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Re: Version 1.0 of Bio2RDF and Chembl webapps released

From: Matthias Samwald <matthias.samwald@meduniwien.ac.at>
Date: Thu, 30 Jun 2011 10:43:44 +0200
Message-ID: <06A1A17DAB594C9F8B13D0E28002D5AD@zetsu>
To: "Peter Ansell" <ansell.peter@gmail.com>, "Bio2Rdf Mailing List" <bio2rdf@googlegroups.com>, "w3c semweb hcls" <public-semweb-lifesci@w3.org>
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?

> 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?

> 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.

Cheers,
Matthias


--------------------------------------------------
From: "Peter Ansell" <ansell.peter@gmail.com>
Sent: Thursday, June 30, 2011 8:58 AM
To: "Bio2Rdf Mailing List" <bio2rdf@googlegroups.com>; "w3c semweb hcls" 
<public-semweb-lifesci@w3.org>
Subject: Version 1.0 of Bio2RDF and Chembl webapps released

> Hi all,
>
> The 1.0.1 version of the Bio2RDF server software has been released on
> Sourceforge. The software is designed to be a Linked Data interface to
> a range of RDF datasources, with the current examples being Bio2RDF
> and Chembl. (There was a small bug fix needed to enable endpoint
> round-robin between 1.0.0 and 1.0.1.)
>
> The Bio2RDF version now contains 1655 namespaces, 111 query types, 455
> data providers and 197 normalisation rules. In addition to the Bio2RDF
> server interface [1], I made up a version suitable for browsing
> through resources located in Egon Willighagen's Chembl RDF dataset [2]
> from http://rdf.farmbio.uu.se/chembl/sparql . I picked this dataset as
> it did not seem to have a linked data interface to go with its URIs.
>
> If anyone has any other RDF or SPARQL datasets that they want to have
> a linked data interface then feel free to either mention them and/or
> experiment with the software yourself based on the Chembl sources (all
> of the Bio2RDF and Chembl configuration files can be found in the
> sourceforge Git repository at [3]). The Bio2RDF configuration files
> may be easier to find examples in, but they are quite large, so you
> may want to start by looking at how Chembl was implemented using the
> software. The software is designed to merge data from different
> locations, so if you want to do a mashup with the data you can make up
> queries/providers/normalisation rules to do it and publish them as a
> server configuration using the configuration interface in the server
> (/admin/configuration/n3 , For example:
> http://config.bio2rdf.org/admin/configuration/n3 ) so that others can
> extend/integrate/re-use them easily in their own instances of the
> software.
>
> The HTML interface for the software is configurable using Apache
> Velocity templates, so don't feel that you have to stick to the
> current design if you want to reuse the software.
>
> This version allows you to optionally perform 303 redirections along
> with the in-built HTTP content negotiation using the Accept header.
> This allows access to the results of queries in the following RDF
> formats:
>
> * RDF/XML - using /rdfxml/ or Accept:application/rdf+xml
> ** For example: http://bio2rdf.org/rdfxml/geneid:12334
> * N3 - using /n3/ or Accept:text/rdf+n3
> ** For example: http://bio2rdf.org/n3/geneid:12334
> * HTML and RDFa - using /page/ or Accept:text/html
> ** For example: http://bio2rdf.org/page/geneid:12334 (RDFa embedded in
> the HTML representation)
> * NTriples - /ntriples/ or Accept:text/plain
> ** For example: E.g. http://bio2rdf.org/ntriples/geneid:12334 (this
> and the following two formats will not work until we actually do the
> upgrade on bio2rdf.org in the next few days.)
> * NQuads  - /nquads/ or Accept:text/x-nquads
> ** E.g. http://bio2rdf.org/nquads/geneid:12334 (The graph names match
> the provider URI that the data came from. I.e., it is not possible to
> see the provenance for each statement in a results document. The
> downside to this is that it can sometimes cause duplicate statements
> to appear if they are located in different graphs, even in the HTML
> representation.)
> * RDF/Json - /json/ or Accept:application/json
> ** E.g. http://bio2rdf.org/json/geneid:12334
>
> 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.
>
> 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.
>
> If you use the server software and/or Bio2RDF datasets it would be
> great if you could cite us using the publications on the wiki at [4]
>
> Thanks,
>
> Peter
>
> [1] 
> http://sourceforge.net/projects/bio2rdf/files/bio2rdf-server/bio2rdf-1.0.1/
> [2] 
> http://sourceforge.net/projects/bio2rdf/files/chembl-server/chembl-webapp-1.0.1/
> [3] 
> http://bio2rdf.git.sourceforge.net/git/gitweb.cgi?p=bio2rdf/bio2rdf;a=tree;f=bio2rdf-webapp/src/main/resources/config;hb=HEAD
> [4] 
> https://sourceforge.net/apps/mediawiki/bio2rdf/index.php?title=Publications
>
>
> 
Received on Friday, 1 July 2011 08:33:48 GMT

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