Difference between revisions of "WormBase-Caltech Weekly Calls"
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** What classes of genes would we want to identify: histones, transcription factors, ion channels, protein kinases | ** 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 | ** 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 |
Revision as of 16:13, 20 September 2018
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
September 6, 2018
Genotype class
- Chris started initial document to draw up ?Genotype class and make appropriate changes to ?Strain class
- 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
- Covered gene set enrichment, WormMine, SPELL, SimpleMine, ParaSite BioMart, Textpresso
- Would be good to show people how to use Textpresso Central
- 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