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[bioontology-support] bulk download of mapping data?

Jennifer Leigh Vendetti vendetti at
Mon Jul 30 09:08:58 PDT 2018

Hello Mark,

On Jul 27, 2018, at 12:45 PM, Miller, Mark <markampa at<mailto:markampa at>> wrote:

I’m user markampa

I would like to download a large number of your high-quality term mappings.  I think I see how to do it thought the API, but would prefer downloading a static file or retrieving the mappings with a SPARQL query.

The open SPARQL endpoint is a beta service that we published a number of years ago, but haven’t had the resources to maintain. The data is entirely out of date. Current ontology data is only available via our REST API.

Apologies that we also don’t make the mappings available as static files.

If you let me know what mappings you’re trying to retrieve, I can help with which API calls to use.

Kind regards,

I see but can’t seem to get the sample queries to work.

I created a query file like this

mark at office:~/apache-jena-3.8.0/bin$ cat > ~/bpmap.rq
PREFIX map: <>
PREFIX rdfs: <>
PREFIX skos: <>
        ?mapping map:target <> .
        ?mapping map:source ?source .

And submitted it with Jena’s remote query command like this, but got an error.

mark at office:~/apache-jena-3.8.0/bin$ ./rsparql --service '' --query  ~/bpmap.rq
HTTP Exeception
HttpException: 500 HTTP 500 error making the query: INTERNAL SERVER ERROR
        at org.apache.jena.sparql.engine.http.HttpQuery.rewrap(
        at org.apache.jena.sparql.engine.http.HttpQuery.execGet(
        at org.apache.jena.sparql.engine.http.HttpQuery.exec(
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execResultSetInner(
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execSelect(
        at org.apache.jena.sparql.util.QueryExecUtils.doSelectQuery(
        at org.apache.jena.sparql.util.QueryExecUtils.executeQuery(
        at arq.rsparql.exec(
        at jena.cmd.CmdMain.mainMethod(
        at jena.cmd.CmdMain.mainRun(
        at jena.cmd.CmdMain.mainRun(
        at arq.rsparql.main(
mark at office:~/apache-jena-3.8.0/bin$
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