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Re: Announcement: Bio2RDF 0.3 released

From: Peter Ansell <ansell.peter@gmail.com>
Date: Sun, 22 Mar 2009 10:42:08 +1000
Message-ID: <a1be7e0e0903211742s23d6b2cfof38ba537bb851a58@mail.gmail.com>
To: Egon Willighagen <egon.willighagen@gmail.com>
Cc: bio2rdf@googlegroups.com, w3c semweb hcls <public-semweb-lifesci@w3.org>, "public-lod@w3.org" <public-lod@w3.org>, Paul Roe <p.roe@qut.edu.au>, James Hogan <j.hogan@qut.edu.au>, Lawrence Buckingham <l.buckingham@qut.edu.au>
2009/3/20 Egon Willighagen <egon.willighagen@gmail.com>:
> Hi Peter,
> On Fri, Mar 20, 2009 at 7:56 AM, Peter Ansell <ansell.peter@gmail.com> wrote:
>> * Some http://database.bio2rdf.org/database:identifier URI's are given
>> by this, but these aren't standard, and are only shown where there is
>> still at least one SPARQL endpoint available which uses them. People
>> should utilise the http://bio2rdf.org/database:identifier versions
>> when linking to Bio2RDF.
> I'm using ChEBI IDs right now to link to your RDF with owl:sameAs:

owl:sameAs fits well for that purpose.

> http://rdf.openmolecules.net/?InChI=1/C12H8O2S/c13-8-5-6-10-11(12(8)14)7-3-1-2-4-9(7)15-10/h1-6,13-14H
> Linking back to rdf.openmolecules.net can be done as shown above with the InChI.

Okay. Will look into doing owl:sameAs links back either dynamically or
by modifying the way ChEBI is converted to RDF.

Do you also provide InChIKey resolution? [1] It is just that InChI's
can get pretty long for complex molecules and it makes it harder for
people to accurately copy and paste them around when needed.
InChiKey's might be better for general use in RDF because they have a
guaranteed identifier length and therefore won't become cumbersome for
complex molecules.

Currently all of the InChI's that I have seen have been as Literals,
but it would be relatively easy to also provide them as URI's to
provide the link since you have a resolver for them set up.

> I'll hook up to your DrugBank and DBPedia later today. Do you already
> make links between ChEBI and DBPedia? I created links by converting
> SMILES into InChIs:

DBpedia provide links to ChEBI as far as I know for at least some
chemical infoboxes that wikipedia provides. Someone went through in
the last 6 months or so finding the properties for common databases
and making them into Bio2RDF URI's.

> http://chem-bla-ics.blogspot.com/2009/02/dbpedia-enters-rdfopenmoleculesnet.html
> Comments most welcome!


Peter Ansell

[1] http://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey
Received on Sunday, 22 March 2009 00:42:48 UTC

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