Thank you very much for your time.
I am running the query against my own virtuoso instance where I have
manually entered the respective Bio2RDF datasets.
The virtuso instance has been built by me on ubuntu. Virtuoso version
07.20.3214, built on October 14, 2015.
Kind regards,
Pantelis Natsiavas
2016-02-17 12:46 GMT+02:00 Hugh Williams <hwilli...@openlinksw.com>:
> Hi Pantelis,
>
> Development are looking into this error as it even occurs running against
> an empty database with the latest develop/7 build …
>
> Best Regards
> Hugh Williams
> Professional Services
> OpenLink Software, Inc. // http://www.openlinksw.com/
> Weblog -- http://www.openlinksw.com/blogs/
> LinkedIn -- http://www.linkedin.com/company/openlink-software/
> Twitter -- http://twitter.com/OpenLink
> Google+ -- http://plus.google.com/100570109519069333827/
> Facebook -- http://www.facebook.com/OpenLinkSoftware
> Universal Data Access, Integration, and Management Technology Providers
>
>
>
> On 17 Feb 2016, at 10:21, Lorenz Bühmann <
> buehm...@informatik.uni-leipzig.de> wrote:
>
> Hello Pantelis,
>
> it looks like a bug of course. The question is which Virtuoso version
> Bio2RDF is currently using. Might be that the bug is fixed in latest
> versions, but if you're not the maintainer of Bio2RDF it seems to be
> impossible to fix it. Might be that there is a workaround, but that's what
> the developers should know.
>
> Kind regards,
> Lorenz
>
> No feedback?
>
> Nobody has seen "Virtuoso 37000 Error SQ156: Internal Optimized compiler
> error : supposed to have ose in bracket outer in rdfinf.c:2636." in the
> past?
> Kind regards,
> Pantelis Natsiavas
>
>
> 2016-02-13 14:40 GMT+02:00 Lorenz Bühmann <
> buehm...@informatik.uni-leipzig.de>:
>
>> Why do you ask this as a response to a totally different question? And
>> what's the relationship to Virtuoso? I think this questions is better for
>> something like answer.semanticweb.com or stackoverflow.
>>
>> By the way, I do not understand the question: What do you mean by "I want
>> to link to find a dataset"?
>>
>> Lorenz
>>
>> Hi every body
>> I am trying to use bio2rdf, but i want to link to find a dataset.
>> This link http://bio2rdf.org/bio2rdf.dataset_vocabulary give me an error.
>>
>> any suggestion of other link could be helpfull.
>> Kind regards
>> Fatma
>>
>> 2016-02-12 14:55 GMT+01:00 Pantelis Natsiavas < <natsia...@gmail.com>
>> natsia...@gmail.com>:
>>
>>> Hi everybody.
>>>
>>> I am trying to execute the query
>>>
>>> PREFIX void: < <http://rdfs.org/ns/void#>http://rdfs.org/ns/void#>
>>> PREFIX dv: <http://bio2rdf.org/bio2rdf.dataset_vocabulary:>
>>> PREFIX dcterms: < <http://purl.org/dc/terms/>http://purl.org/dc/terms/>
>>> PREFIX drugbank: < <http://bio2rdf.org/drugbank_vocabulary>
>>> http://bio2rdf.org/drugbank_vocabulary:>
>>> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
>>>
>>> SELECT ?drug
>>> ?drugTitle
>>> ?brandTitle
>>> WHERE {
>>> ?drug a drugbank:Drug .
>>> OPTIONAL { ?drug dcterms:title ?drugTitle .
>>> ?drugTitle bif:contains "'Ibuprofen'"} .
>>> OPTIONAL { ?drug drugbank:brand ?brand .
>>> ?brand bif:contains "'Ibuprofen'"} .
>>> OPTIONAL { ?brand dcterms:title ?brandTitle .
>>> ?brandTitle bif:contains "'Ibuprofen'"} .
>>> }
>>>
>>> which uses bif:contains inside optionals.
>>>
>>> I get the error:
>>>
>>> Virtuoso 37000 Error SQ156: Internal Optimized compiler error : supposed to
>>> have ose in bracket outer in rdfinf.c:2636.
>>> Please report the statement compiled.
>>>
>>> SPARQL query:
>>>
>>> #output-format:text/html
>>> PREFIX void:
>>> PREFIX dv:
>>> PREFIX dcterms:
>>> PREFIX drugbank:
>>> PREFIX rdf:
>>>
>>> SELECT ?drug
>>> ?drugTitle
>>> ?brandTitle
>>> WHERE {
>>> ?drug a drugbank:Drug .
>>> OPTIONAL { ?drug dcterms:title ?drugTitle .
>>> ?drugTitle bif:contains "'Ibuprofen'"} .
>>> OPTIONAL { ?drug drugbank:brand ?brand .
>>> ?brand bif:contains "'Ibuprofen'"} .
>>> OPTIONAL { ?brand dcterms:title ?brandTitle .
>>> ?brandTitle bif:contains "'Ibuprofen'"} .
>>> }
>>>
>>> Is this an invalid query? I tried the same query with only the first
>>> optional clause in place and I don't get the error, but I don't get any
>>> results either. It seems it takes too long to execute (more than 10
>>> minutes).
>>>
>>> Could you please point me on how I could use such a restriction with
>>> multiple optional clauses in a performance suitable manner?
>>>
>>> Kind regards,
>>> Pantelis Natsiavas
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>> _______________________________________________
>>> Virtuoso-users mailing list
>>> Virtuoso-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/virtuoso-users
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup
>> Now!http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>
>>
>>
>> _______________________________________________
>> Virtuoso-users mailing
>> listVirtuoso-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/virtuoso-users
>>
>> --
>> Lorenz Bühmann
>> AKSW group, University of Leipzig
>> Group: http://aksw.org - semantic web research center
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> Virtuoso-users mailing list
>> Virtuoso-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/virtuoso-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup
> Now!http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>
>
>
> _______________________________________________
> Virtuoso-users mailing
> listVirtuoso-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/virtuoso-users
>
> --
> Lorenz Bühmann
> AKSW group, University of Leipzig
> Group: http://aksw.org - semantic web research center
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> Virtuoso-users mailing list
> Virtuoso-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/virtuoso-users
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Virtuoso-users mailing list
> Virtuoso-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/virtuoso-users
>
>
------------------------------------------------------------------------------
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
_______________________________________________
Virtuoso-users mailing list
Virtuoso-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/virtuoso-users
