WormBase-Caltech Weekly Calls

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February 11, 2016

Postgres data not in ACEDB

  • Should we this data get into ACEDB to be converted to Datomic (via the existing pipeline)? Maybe, but only temporarily
  • We will need to learn to model in Datomic to start building curation tools that run off of Datomic
  • Juancarlos has access to Colonnade & trAceView (table maker tool and web interface to view Datomic data like in ACEDB)
  • For long term, we will want to build a curation tool directly on top of Datomic; will need to model currently un-dumped fields in Datomic
  • Juancarlos has a few action items to test reading from and writing to Datomic in a simple manner
  • Paper editor may be best form to start Datomic transition, since it doesn't deal with N1-objects changing with N2-other-objects
  • Bulk updates of data not edited through the OA may be another good starting point, as those pipelines will need to change Datomic directly

CITace upload

  • Upload files to Wen by Tuesday Feb 16, 10am

Life stage ontology update

  • To accommodate flat worms, will make "worm life stage" root node with "platyhelminth (flatworm)..." and "nematode (roundworm)..." children


  • Data in OA's has timestamp history, but all data first imported in bulk has one 'epoch' timestamp
  • Chris looking into older timestamps from older versions of WS/ACEDB
  • Will be good to clarify how older timestamps will be stored in Datomic going forward (i.e. a timestamp field separate from a Datomic intrinsic timestamp?)
  • Would be best to have as many original timestamps as possible