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[bioontology-support] familiarization with back-end components

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Dec 19 11:33:16 PST 2019


Hello Mark,


On Dec 17, 2019, at 5:51 PM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

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)


In terms of troubleshooting the cell ontology, you could look at the contents of the parsing log file (“parsing.log” is located in the folder /srv/ncbo/repository/{ontology acronym}/{submission id}).

If for some reason the ontology never parsed, we have instructions on our wiki for how you could re-parse it manually:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#Ontology_Parsing



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


The BioPortal front end is a Rails application. We only use the view and controller pieces though, since all of the ontology data is stored in the 4store triplestore. Hence, not much of interest in the relational database.


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 think this bit from the 4store documentation helps to clarify:

"When you run a 4s-httpd and connect it to a 4store backend you will no longer be able to use the 4s- command line tools. You can however use ​sparql-query (or any other SPARQL client) to issue queries, and curl to add/remove graphs…”

Example curl syntax for updates:

curl -i -d 'update=INSERT+DATA+{+GRAPH+<http://example.com/G>+{+<http://example.com/s>+<http://example.com/p>+"o"+}+}' http://localhost:8000/update/


I have years of experience with Virtuoso, GraphDB, Stardog and Blazegraph, but I know nothing about 4store.


Unfortunately, 4store is no longer being developed / maintained. As time allows, we’ve been working on transitioning BioPortal to AllegroGraph.

If you want to know more about 4store, you might find it useful to clone the GitHub repository:

https://github.com/4store/4store

There’s a directory called “website” where someone put a copy of all the files from the old 4store site that had documentation for some of what you asked about above, e.g., this file:

https://github.com/4store/4store/blob/master/website/trac/wiki/SparqlServer/index.html

Kind regards,
Jennifer

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