[Bioperl-l] A perl regex query

Stefan Kirov stefan.kirov at bms.com
Tue Sep 18 14:54:49 EDT 2007


Actually, smiles can be tricky too- you can easily generate
non-canonical keys, where InChi is unique (as I understand it at least).
It is promoted by IUAPC:
http://www.iupac.org/inchi/
and can be generated by OpenBabel.
My take is that if you need to map between small molecules InChi might
be the best way..
Stefan

Chris Fields wrote:
> On Sep 18, 2007, at 8:26 AM, Roy Chaudhuri wrote:
>
>   
>>> My actual problem is a bit more complicated.
>>> It is not just one string, nut lakhs of them, they are actually  
>>> names of
>>> chemical compounds.
>>>
>>> THe problem is there are 2 different data sources, I need to match  
>>> the
>>> compond names between them, but the problem is though the compound  
>>> may
>>> be the same in the two, they use different naming formats for them.
>>>       
>> Unless you can define in simple and precise terms exactly which  
>> parts of
>> the string you need then there is no way that you will be able to  
>> code a
>> solution in Perl.
>>
>> Maybe you could look for a database that contains the synonyms for  
>> each
>> molecule? A quick Google finds ChEBI (http://www.ebi.ac.uk/chebi),  
>> which
>> is available to download as flat files.
>>
>> Roy.
>> --
>> Dr. Roy Chaudhuri
>> Department of Veterinary Medicine
>> University of Cambridge, U.K.
>>     
>
> D'oh!  Roy beat me to it; that's what I was going to suggest.  I  
> agree; don't trust simple word munging to always get you the correct  
> answer in this case, it's just too complicated to try and catch every  
> case.
>
> ChEBI is a good choice; Stefan's suggestion of OpenBabel is also a  
> good one.  I would also try not to reinvent the wheel; there may be  
> some modules available via CPAN which do what you need, such as these:
>
> http://search.cpan.org/search?query=chem&mode=module
>
> or this:
>
> http://search.cpan.org/~ghutchis/Chemistry-OpenBabel-1.2.0/
>
> chris
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>
>   



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