[BioPython] [Biopython-dev] Bio.CDD, anyone?
Chris Fields
cjfields at uiuc.edu
Thu Jun 19 10:45:05 EDT 2008
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
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