment

  • We had discussed last week having either of two models in the ?Variation class
  • First:
?Variation   Variation_effect  Null  ?Text  #Evidence
  • Second:
?Variation   Variation_effect  Null  ?Paper  #Evidence
  • The first option can keep things as they are and can allow a remark in the ?Text entry, with paper or person evidence coming from the #Evidence hash
  • The second option likely requires that we consider person evidence/communication as ?Paper objects
  • Many entries in the Phenotype OA coming from Jonathan Hodgkin are from the C. elegans I and II books
    • Would be good to create ?Paper objects for C. elegans I and II and reference them accordingly
      • Already exist:
        • C. elegans II WBPaper00004071
        • C. elegans I WBPaper00004052
  • Probably best to go with
?Variation   Variation_effect  Null  ?Text  #Evidence
  • Going forward we can encourage people to micropublish if they want to submit personal communication

Blog posts for WormMine

  • Not quite ready; Chris will contact Ranjana about it when ready

WormMine templates

  • Todd had encouraged development of template queries
  • Older templates are still difficult to access and edit, but new queries going forward are OK

New Server

  • New WormBase server (@ Catlech) is online
  • Let Raymond know if anyone has uses for the server
  • Anything that needs to be running 24-7 (e.g. services) can be considered

Supplement for AGR

  • Proposing tuning up of orthology calls
  • Paul S. wants to get Gene Orienteer back up, and have RNASeq analysis pipeline
  • Pull in WormNet data (predicted interactions)

July 27, 2017


  • Discussion of new AGR GO slim and representation of C. elegans genes
  • Modification to AGR slim
  • Key to graphs
    • Red = AGR slim
    • Orange = C. elegans orphans
    • Multi-colors = Other organism orphans, as well

August 3, 2017

WB grant

  • Progress (maintenance stuff) can be written as of last grant cycle
  • Current projects and report the steady state

CRISPR alleles

  • Some authors not reporting CRISPR alleles with standard nomenclature
  • Some in Paul's lab creating same knockin with same name (should be distinct)
  • Some (e.g. Bruce Bowerman) knock-in GFP in frame and use RNAi against GFP to knockdown endogenous gene
    • RNAi mapping pipeline not setup to handle this
    • Could maybe use endogenous sequence near insertion site (not ideal, for off-target effects)
    • Maybe best, once new ?Phenotype_experiment model is in place, to just refer to perturbed gene

Ontology Browser

  • Has been less stable lately; Raymond has needed to restart machine
  • Being served from Dell server (in Braun building)