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[bioontology-support] bulk download of mapping data?

Miller, Mark markampa at pennmedicine.upenn.edu
Fri Jul 27 12:45:15 PDT 2018


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.

I see https://www.bioontology.org/wiki/SPARQL_BioPortal 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: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT
*
WHERE {
        ?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .
        ?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 'http://sparql.bioontology.org/mappings/sparql/?apikey=9cf735c3-a44a-404f-8b2f-c49d48b2b8b2' --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(HttpQuery.java:370)
        at org.apache.jena.sparql.engine.http.HttpQuery.execGet(HttpQuery.java:336)
        at org.apache.jena.sparql.engine.http.HttpQuery.exec(HttpQuery.java:288)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execResultSetInner(QueryEngineHTTP.java:352)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execSelect(QueryEngineHTTP.java:344)
        at org.apache.jena.sparql.util.QueryExecUtils.doSelectQuery(QueryExecUtils.java:196)
        at org.apache.jena.sparql.util.QueryExecUtils.executeQuery(QueryExecUtils.java:79)
        at arq.rsparql.exec(rsparql.java:76)
        at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
        at arq.rsparql.main(rsparql.java:44)
mark at office:~/apache-jena-3.8.0/bin$
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