WormBase-Caltech Weekly Calls December 2017

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December 7, 2017

Next Citace upload

  • Submit files to Wen by Jan 16, 2018
  • There shouldn't be model changes (that affect Caltech) for this next upload
  • Juancarlos goes on vacation Dec 19th

WB Curator candidate

  • April, could join WB for 1-2 years
  • Could possibly interview next Thursday
  • Could curate sequence features, enhancers, alleles/mutations/variations?
  • Could start in January

Expression clusters

  • Wen and Raymond discussed; will add an "uncertain" tag or something similar
  • Tag can be used to filter out datasets that are complex (like mixed cell/tissue types)

Automated descriptions & expression clusters

  • Many expression clusters are associated with infection
  • Such data not currently incorporated into automated gene descriptions
  • Wen can talk with Ranjana to incorporate (particularly for info-sparse genes)
  • Can use GO terms, but need to be careful about how they are applied (what relationships they have) to genes

Author First Pass Form

Overall approach

  • AFP form would move from being just a flagging pipeline towards a validation and data entry pipeline
  • Also move from free text boxes towards autocompletes, controlled vocabularies
  • If this is a validation and a portal for data entry forms, should we display everything we can mine?
  • Idea is to eventually create data entry forms for as many data types as possible
  • Long term goal would include linking to TPC and evidence sentences for validation
  • Data types not curated by WB would need to be re-evaluated: continue to mine but share with other curation groups? no longer mine? new WB objects or pages?
  • Periodically review the form and add/remove data types and curation forms as needed
  • Would be good to ask authors if they had to omit data from the recently published paper and if they want to micropublish

Questions

  • Question for WB curators: Are we missing data types?
  • Question for WB curators: Are there data types that we don't curate (e.g. domain analysis) but for which we could share mining information with other groups, e.g. UniProt?
  • Question for WB curators: Are there data types we should no longer mine?
  • Question for Wen: Does it make sense to include an afp flag for expression cluster?
  • Question for Karen: What afp tables are populated from the Genetics/G3 pipeline?
Details here: http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass
Screen Shot 2017-12-07 at 9.28.56 AM.png

Thoughts

  • Could we add to citation index score as incentive to provide validation/data?
  • How do we make sure we are not turning off/overwhelming users/participants/authors?
  • Can gamify the forms; give points?
  • Create an app that has user-friendly data submission tools/forms?


December 14, 2017

MOD data in Data Commons

  • NIH Data Commons wants DB data in common formats
  • We've wanted APIs or web service to allow access all data in standard format
  • Good to have one place for all data from all MODs
  • This should be a work product of the AGR
  • Consider priority: data site, website
  • AGR working groups work towards data standards
  • GAF (gene association file) could be used now; what can we learn about the GAF: development, usage?
  • GAF hasn't changed much in last ~10 years

Contingency plan for Juancarlos' vacation

  • If Tazendra crashes/dies, we can perform a hard drive swap at Caltech

Essential genes

  • David Fay asked for list of essential C. elegans genes
  • David asked for genes whose mutants are inviable as homozygotes, ignoring RNAi
  • Could we generate a file for users? Can we make a conservative list with ~no false positives
  • What are all the criteria (that are curated) that could be used to decide whether a gene is essential?
  • How does any user define "essential"? What are the cutoffs/thresholds?
  • Best option may be to provide a table with all relevant phenotype annotation attributes and let user decide based on filters

Expression certainty

  • Proteomics experiments have subjective thresholds
  • How do we handle cases where one peptide maps to multiple genes?
  • How should large scale expression data be incorporated into enrichment analysis?

GitHub tracker for Caltech curation issues

  • "Caltech curation" repository - primarily used for creating curation tool set for Caltech team
  • "WormBase curation" repository - last used in 2015
  • Should there be a single repository for tracking? Yes, use the "wormbase-curation" repository
  • Curators will start submitting tickets in the "wormbase-curation" repository
  • OA code is in there now
  • We should add OA dumper code as well


December 21, 2017

Upload

  • Jan 19th citace upload to Hinxton
  • Get .ace files to Wen by Tuesday Jan 16th, 10am PST

Wen's outreach slides

  • Wen created slides for presenting at San Diego area worm meeting
  • Meeting on Jan 12, 2018
  • Wen recreated her slides based on feedback from Sternberg lab meeting
  • Slides cover step-by-step tutorials for using Wormbase website
  • For future outreach meetings/presentations, we can reach out ahead of time to find out what topics would be of greatest interest
  • Curators, review Wen's slides and send her feedback
  • Can take a look at WormBase YouTube channel for existing videos
  • Chris can send WormMine tutorial videos and/or slides to Wen to share with audience

Karen and Daniela going to Bay Area meeting

  • January meeting
  • WormBase outreach, micropublications

April will start in January

  • Will start on transcriptional regulation
  • May work on allele phenotypes

Any curation issues (tool bugs etc.)

  • While Juancarlos is gone, submit tickets to GitHub
  • Raymond will take a look at