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

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
https://myexperiment.org/workflows/25/download?version=3
[ More InfoExpand ]


Information Workflow Components

Inputs (2)
Processors (3)
Beanshells (0)
Outputs (2)
Links (6)
Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 3 (latest) (of 3)

View version:

Information Credits (0)

(People/Groups)

None

Information Attributions (0)

(Workflows/Files)

None

Information Tags (4)

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

 

Citations (0)

None


Version History

In chronological order:



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (9)

Log in to make a comment

  • 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 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

  • 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.

    cheers,

    Paul.

     

     

  • Saturday 21 August 2010 11:46:13 (UTC)
    great
  • Saturday 21 August 2010 11:53:35 (UTC)
    great
  • Monday 23 August 2010 14:06:38 (UTC)
    great
  • Monday 23 August 2010 14:07:13 (UTC)
    great
  • Monday 23 August 2010 14:10:28 (UTC)
    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
  • 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.

    Katja 




Workflow Other workflows that use similar services (30)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.


Uploader

Workflow Escherichia coli : From cDNA Microarray Ra... (1)

Thumb
This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed changes in the microarray data. By identifying the candidate pathways, more detailed...

Created: 2008-05-08 | Last updated: 2008-05-12

Credits: User Saeedeh User Paul Fisher

Attributions: Workflow HUMAN Microarray CEL file to candidate pathways

Workflow NCBI_QBLAST (2)

Thumb
Perform an NCBI BLAST sequence similarity search using NCBI's QBLAST service (see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

Created: 2008-06-07 | Last updated: 2008-06-07

Credits: User Hamish McWilliam