[BioPython] [Biopython-dev] Bio.CDD, anyone?

[Chris Fields]

They don't, though you can get esummary XML information (which  
includes description), and I believe you can use elink to grab other  
information (including proteins with the specified domain).

chris

On Jun 19, 2008, at 8:38 AM, Peter wrote:

>> Bio.CDD is a module with a parser for CDD (NCBI's Conserved Domain  
>> Database)
>> records. The parser parses HTML pages from CDD's web site. Since  
>> the parser
>> was written about six years ago, the CDD web site has changed  
>> considerably.
>> Bio.CDD therefore cannot parse current HTML pages from CDD.
>
> A couple of years ago, I wanted to get the CDD domain name and
> description and ended up writing my own very simple and crude parser
> to extract just this information.  Doing a proper job would mean
> extracting lots and lots of fields, e.g.
> http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=29475
>
> I wonder if the NCBI make any of this available as XML via Entrez?  I
> had a quick look and couldn't find anything.
>
> Peter
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign