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Re: Version 1.0 of Bio2RDF and Chembl webapps released

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Thu, 7 Jul 2011 11:54:52 +0200
Message-ID: <CACHzV2M5dwoidLo-bC0-a11RzTHoEL1ECRyQ0qDi8b+9hZPYiQ@mail.gmail.com>
To: Peter Ansell <ansell.peter@gmail.com>
Cc: Matthias Samwald <matthias.samwald@meduniwien.ac.at>, Bio2Rdf Mailing List <bio2rdf@googlegroups.com>, w3c semweb hcls <public-semweb-lifesci@w3.org>, "Eric Prud'hommeaux" <eric@w3.org>
Hi Peter,

You could probably use SWObjects as an interpreter for your SPARQL
Constructs while speaking with your Sesame SPARQL endpoint as a graph
service. SWObjects makes use of SPARQL Constructs to chain rules and
effectively create views or mappings of either triplestores or
relational databases. I think that it has support for the SPARQL 1.1
functions - at least, I've seen several of the functions in your
example. Not sure about encode_for_uri() though.

If that sounds interesting to you, checkout:
http://www.w3.org/2010/Talks/1208-egp-swobjects/
See also: http://tinyurl.com/swobjects-swat4ls

Cheers,
Scott

-- 
M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
http://staff.science.uva.nl/~marshall

On Thu, Jun 30, 2011 at 1:07 PM, Peter Ansell <ansell.peter@gmail.com> wrote:
> On 30 June 2011 18:43, Matthias Samwald
> <matthias.samwald@meduniwien.ac.at> wrote:
>> Hi Peter,
>>
>> Great work! On the example page you provided
>> (http://bio2rdf.org/page/geneid:12334) I also see properties such as
>> http://purl.org/science/owl/sciencecommons/describes_gene_or_gene_product_mentioned_by
>> which come from the Science Commons KB (and the HCLS Knowledge Base
>> developed in the first charter of the HCLS interest group). Did those
>> properties go into Bio2RDF because you imported some data from the Science
>> Commons KB, or did you deliberately choose to re-use those properties
>> because you considered them useful?
>
> Those triples are directly sourced from
> http://sparql.neurocommons.org/sparql , without changing the
> properties.
>
>>> If you want to make changes to any of the datasources, you can
>>> normalise results (and denormalise queries) using rules. This version
>>> allows you to use XSLT and SPARQL in addition to Regular Expressions
>>> that were already supported. For example this now means that if there
>>> are XML datasources, you can convert them to RDF using the
>>> normalisation rules in the server. The software now uses Sesame 2.4.0
>>> which contains support for SPARQL Query 1.1 so any SPARQL rules that
>>> are applied to intermediate results can be transformed using the new
>>> functions and language features. In particular, SPARQL 1.1 allows you
>>> to create new URIs inside queries, so if you know that there are
>>> literals in an rdf document that you could create a URI out of, you
>>> can do it using a SPARQL normalisation rule for that datasource.
>>
>> Do you have an example of how this could be done with SPARQL 1.1?
>
> According to the SPARQL 1.1 specifications, the following should
> hypothetically work, but it doesn't seem to work right now with the
> Sesame 2.4.0 library.
>
> CONSTRUCT {
> ?myUri <http://bio2rdf.org/bio2rdf_resource:genesymbol> ?symbolUri .
> } WHERE {
> ?myUri <http://purl.org/science/owl/sciencecommons/ggp_has_primary_symbol>
> ?primarysymbol .
> bind(iri(concat("http://bio2rdf.org/symbol:",encode_for_uri(lcase(str(?primarySymbol)))))
> AS ?symbolUri)}
>
> BIND : http://www.w3.org/TR/sparql11-query/#bind
> IRI : http://www.w3.org/TR/sparql11-query/#func-iri
> CONCAT : http://www.w3.org/TR/sparql11-query/#func-concat
> ENCODE-FOR-URI : http://www.w3.org/TR/sparql11-query/#func-encode
> LCASE : http://www.w3.org/TR/sparql11-query/#func-lcase
>
> Maybe I am doing something wrong so far. It is complaining about
> something being wrong after concat but it looks okay to me.
>
>>> In addition, if anyone wants to suggest a way to do any other rule
>>> based normalisation I would be happy to extend the software to support
>>> it. I have always had RIF rules in the back of my head, but have not
>>> experimented with them yet. If anyone uses RIF rules in their work, it
>>> would be great to get some example code to guide a future extension to
>>> this software.
>>
>> Did you consider using SPARQL Inference Notation (SPIN,
>> http://spinrdf.org/)? I don't think there is an implementation for Sesame
>> out there yet, though.
>
> I will look at it again. Is there an open source implementation by the
> way? I have been using SPARQL CONSTRUCT queries to do virtually
> everything that I thought SPIN could do, with a more familiar
> notation. I didn't find the SPIN notation easy to understand.
>
> Cheers,
>
> Peter
>
>
Received on Thursday, 7 July 2011 09:55:22 GMT

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