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[bioontology-support] [BioPortal] Feedback from SB

Samson Tu swt at stanford.edu
Sun Jun 25 01:02:16 PDT 2017


Hi,

Your SPARQL query is incorrect syntactically so that the SPARQL query processor couldn't parse the query.

The BioPortal SPARQL endpoint is not a good place to learn SPARQL, I myself learned SPARQL using the book  DuCharme, Bob. Learning SPARQL, O’Reilly Press. I highly recommend it. It recommends that you download a free SPARQL processor (e.g., Apache Jena ARQ [1][2]) and run queries against file-based data. There are numerous SPARQL tutorials online but the endpoints on which you can make associated queries may be out-of-date.

If you want to query against ontologies of your choice, Protege’s SPARQL and SNAP SPARQL query tabs/views are reasonable placed to test your queries. Note that the SPARQL Query tab is a SPARQL 1.0 processor that only support simple entailment (no reasoning), whereas the SNAP SPARQL tab/view does not support all of SPARQL 1.1 constructs but supports the OWL 2 entailment regime.  

If you have problem with your Protege installation or the Protege’s SPARQL tabs, you can get help on the Protege-user mailing list. I saw that you’ve already posted a question on that list.

With best regards,
Samson

[1] https://jena.apache.org/documentation/query/index.html
[2] apache-jena-3.3.0.zip <http://mirror.cc.columbia.edu/pub/software/apache/jena/binaries/apache-jena-3.3.0.zip>

> On Jun 23, 2017, at 5:11 PM, support at bioontology.org wrote:
> 
> Name: SB
> 
> Email: selenb at gmail.com
> 
> Location: http://sparql.bioontology.org/
> 
> 
> Feedback:
> 
> Dear all, 
> When I execute the query below, I have an error message as a response: 
> "*Internal error, please contact administrator. Error with SPARQL query: 
> 400 Parser error*
> 
> QUERY: I guess it is because of FILTER... 
> PREFIX rdfs: 
> SELECT DISTINCT ?concept ?subClassOf ?Synonym 
> WHERE { 
> GRAPH 
> { 
> { ?term a ; 
> ?concept. } 
> ?subclass rdfs:subClassOf ?class. 
> ?class ?subClassOf. 
> } 
> FILTER (?term = ?subclass) 
> }
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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