WormBase-Caltech Weekly Calls
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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