WormBase-Caltech Weekly Calls

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

2018 Meetings









September 6, 2018

Genotype class

Citace Upload

  • Send citace files to Wen by Sept 18, 10am Pacific

Automated gene descriptions

  • Group making improvements
  • Added disease, protein domains
    • When direct experimental evidence for disease relevance, will say "gene has been used to study"
  • When minimal data (information-poor genes), we can refer to human ortholog and data stored for that human gene in Alliance
  • Continue to receive feedback from users; include enrichment information, etc.
  • Now have good trimming algorithms to retain important info without flooding a description with too many granular terms
  • Will not store automated descriptions in Postgres
  • Wen will modify SimpleMine scripts to accommodate change
  • Would be good to write a paper on automated concise descriptions
  • Came up at GO meeting/hackathon: Translating GO-CAM models into concise descriptions?
    • Should be doable; just need to develop code when we're ready to do that

Textpresso presentation at next Alliance all-hands call

  • Who should present? Maybe have several people? Kimberly, Valerio, Michael for sections?
  • We can discuss at next Textpresso meeting
  • Should cover techniques and software, but keep it generally simple and comprehensible for a larger audience

September 13, 2018

Citace upload

  • Send files to Wen by 10am Tuesday (18th)

Genotype class

  • ?Genotype class proposal
  • Genotype_name tag: free text summary of the genotype
    • Can this be automatically generated from components? Ideally, yes, but may be difficult
    • Otherwise, can be manually written, as we have been doing, but is a bit denormalized and may require maintenance
  • Genotype_description tag: free-text description of the genotype
    • No precedent and probably not going to start now, so will remove from model
  • Genotype_components supertag: to collect genotype component objects and, where necessary, free text
    • We want to be able to express zygosity for each referenced object, likely requires a #Zygosity hash (and hence a ?Zygosity model)
    • ?Zygosity model can have three main tags: "Homozygous", "Heterozygous_with_wild_type", or "Heteroallelic_combination_with"
      • Heteroallelic_combination_with tag could further specify the type and identity of the object that is in heteroallelic combination with the original object
      • Since it is not ideal to store an arbitrary component in the #Zygosity hash, we should probably just state the zygosity as "Heteroallelic_combination" and for display purposes have an automated way to calculate which components affect the same locus/loci (if necessary)

September 20, 2018

Kimberly's talk at Rutgers

  • Kimberly went to worm meeting at Rutgers (10 labs using C. elegans? 6-7 totally worm-centric)
  • 30-40 attendees (PIs, postdocs, grad students)
  • Discussed tools and features at WB
  • Presented Alliance pages and Textpresso
  • PIs are enthusiastic about WB
  • Monica Driscoll made a good plug for Textpresso
  • People requesting FAQs and user guides (text and videos)
  • Monica suggested a WB tutorial for PIs ;p
  • Some people surprised about what they can accomplish using the tools available, like SimpleMine
  • Covered gene set enrichment, WormMine, SPELL, SimpleMine, ParaSite BioMart, Textpresso
  • Would be good to show people how to use Textpresso Central
  • Discussed micropublications, asked about negative results (precedent?)
  • Some asked about WB funding and Alliance plans
  • Can we make a within-page search available to find, for example, field names etc.
  • Some challenges in find genes/proteins of certain class
    • Had question about histone genes recently
    • Repeatedly have had questions about finding "ion channels"
    • Searching gene class with text pulls out lots of false positives
    • Could perform an analysis on particular classes of genes (e.g. histones or ion channels) and generate a micropublication providing the curated list
    • Can generate a WormMine template query to pull these out for each release
    • What classes of genes would we want to identify: histones, transcription factors, ion channels, protein kinases
    • Chris will look into WormMine templates using gene class info and look into pulling in protein motif information
    • We will ask other MODs and UniProt about how they deal with this issue

September 27, 2018

Update on the new AFP form and pipeline

  • Daniela, KImberly, Juancarlos, and Valerio will update on the current status of the new AFP form and pipeline
    • Overall, the goal has been to incorporate as much Textpresso-based entity and data-type flagging as possible into the form
    • Move from author data flagging to author data validation wherever we can
    • Provide opportunities for authors to submit more detailed curation if they want