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InviteWorkflow Entry: Basic eSearch/eFetch cycle
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 Version 1
(of 1)
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Version created on:
04/12/08 @ 22:47:43
by:
Giovanni Dall'Olio
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Revision comments 
Last edited on: 04/12/08 @ 22:51:43 by: Giovanni Dall'Olio
Title: Basic eSearch/eFetch cycle
Type: Taverna 1
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Description
This is a basic eSearch/eFetch workflow created with taverna and using eUtils from NCBI.
It accepts a query term as input (at the moment, for testing purposes, this is a fixed string), interrogate eSearch to retrieve the list of related sequences on the Nucleotide database, and use eFetch to retrieve the corresponding sequences.
I wrote this workflow one year ago, when I was trying to understand how taverna and eUtils work; I suspect it broken, and of course it could be enhanced, so I am putting it here and you are free to copy and modify it, and any suggestion is highly appreciated.
I believe this is a good workflow to study if you want to understand how the eUtils and their mechanism of WebEnv and QueryKey work.
I also putted it on my github repository: http://github.com/dalloliogm/taverna_workflows/tree/master/eUtils
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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/592/download?version=1
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Original Uploader |
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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.
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Created: 17/03/10 @ 10:53:02
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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
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Linked Data
Non-Information Resource URI: http://www.myexperiment.org/workflows/592
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