WormBase-Caltech Weekly Calls

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January

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 & TRACE-view (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

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

Timestamps

• 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