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| | [[WormBase-Caltech_Weekly_Calls_November_2017|November]] | | [[WormBase-Caltech_Weekly_Calls_November_2017|November]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_December_2017|December]] |
| − | == December 7, 2017 ==
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| − | | |
| − | === Next Citace upload ===
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| − | * Submit files to Wen by Jan 16, 2018
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| − | * There shouldn't be model changes (that affect Caltech) for this next upload
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| − | * Juancarlos goes on vacation Dec 19th
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| − | | |
| − | === WB Curator candidate ===
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| − | * April, could join WB for 1-2 years
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| − | * Could possibly interview next Thursday
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| − | * Could curate sequence features, enhancers, alleles/mutations/variations?
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| − | * Could start in January
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| − | | |
| − | === Expression clusters ===
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| − | * Wen and Raymond discussed; will add an "uncertain" tag or something similar
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| − | * Tag can be used to filter out datasets that are complex (like mixed cell/tissue types)
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| − | | |
| − | === Automated descriptions & expression clusters ===
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| − | * Many expression clusters are associated with infection
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| − | * Such data not currently incorporated into automated gene descriptions
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| − | * Wen can talk with Ranjana to incorporate (particularly for info-sparse genes)
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| − | * Can use GO terms, but need to be careful about how they are applied (what relationships they have) to genes
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| − | | |
| − | === Author First Pass Form ===
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| − | *[https://docs.google.com/spreadsheets/d/1sS_uAjBJ2r5H90Lam62Ai0HunjwvfjnklkFNrDoNXeU/edit Analysis of current flags and numbers of entries]
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| − | | |
| − | ==== Overall approach ====
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| − | *AFP form would move from being just a flagging pipeline towards a validation and data entry pipeline
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| − | *Also move from free text boxes towards autocompletes, controlled vocabularies
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| − | *If this is a validation and a portal for data entry forms, should we display everything we can mine?
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| − | *Idea is to eventually create data entry forms for as many data types as possible
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| − | *Long term goal would include linking to TPC and evidence sentences for validation
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| − | *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?
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| − | *Periodically review the form and add/remove data types and curation forms as needed
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| − | * Would be good to ask authors if they had to omit data from the recently published paper and if they want to micropublish
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| − | | |
| − | ==== Questions ====
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| − | *Question for WB curators: Are we missing data types?
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| − | *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?
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| − | *Question for WB curators: Are there data types we should no longer mine?
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| − | *Question for Wen: Does it make sense to include an afp flag for expression cluster?
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| − | *Question for Karen: What afp tables are populated from the Genetics/G3 pipeline?
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| − | **journal first pass forms : http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?
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| − | Details here: http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass
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| − | | |
| − | [[File:Screen_Shot_2017-12-07_at_9.28.56_AM.png]]
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| − | | |
| − | ==== Thoughts ====
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| − | * Could we add to citation index score as incentive to provide validation/data?
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| − | * How do we make sure we are not turning off/overwhelming users/participants/authors?
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| − | * Can gamify the forms; give points?
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| − | * Create an app that has user-friendly data submission tools/forms?
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| − | | |
| − | | |
| − | == December 14, 2017 ==
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| − | | |
| − | === MOD data in Data Commons ===
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| − | * NIH Data Commons wants DB data in common formats
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| − | * We've wanted APIs or web service to allow access all data in standard format
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| − | * Good to have one place for all data from all MODs
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| − | * This should be a work product of the AGR
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| − | * Consider priority: data site, website
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| − | * AGR working groups work towards data standards
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| − | * GAF (gene association file) could be used now; what can we learn about the GAF: development, usage?
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| − | * GAF hasn't changed much in last ~10 years
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| − | | |
| − | === Contingency plan for Juancarlos' vacation ===
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| − | * If Tazendra crashes/dies, we can perform a hard drive swap at Caltech
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| − | | |
| − | === Essential genes ===
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| − | * David Fay asked for list of essential C. elegans genes
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| − | * David asked for genes whose mutants are inviable as homozygotes, ignoring RNAi
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| − | * Could we generate a file for users? Can we make a conservative list with ~no false positives
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| − | * What are all the criteria (that are curated) that could be used to decide whether a gene is essential?
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| − | * How does any user define "essential"? What are the cutoffs/thresholds?
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| − | * Best option may be to provide a table with all relevant phenotype annotation attributes and let user decide based on filters
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| − | | |
| − | === Expression certainty ===
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| − | * Proteomics experiments have subjective thresholds
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| − | * How do we handle cases where one peptide maps to multiple genes?
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| − | * How should large scale expression data be incorporated into enrichment analysis?
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| − | | |
| − | === GitHub tracker for Caltech curation issues ===
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| − | * "Caltech curation" repository - primarily used for creating curation tool set for Caltech team
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| − | * "WormBase curation" repository - last used in 2015
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| − | * Should there be a single repository for tracking? Yes, use the "wormbase-curation" repository
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| − | * Curators will start submitting tickets in the "wormbase-curation" repository
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| − | * OA code is in there now
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| − | * We should add OA dumper code as well
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| − | | |
| − | | |
| − | == December 21, 2017 ==
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| − | | |
| − | === Upload ===
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| − | * Jan 19th citace upload to Hinxton
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| − | * Get .ace files to Wen by Tuesday Jan 16th, 10am PST
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| − | | |
| − | === Wen's outreach slides ===
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| − | * Wen created slides for presenting at San Diego area worm meeting
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| − | * Meeting on Jan 12, 2018
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| − | * Wen recreated her slides based on feedback from Sternberg lab meeting
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| − | * Slides cover step-by-step tutorials for using Wormbase website
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| − | * For future outreach meetings/presentations, we can reach out ahead of time to find out what topics would be of greatest interest
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| − | * Curators, review Wen's slides and send her feedback
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| − | * Can take a look at WormBase YouTube channel for existing videos
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| − | ** https://www.youtube.com/user/WormBaseHD/featured
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| − | * Chris can send WormMine tutorial videos and/or slides to Wen to share with audience
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| − | | |
| − | === Karen and Daniela going to Bay Area meeting ===
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| − | * January meeting
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| − | * WormBase outreach, micropublications
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| − | | |
| − | === April will start in January ===
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| − | * Will start on transcriptional regulation
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| − | * May work on allele phenotypes
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| − | | |
| − | === Any curation issues (tool bugs etc.) ===
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| − | * While Juancarlos is gone, submit tickets to GitHub
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| − | * Raymond will take a look at
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