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InviteWorkflow Entry: Perform a search through NCBI eUtils eSearch
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 Version 3 (latest)
(of 3)
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Version created on:
27/11/09 @ 14:44:11
by:
Paul Fisher
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Revision comments 
Last edited on: 03/12/09 @ 16:32:27 by: Paul Fisher
Title: Perform a search through NCBI eUtils eSearch
Type: Taverna 1
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Description
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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Option 1:
Launch in TavernaNote: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.
Option 2:
Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/25/download?version=3
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Earliest Version:
[1] - Perform a search through NCBI eUtils eSearch
Previous Versions:
[2] - Perform a search through NCBI eUtils eSearch
Latest Version:
[3] - Perform a search through NCBI eUtils eSearch
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Original Uploader |
Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41
Credits:
Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.
Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 43 times | Downloaded: 23 times Tags (30): |
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Original Uploader |
Created: 17/03/10 @ 10:53:02
Credits:
Attributions:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs
Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 150 times | Downloaded: 2 times Tags (21): |
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Linked Data
Non-Information Resource URI: http://www.myexperiment.org/workflows/25
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Copyright © 2007 - 2011 The University of Manchester and University of Southampton
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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?
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
Hi Guys,
Sorry for the late reply.
I have uploaded a new verison, which should cater for your requirements.
cheers,
Paul.