WormBase-Caltech Weekly Calls August 2014
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- 1 August 7, 2014
- 2 August 14, 2014
- 3 August 21, 2014
- 4 August 28, 2014
August 7, 2014
- 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
- 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
Generating a Site-Map for WormBase
- Use a crawler to generate? Output would need to be made human-readable
- We could use the legacy site as a site map
Citace upload report modifications
- wikipage here: Citace_upload_report
- Goals of this report
- Summary of the uploaded data classes/objects - this summary should be blind to requests from curators and should alert Caltech to missing data classes or severe changes in numbers of objects within preexisting data classes
- Summary of curation work - this summary should be curator driven, in some cases the summary will require a more involved aceperl query to get at the actual annotation rather than a straight data class object number.
- Can we get a comparison for those data that are curated through postgres? It would be very helpful to be able to compare the changes in postgres with the changes in the Citace upload.
- Can we automate the generation of this report to make it easier to change and track?
- Regardless of manual or automated report generation when there is a model change or data class addition/subtraction, the responsible curator needs to inform Wen of the need for compensatory modification in the report.
August 28, 2014
Curation Statistics for SAB
- Curators should send Chris all stats for their respective data types: total papers curated, total backlog, false positives
- Can we ignore SVM results for certain data types?
- Can we include Textpresso search results for relevant data types?
- Curators that use a Textpresso pipeline: Karen, Ranjana, Xiaodong, (Daniela?), Mary Ann
- Can we get detailed web usage statistics on particular datatypes?
- We want to articulate our priorities to the SAB; get feedback
- RNAi curation could get up to speed in 5 years if we have two FTEs on RNAi curation
- Are there certain genes that have less phenotype coverage that we should prioritize?
Database migration call
- MongoDB, CouchDB, Neo4J, Datomic, OrientDB, postgreSQL, Cassandra candidates
- Neo4J likely ruled out because of slow performance
- Will compare performance of Datomic vs. Postgres and ACEDB, etc.
- Datomic has good history tracking
- Thomas Down has experience with Datomic
- Probably won't go with a relational database
- We should use the Gene page (webpage) as a demo/example of what we want to try to emulate
- Adam (from Lincoln's group) working with OrientDB (graph database)
Citace Upload Report
- Classes/datatypes missing from Citace Upload Report
- Karen started a Wiki page to capture this info: Citace_upload_report
- Curators should take a look and make sure it is properly filled out for their data types
- Columns are present in the table to make requests for certain numbers in Citace Upload Report and/or the Build Report
- Wen will take requests for queries to Citace etc. to add data to report
- UniProt would like us to add information about some specific curated datatypes to a file we already supply that maps paper and gene identifiers
- Kimberly and Juancarlos will work on this
- Need to clarify with UniProt how links back to WormBase can/will be implemented
Paul S going to NIH for data science meeting next week
FlyBase pushing human disease curation
LEGO backend updates
- Still need to get some backend logistics sorted out
- Communication between Michael Muller and Chris Mungall
- OA-like interface for Noctua?