WormBase-Caltech Weekly Calls

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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.
  • SAB
    • 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 linking to and from WormBase
  • 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?