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Re: PharmaOntology / TMO KB Wiki Demo Page.... BROKEN sparql endpoint

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Thu, 2 Jan 2014 10:15:41 -0800
Message-ID: <CALcEXf7S3EOxM1zO9kDFftx2=_SOuiqcJxvr2T0dekS5FFrssw@mail.gmail.com>
To: "Luciano, Joanne S." <luciaj2@rpi.edu>
Cc: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, "ericp@w3.org" <ericp@w3.org>
Hi Joanne,
  Happy New Year!

  As you and everybody on this list is already aware, it is challenging
(and arguably impossible) to maintain SPARQL endpoints indefinitely (and
certainly without any business plan to support it). We put up this server
for demonstration purposes in support of our paper [1], primarily so that
reviewers could reproduce the answers to our queries at the time of review.
The main outcome of our paper was not the availability of the SPARQL
endpoint, but the emphasis that a global ontology could be used to
integrate other ontologies and linked open data for biomedical research.
 Since we cannot guarantee access to that SPARQL endpoint, those with
sufficient expertise can reconstruct our experiment using the data which we
made available on the Google Code site [2] (also indicated in the paper).
The only tricky part when using Virtuoso is to create the ruleset "infer"
so as to generate the transitive closure for the subclass hierarchy.



[1] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102889/
[2] https://code.google.com/p/translationalmedicineontology/

On Tue, Dec 24, 2013 at 4:23 AM, Luciano, Joanne S. <luciaj2@rpi.edu> wrote:

>  Hi,
>  I’d hoped to use some of the work we did for the TMO / TMOKB in a course
> I’m teaching (now [*]) however I’m finding broken links on this page:
>   http://www.w3.org/wiki/HCLSIG/PharmaOntology/TMKB
>  Virtuoso provisions a :
>    - SPARQL endpoint : http://tm.semanticscience.org/sparql
>    - Full text faceted browser: http://tm.semanticscience.org/fct
>  And..
> We can pose SPARQL Queries<http://www.w3.org/wiki/HCLSIG/PharmaOntology/Queries> questions
> to the SPARQL endpoint.   /// The page with the queries is there,
> however…..
> none can be run.
>  I had hoped it was a momentary glitch, but it’s now been at least a few
> days.
> Season’s Greetings to all!
>  Joanne
>  —— Not Found
> The requested URL /sparql was not found on this server.
> ------------------------------
> Apache/2.4.6 (Ubuntu) Server at tm.semanticscience.org Port 80
>  [The class is being held in Israel at Ben-Gurion University of the
> Negev, which is open at this time.]

Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
Received on Thursday, 2 January 2014 18:16:30 UTC

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