WormBase-Caltech Weekly Calls

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2018 Meetings

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September 6, 2018

Genotype class

• Chris started initial document to draw up ?Genotype class and make appropriate changes to ?Strain class
  • https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
• Would be good for people to look at so we can discuss next time
• Would also be good to have Kevin H take a look and provide feedback

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