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.
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edwardbeaty •
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
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.
You can always transform the XML to genbank using xslt but that would be excessive...
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"as an xml file in the genbank .gb format" does not make sense. The output file is either XML or Genbank format.