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Re: Announcement: Bio2RDF 0.3 released

From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sun, 22 Mar 2009 10:50:17 +0100
Message-ID: <6aeb064b0903220250q42c1d0abuae120054c8ed1fff@mail.gmail.com>
To: Peter Ansell <ansell.peter@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>
Hi Peter,

On Sun, Mar 22, 2009 at 1:42 AM, Peter Ansell <ansell.peter@gmail.com> wrote:
> 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.

Thanx.

> Do you also provide InChIKey resolution?

No. That requires look up, so only works against an existing database.
Chemspider is doing this, but is not a general solution. InChIKey's
are not unique, though clashes rare, and not observed so far.

> [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.

Indeed. However, InChIKey is less precise. RDF allowing us to be do
things in an exact manner, I rather use InChI.

> 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.

But can never be used for owl:sameAs like relations.

> 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.

That was precisely the reason why I started the service.

Egon

-- 
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
Received on Sunday, 22 March 2009 09:50:53 UTC

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