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[bioontology-support] familiarization with back-end components

Miller, Mark markampa at pennmedicine.upenn.edu
Tue Dec 17 17:51:13 PST 2019


building upon an earlier query from today "term mapping experience in BioPortal appliance"

I have an AWS Bioportal Appliance, with 1) LOINC  loaded, parsed, indexed, etc. 2) the cell ontology uploaded (but nothing else has happened in 5 hours)

I have been able to pull keys from Redis and browse Solr

HOWEVER: 1) Although I can connect to MySQL, the bioportal_ui database doesn't seem to have any tables 2) Although I can submit a query to 4store via the web interface at http://server.address:8081/test/<http://52.87.183.221:8081/test/>,  I can't figure how to submit queries programatically. I would like to use R's SPARQL library or CURL, but even the built in query command gives an error. Is there some kind of client locking? I have years of experience with Virtuoso, GraphDB, Stardog and Blazegraph, but I know nothing about 4store.

$ 4s-query ontologies_api
4s-client.c:309 kb=ontologies_api waiting for lock on segment 0 on 127.0.0.1 port 6734

thanks!
Mark

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