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Re: Announcement: Bio2RDF 0.3 released

From: Peter Ansell <ansell.peter@gmail.com>
Date: Mon, 23 Mar 2009 09:09:14 +1000
Message-ID: <a1be7e0e0903221609m18410b5ex2a90415787e10124@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>
2009/3/22 Egon Willighagen <egon.willighagen@gmail.com>:
> 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.

I didn't think it required a lookup to derive an InChIKey given an
InChI. I realise that clashes are rare but possible, just wondering
whether it would be supported. Leaving them out altogether just seems
like missing possibly extra information.

>> [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.

Having them as properties could give someone a quick clue as to
whether they are looking at the same molecule. Humans do interact with
RDF (inevitably), and having short hash values can still be valuable.
Given that hashes are usually designed to amplify small changes, it is
easier than reading a 10 line InChiKey to determine whether there was
a difference.

>> 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.

Good work.

Cheers,

Peter Ansell
Received on Sunday, 22 March 2009 23:09:51 UTC

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