WormBase-Caltech Weekly Calls August 2014

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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.


  • 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

  • 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?