Perform a search through NCBI eUtils eSearch

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

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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Comments Comments (9)

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  • 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?

  • Tuesday 04 March 2008 10:02:54 (UTC)

    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 the moment the xml splitter just isn't doing the don't happen to have a "esearch output to efetch input parser" processor lying around do you? Any help would be appreciated.

    Cheers, Jonathan

  • Friday 27 November 2009 14:37:30 (UTC)

    Hi Guys,

    Sorry for the late reply.

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





  • Saturday 21 August 2010 11:46:13 (UTC)
  • Saturday 21 August 2010 11:53:35 (UTC)
  • Monday 23 August 2010 14:06:38 (UTC)
  • Monday 23 August 2010 14:07:13 (UTC)
  • Monday 23 August 2010 14:10:28 (UTC)
  • Wednesday 23 January 2013 15:07:27 (UTC)

    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.


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