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Re: Announcement: Bio2RDF 0.3 released

From: Kei Cheung <kei.cheung@yale.edu>
Date: Mon, 23 Mar 2009 10:37:04 -0400
To: Egon Willighagen <egon.willighagen@gmail.com>
Cc: Peter Ansell <ansell.peter@gmail.com>, 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>
Message-id: <49C79E90.3050507@yale.edu>
As part of the biordf query federation task, we are currently exploring 
a federation scenario involving integration of neuroreceptor-related 
information. For example, IUPHAR provides information for different 
classes of receptors. For example, in the table shown at  
http://www.iuphar-db.org/GPCR/ReceptorListForward?class=class%20A, 
ligands are provided for receptors but not InChI codes ...

-Kei

One types of Egon Willighagen wrote:
> On Mon, Mar 23, 2009 at 12:09 AM, Peter Ansell <ansell.peter@gmail.com> wrote:
>   
>> 2009/3/22 Egon Willighagen <egon.willighagen@gmail.com>:
>>     
>>> On Sun, Mar 22, 2009 at 1:42 AM, Peter Ansell <ansell.peter@gmail.com> wrote:
>>>       
>>>> 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.
>>     
>
> Ah, sorry. InChIKey can be computed, but I thought you meant resolving
> what structure has a given InChIKey... going from InChIKey to
> structure does require lookup, generation from InChIKey from structure
> (or InChI) does not.
>
>   
>> 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.
>>     
>
> I'll add them where missing.
>
>   
>>>> [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.
>>     
>
> Agreed.
>
>   
>>>> 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.
>>     
>
> Thanx for the feedback!
>
> Egon
>
>   
Received on Monday, 23 March 2009 14:37:52 UTC

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