Perform a search through NCBI eUtils eSearch

Created: 2009-11-27 14:44:11 Last updated: 2009-12-03 16:32:26

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This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term.

Example input for this workflow are given below:

database: pubmed

terms: cancer AND diabetes

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Workflow Components

Inputs (2)

Name	Description
terms
database

Processors (3)

Name	Type	Description
parametersXML	local
NCBI_eSearch	arbitrarywsdl
parametersXML1	local

Beanshells (0)

Outputs (2)

Name	Description
xml_output
IdList

Links (6)

Source	Sink
database	parametersXML:db
parametersXML:output	NCBI_eSearch:parameters
terms	parametersXML:term
NCBI_eSearch:parameters	parametersXML1:input
NCBI_eSearch:parameters	xml_output
parametersXML1:IdList	IdList

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Taverna 1

Information Uploader

Paul Fisher

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Information Version 3 (latest) (of 3)

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Version History

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Perform a search through NCBI eUtils eSearch

Created by Paul Fisher on Wednesday 03 October 2007 18:36:07 (UTC)
Perform a search through NCBI eUtils eSearch

Created by Paul Fisher on Wednesday 03 October 2007 18:36:07 (UTC)

Last edited by Paul Fisher on Tuesday 13 November 2007 16:11:50 (UTC)
Perform a search through NCBI eUtils eSearch

Created by Paul Fisher on Friday 27 November 2009 14:44:11 (UTC)

Last edited by Paul Fisher on Thursday 03 December 2009 16:32:27 (UTC)

Revision comment:

Added a processor to extract ids from the xml output

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Comments (9)

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Jelle Scholtalbers	Tuesday 04 March 2008 09:35:59 (UTC)
	Did you try to get the ID list from the xml? I doesn't seem to work. Since I'm no java programmer I did not yet try to parse the output myself. If you do get the ID list from the XML could you show me how?

Jmframpton

Hi Paul, I've got the same probs as Chewy. I'm trying to split the ID list from esearch so that I can feed that into the efetch utility...at the moment the xml splitter just isn't doing the job...you don't happen to have a "esearch output to efetch input parser" processor lying around do you? Any help would be appreciated.

Cheers, Jonathan

Paul Fisher

Hi Guys,

Sorry for the late reply.

I have uploaded a new verison, which should cater for your requirements.

cheers,

Paul.

Liyinji
Saturday 21 August 2010 11:46:13 (UTC)

great
Liyinji
Saturday 21 August 2010 11:53:35 (UTC)

great
Liyinji
Monday 23 August 2010 14:06:38 (UTC)

great
Liyinji
Monday 23 August 2010 14:07:13 (UTC)

great

Liyinji	Monday 23 August 2010 14:10:28 (UTC)
	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh

Katja Vouk

Hi Paul, running this workflow, I only get the first 20 IDs. Is it possible to adapt the workflow to get the list of all the IDs resulting from particular search?

Thank you in advance for your help.

Katja

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