WormBase-Caltech Weekly Calls

From WormBaseWiki
Revision as of 21:59, 23 May 2018 by Vanaukenk (talk | contribs)
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

GoToMeeting link: https://www.gotomeet.me/wormbase1

2018 Meetings





May 3, 2018

SimpleMine output

  • Wen was working on simplification of SimpleMine output
  • Considering removing general terms in an ontology when more specific terms exist
  • Concern that we would be removing information; will keep terms

SPELL topics

  • Topics in SPELL need some organization, possibly trimming
  • We could create a graph (SObA) display of topics (based on GO process)

SPELL problem with WS265

  • Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340)
  • Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
  • Wen will write to Matt Hibbs to ask how to deal with
  • Will Alliance work together on a system to analyze large scale expression data?

Curator candidate

  • Will arrive at 10am
  • Skype calls with remote curators
  • Curators will send group Skype handle and requested time to talk

May 10, 2018

ECO terms for genome editing

  • Asking group's feedback on ECO terms for genome editing (Daniela)
  • What would be used for fly-enhancer trap experiment?
  • Genomically encoded GFP, for example
  • ECO: GFP localization
  • ECO term, example: Fluorescent protein transcript localization evidence
  • Single copy transgene? Endogenous locus?
  • Whether it is CRISPR or not may not be relevant
  • May request ECO terms that capture distinct types of transgenes evidence
  • Will use generic term for now
  • Do other MODs use ECO?
  • May want to capture endogenous/non-endogenous, multi-copy/single-copy distinctions
  • Many of these features are captured in the transgene and construct objects already; specific ECO code redundant?


  • Significant involvement in Alliance
  • Interest in micropublications; will push a pilot
  • June 19, moving from older DB to Postgres
  • Investigating automation for some curation processes
  • Students review which papers to include; acquire PDF
  • Curate paper-by-paper


  • Supplement request for year 3, due soon (May 15)
  • Formal report from NHGRI, 18-month plan looks good
  • Further future plans (from NHGRI perspective) aren't quite clear
  • Software infrastructure?
  • Central- vs. MOD-control of resources questions
  • Likely will have to write a NIH proposal in Fall or Winter
  • How much is Alliance going to handle human variants?
  • NHGRI interested in metabolomics; Alliance plans?

Genome-wide screens

  • Had help desk question about phenotypic screens in organisms other than worms, flies, yeast, bacteria
  • There have been human cell line phenotypic screens (e.g. siRNA/shRNA); who curates these, if anyone?
  • Also, induced pluripotent stem cell experiments

Nameserver issues

  • Issue came up about assigning unique WBStrain IDs
  • Can use a nightly nameserver dump from Hinxton to populate Postgres/OA
  • Will need to clean up existing strains in Postgres
  • Also, considering unique IDs for genotypes
  • Mechanics of naming and managing naming of objects
    • Nightly syncing (cronjob) to nameserver
    • Ideally, we would have instant updates; Hinxton firewall prevents direct access; Matt working on establishing a separate nameserver location to gain direct access
    • Strain names (at least historically) have been updated quarterly from CGC file
    • Curators need mechanism to create and use strain (and variation) names right away
    • Current system requires manual denormalization step; has worked so far

May 17, 2018


  • Create a strain OA? Central curation tool for strain data?
  • Would need to maintain synchrony with CGC and Hinxton
  • Postgres/Tazendra variation adding CGI: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
  • Will add similar link for Strains, adding info to obo_name_strain and obo_data_strain as well as a tempfile, which will those objects in postgres when the nightly_geneace.pl updates the OA strain info

SAB 2018

  • Who will present? Present what?
  • We can generate a central document with stats to give to SAB
  • Ask SAB for opinions and guidance?
  • Would be good to assess current efforts and priorities, ask if we should stay the course or make modifications to our approach

May 24th, 2018