Thursday, March 22, 2007

As announced on nodalpoint, I've put together a web site called which, rather grandly, is an attempt to bootstrap the biodiversity Semantic Web by providing resolvable URIs for biological objects, such as publications, taxonomic names, nucleotide sequences, and specimens. These URIs (or "GUIDs") can be resolved by a web browser to display HTML, but under the hood are resolved to RDF (which you can see by viewing the source of the web page you get for a URI).

Tuesday, March 13, 2007

More 3store3

Had a little fun with 3store3 on Fedora Core 4, which is what I run on my servers. 3store3 builds easily on Fedora (in constrast to the fun had building 3store3 on a Mac. However, any SPARQL query beyond a simple listing of all triples just bailed out with scary errors. For example:

ts-explain "PREFIX dc:
dc:title ?o . } LIMIT 10"
SQL error 2013: Lost connection to MySQL server during query at util.c:55
SQL error 2002: Can't connect to local MySQL server through socket
'/var/lib/mysql/mysql.sock' (111) at query.c:316
Warning cannot calculate complexity
Complexity: 0
SELECT DISTINCT v0.lexical AS `s`, v1.lexical AS `o`, v1.datatype AS
o_dt, v1.language AS o_lang
FROM (SELECT DISTINCT t0.object AS `o`, t0.subject AS `s`
FROM triples t0
WHERE t0.predicate=-8024650864867163606
LIMIT 10) AS `tmp0_202a`, symbols v0, symbols v1
WHERE tmp0_202a.s=v0.hash && tmp0_202a.o=v1.hash

After much cursing, rebuilding,trying different versions of 3store3 and the Redland libraries, gave up and contemplated a crude hack. The SQL query itself works fine in MySQL, but not when 3store3 tries to call MySQL. But, before writing a crude hack I mailed the 3store3 mailing list this morning, and by 9:30 the same morning Steve Harris had given me the solution. I was running MySQL version 4.1.11, and according to Steve there's a bug in early verisons of MySQL 4. He recommended upgrading, so off to do yum install mysql. Sure enough, I get MySQL 4.1.20, and everything works. Yay!

Tuesday, March 06, 2007


Stumbled across Bio2RDF by Fran├žois Belleau. Here's the blurb:
It is now possible to query Bio2RDF triple store using Sesame's SeRQL query engine. The actual triple store contains all annotations about human and mouse from UniProt, Affymetrix and GeneID. It also contains all GO term definitions and OMIM disease description. It contains 50 millions triples and the native RDF store in sesame weigths 3 Go. Watch for the speed of it ! Thanks for the Sesame team for their great work.

There's a blog, and a SourceForge project. The Bio2RDF website itself displays RDF as tables. It doesn't have a query interface but it's a bit hidden. Try here, based on this blog post.
It uses Seasame, JSP, and SeRQL -- not my favourite technologies -- but is an example of people thinking about RDF and triple stores, and actually making stuff. Must polish up my creaking ant demo and play some more with this.
On the subject of ants, Terry Catapano has been playing with Simile, and come up with this demo.

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