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Question: Retrieving Genbank Xml Through Efetchseq (Or Another Entrez Web Service?)
0
gravatar for edwardbeaty
7.0 years ago by
edwardbeaty • 0
edwardbeaty • 0 wrote:

Hello! I have a question about using the Entrez Utility Web Service to retrieve records in genbank XML format.

I’m using C# to access the eFetchSeq service at http://eutils.ncbi.nlm.nih.gov/soap/v2.0/efetch_seq.wsdl like so:

 eFetchSeq.eUtilsServiceSoapClient serv = new eFetchSeq.eUtilsServiceSoapClient();
 eFetchSeq.eFetchRequest req = new eFetchSeq.eFetchRequest();
 req.db = "nuccore";
 req.id = "HV982480.1";
eFetchSeq.eFetchResult res = serv.run_eFetch(req);

…which is giving me the eFetchResult. However, I would like to dump the entire record and all its fields directly as an xml file in the genbank .gb format. Is there a way to do this from an eFetchResult? Or is there a different service I should use to retrieve my results in that format?

Thanks for your help.
entrez • 1.7k views
ADD COMMENT • link •
modified 7.0 years ago by Pierre Lindenbaum ♦ 126k • written 7.0 years ago by edwardbeaty • 0

"as an xml file in the genbank .gb format" does not make sense. The output file is either XML or Genbank format.

ADD REPLY • link written 7.0 years ago by Neilfws ♦ 48k
1
gravatar for Pierre Lindenbaum
7.0 years ago by
Pierre Lindenbaum ♦ 126k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 126k wrote:

I don't see the retmode param in the XSD for efetch, so I'm not sure the following solution will run.

req.rettype = "gb";
req.retmode = "txt";

But you can always use REST based service instead of SOAP:

 curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=HV982480.1&retmode=txt&rettype=gb"

LOCUS       HV982480                  19 bp    DNA     linear   PAT 13-FEB-2013
DEFINITION  JP 2011201887-A/6577: iRNA CONJUGATES.
ACCESSION   HV982480
VERSION     HV982480.1  GI:449784475
KEYWORDS    JP 2011201887-A/6577.
SOURCE      Hepatitis C virus
  ORGANISM  Hepatitis C virus
            Viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae;
            Hepacivirus.
REFERENCE   1  (bases 1 to 19)
  AUTHORS   Harborth,J., Manoharan,M. and Elbashir,S.
  TITLE     iRNA CONJUGATES
  JOURNAL   Patent: JP 2011201887-A 6577 13-OCT-2011;
            Alnylam Pharmaceuticals Inc
COMMENT     OS   Human hepatitis C virus
            PN   JP 2011201887-A/6577
            PD   13-OCT-2011
            PF   21-APR-2011 JP 2011095517
            PR   10-OCT-2003 US    60/510318,09-OCT-2003 US    60/510246, PR
            26-SEP-2003 US    60/506341,11-AUG-2003 US    60/494597, PR
ADD COMMENT • link written 7.0 years ago by Pierre Lindenbaum ♦ 126k

Thanks, I might try the REST service. I didn't see a "retmode" parameter either; also there wasn't an obvious way to pull the results from the eFetchResult object that gets returned.

ADD REPLY • link written 7.0 years ago by edwardbeaty • 0

You can always transform the XML to genbank using xslt but that would be excessive...

ADD REPLY • link written 7.0 years ago by Pierre Lindenbaum ♦ 126k
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