WormBase-Caltech Weekly Calls
From WormBaseWikiJump to navigationJump to search
August 7, 2014
- Topic Curation
- Working out pipeline for curation
- Collecting model/pathway diagrams from papers and reviews: should we make ?Picture objects for these?
- Do we want to display these published diagrams on ?Paper pages and/or ?Topic pages
- We need to determine copyrights/accessibility to images
- Would be good to automate identification of Review articles (or "non-primary" in general) in the Topic OA
- This could be done at the bulk import step
- Would require a new (possibly read-only) field in the Topic OA to indicate "primary" or "non-primary"
- Chris will look into whether "non-primary" articles are automatically excluded from the Curation Status Form
- The "Curation Status Omit" toggle in the Topic OA may become obsolete once we have a field/column for primary/non-primary status
- Current topic : Wnt signaling
- We have a list of 282 papers from PubMed search using "Wnt" search term (not Mesh term) and C. elegans (Mesh term)
- Finding all papers for a category/topic remains an ad hoc approach; different topics are harder or easier to find all papers for
- We can create a Textpresso category for topics, like "Wnt signaling"
- WormBase Ontology Browser
- Needs documenting
- Once everything is clarified, will be pushed to the live site
August 14, 2014
- WormBase Ontology Browser (WOBr)
- Should be ready but may need some additional testing before pushing to staging site
- Juancarlos will push to staging during meeting
- Curators should test this afternoon (on staging) and report any issues before 5pm
- DataBase call this morning (and every Thursday that doesn't have a site-wide call)
- Thomas Down testing Datomic (costs money) and Neo4J (very slow)
- May look again at DynamoDB
- No DB has been officially chosen
- Will have an Amazon AWS for collaboration.
- Expand smallace into bigger mediumace.
- Demo off one database for advisory board meeting.
- Paul Sternberg back next week; will settle travel plans then
- What advisors are attending?
- What feedback do we want to get from advisors?
- How to show curation/DB progress? What stats/numbers to show?
- We want big picture feedback from biologist advisors; what's useful to the community? What should we prioritize?
- Karen: Perhaps a question to ask is "what are the main questions they are trying to answer when they go to the website?". When they explore a gene or protein function, what is it that they would want to see, and how? I don't think we are missing information so much as a lack of integration of the information at the model level, for example, variation phenotype affects linked to altered protein domain function
- Belated apologies from Mary Ann - clash of evening events.
August 21, 2014
- Topic 1
- Topic 2
August 28, 2014
- Topic 1
- Topic 2