WormBase-Caltech Weekly Calls
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Contents
Previous Years
2017 Meetings
December 7th, 2017
Next Citace upload
- Submit files to Wen by Jan 16, 2018
- There shouldn't be model changes (that affect Caltech) for this next upload
- Juancarlos goes on vacation Dec 19th
WB Curator candidate
- April, could join WB for 1-2 years
- Could possibly interview next Thursday
- Could curate sequence features, enhancers, alleles/mutations/variations?
- Could start in January
Expression clusters
- Wen and Raymond discussed; will add an "uncertain" tag or something similar
- Tag can be used to filter out datasets that are complex (like mixed cell/tissue types)
Automated descriptions & expression clusters
- Many expression clusters are associated with infection
- Such data not currently incorporated into automated gene descriptions
- Wen can talk with Ranjana to incorporate (particularly for info-sparse genes)
- Can use GO terms, but need to be careful about how they are applied (what relationships they have) to genes
Author First Pass Form
Overall approach
- AFP form would move from being just a flagging pipeline towards a validation and data entry pipeline
- Also move from free text boxes towards autocompletes, controlled vocabularies
- If this is a validation and a portal for data entry forms, should we display everything we can mine?
- Idea is to eventually create data entry forms for as many data types as possible
- Long term goal would include linking to TPC and evidence sentences for validation
- 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?
- Periodically review the form and add/remove data types and curation forms as needed
- Would be good to ask authors if they had to omit data from the recently published paper and if they want to micropublish
Questions
- Question for WB curators: Are we missing data types?
- 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?
- Question for WB curators: Are there data types we should no longer mine?
- Question for Wen: Does it make sense to include an afp flag for expression cluster?
- Question for Karen: What afp tables are populated from the Genetics/G3 pipeline?
- journal first pass forms : http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?
Details here: http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass