Querying Neurolex database from Python

[Thierry]

Hi all,

Is there a way to extract Neurolex data from a program written in
Python ?

Cordially,

Thierry Brizzi.

[Stephen Larson]

Hi Thierry,

   Yes; you can use the SPARQL endpoint which is documented here: http://neurolex.org/wiki/NeuroLex_SPARQL_endpoint.  The SPARQL protocol can be called over HTTP, so it is straightforward to utilize via any programming language.  Additionally I believe you can google for some Python SPARQL wrappers.

   A more structured version of the NeuroLex data is available here: https://confluence.crbs.ucsd.edu/display/NIF/Sparql+endpoint as a structured ontology.

   Please let us know if you have additional questions.

Thanks,

  Stephen

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[Finn Aarup Nielsen]

Hi Thierry,

On Tue, 5 Apr 2011, Thierry wrote:

> Is there a way to extract Neurolex data from a program written in
> Python ?

Neurolex uses Semantic MediaWiki so it should be possible to query that
extension and get back, e.g., CSV. (I haven't tried)

In this file
http://www2.imm.dtu.dk/pubdb/views/edoc_download.php/5936/pdf/imm5936.pdf
you can see an example on calling a Semantic MediaWiki from Python.

You probably need to formulate a query in the Semantic MediaWiki query
language on the wiki as the construction of the query URL seems to be
obscure.

best regards
Finn

___________________________________________________________________

Finn Aarup Nielsen, DTU Informatics, Denmark
Lundbeck Foundation Center for Integrated Molecular Brain Imaging
http://www.imm.dtu.dk/~fn/ http://nru.dk/staff/fnielsen/
___________________________________________________________________

[Raphael Ritz]

On 4/5/11 6:58 PM, Stephen Larson wrote:

Hi Thierry,

   Yes; you can use the SPARQL endpoint which is documented here: http://neurolex.org/wiki/NeuroLex_SPARQL_endpoint.  The SPARQL protocol can be called over HTTP, so it is straightforward to utilize via any programming language.  Additionally I believe you can google for some Python SPARQL wrappers.

e.g.,

http://pypi.python.org/pypi/SPARQLWrapper/
http://sparql-wrapper.sourceforge.net/

Raphael