Basic eSearch/eFetch cycle

Created: 2008-12-04 22:47:43 Last updated: 2008-12-04 22:51:42

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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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Workflow Components

Inputs (0)

Processors (3)

Name	Type	Description
sample_data	workflow
eSearch	workflow
eFetch	workflow	Given a list of Yeast genes IDs, returns a file with their sequences.

Beanshells (0)

Outputs (4)

Name	Description
eFetch_output
WebEnv
Result_List
WebEnv_in_EFetch

Links (9)

Source	Sink
eFetch:WebEnv_in_eFetch	WebEnv_in_EFetch
eFetch:seq	eFetch_output
eSearch:Query_key	eFetch:query_key
eSearch:Result_List	Result_List
eSearch:WebEnv	WebEnv
eSearch:WebEnv	eFetch:WebEnv
sample_data:db	eFetch:db
sample_data:db	eSearch:db
sample_data:term	eSearch:term

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Taverna 1

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Giovanni Dall'Olio

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Giovanni Dall'Olio

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Basic eSearch/eFetch cycle

Created by Giovanni Dall'Olio on Thursday 04 December 2008 22:47:43 (UTC)

Last edited by Giovanni Dall'Olio on Thursday 04 December 2008 22:51:43 (UTC)

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