WormBase-Caltech Weekly Calls August 2017

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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). Mary Ann to update nomenclature guidelines.
  • 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)

August 10, 2017

WormBase grant

  • Neuronal wiring with Scott Emmons? Maybe not for this round
  • Transcription regulatory networks? Is a priority
  • Paul will assemble existing parts and send around for review

Entity markup

  • InSilico entity linking project requires curator link checking - for missing links as well as for faulty links - bad links are already an issue when ambiguities exist and this will grow as an issue when we start marking up multiple mod entities in the same paper
  • There is a brief summary table outlining the link URLs and predicted quality - this is a useful feature of the current system set up by Arun, we are creating the same type of feature in the new inteface
  • Could Cecilia check links?
  • New interface will come out in a few months; if anyone starts now, they'll have to relearn when the new interface comes out
  • Eventually markup should be job of authors during the process of writing. Need an authoring tool - this can be made - there needs to be more discussion between wormbase, and insilico if this is going to be part of the insilico phase II or not

Sequence features

  • Should we have a standard human readable names for sequence features?
  • Should we consolidate several features associated with the same gene when displaying in network views?
  • Is there an automated way to give them public names?
  • Maybe name automatically, but then allow manual overwriting
  • Use gene name when experimentally demonstrated connection
  • Needs to be automated, rule-based
  • Could name based on neighboring gene(s)

Person lineage graph

  • Progress made in development, direct lineage running off of Datomic. All of it will need to be completed before it can go into production.

Docker container system

  • Potentially very useful for WB web services

Consider content for NAR paper

  • Send ideas to Raymond


  • Input for the WB grant?
  • Could discuss microreviews

Concise descriptions

  • Automated descriptions good for genes with little info
  • Human-written descriptions good for genes with lots of info; don't change too frequently
  • Some have suggested including protein domain info

August 17, 2017

Citace Upload

  • Citace upload August 29th (most likely)

AGR 1.0 Disease data

  • Discussion of cutting back scope to only gene-disease associations versus pushing back deadline
  • Problems stem from the fact that gene objects have already been instantiated as objects with human-readable names, synonyms, etc.
  • Objects like strains, genotypes, fish, etc. still need to be instantiated with symbols, synonyms etc. and so will be difficult to get set up for human-readable display and linking to MOD pages
  • We've already pushed back the deadline twice before, so we probably don't want to do that again
  • We can put up disclaimers or notifications that we are only showing gene-disease associations for now, but other associations (to genotypes, strains, etc.) will come soon

NAR paper community curation?

  • Not much has changed about community curation fundamentally since last NAR paper
  • Chris will write up update with specific numbers (response rates, annotation numbers, etc.) for NAR paper

Community curation submission requests

  • Chris & Juancarlos updated request pipeline
  • Now focusing just on first authors; allows more emails to go out each month
  • Have sent 333 emails since beginning of August, have received annotations for 20 papers so far (6% response, but still early; average tends to be 16%)
  • Sending out more emails should result in more responses in absolute number

Author First Pass (AFP) pipeline

  • Karen brought up that the wrong author was emailed for AFP (Author First Pass)
  • Probably an issue that last author happened to not be the corresponding author, may have thrown off automated detection of corresponding author
  • To what extent do we and community benefit from the AFP pipeline?
  • There may be cases where AFP flags a paper for a data type that was missed/false negative by SVM
  • We can optimize/update the AFP form, leave it as is, or possibly abandon it
  • Maybe Chris can take over over-seeing emails sent to authors for various requests

WB Grant

  • Would like more specifics on future plans
  • Chris will send Paul some details on future plans for community annotation

August 31, 2017


  • Mitani has submitted some for allele-phenotype and sequence change; we will not store the raw data for the sequence reads

author first pass

  • we will keep for now, but re-evaluate more thoroughly in the coming weeks, particularly wrt possible links to the micropublication platform

the grant

  • Paul will send around a version soon and will contact specific people if he needs more info on a certain section

topic lists for SPELL and SpellMine

  • we should take advantage of GO ontology structure for browsing topic lists

new cuator

  • Jae will start at WB on the 1st of September
  • he'll work on PPI and possibly phenotype curation first, will add GO curation a bit later