Workflow Entry: Pathway to Pubmed

Created at: 09/03/08 @ 15:03:12 Last updated: 08/07/08 @ 12:13:06

Version 2 (latest) (of 2)

Version created on: 09/03/08 @ 15:03:11 by: Paul Fisher | Revision comments Expand

Last edited on: 08/07/08 @ 12:13:06 by: Paul Fisher

Title: Pathway to Pubmed

Type: Taverna 1

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Description

This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

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Option 1:

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Option 2:

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http://www.myexperiment.org/workflows/172/download?version=2
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Workflow Components

Inputs (1)

Name	Description
pathway_descriptions

Processors (8)

Name	Type	Description
regex	stringconstant
merge_outputs_2	local
remove_nulls	beanshell
split_search_terms	local
pathway_and_abstract	beanshell
extract_terms	beanshell
add_MeSH_to_string	beanshell
Search_PubMed	workflow	This workflow takes in a list of KEGG pathway descriptions and a stop_list of KEGG pathway descriptions. These patwhays are then compared, and those in the stop list are removed. The workflow then extracts the pathway process from the KEGG formatted pathway descriptions output. It takes in a list of KEGG pathway descriptions and returns a list of pathways, without the KEGG pathway identifier or the species from which it came (e.g. - mus musculus (mouse) ). These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Outputs (1)

Name	Description
pathway_abstracts

Links (10)

Sink	Source
pathway_and_abstract:abstracts	Search_PubMed:concat_data
split_search_terms:string	add_MeSH_to_string:output
add_MeSH_to_string:input	extract_terms:output
extract_terms:input	pathway_descriptions
pathway_abstracts	merge_outputs_2:concatenated
remove_nulls:input	pathway_and_abstract:output
split_search_terms:regex	regex:value
merge_outputs_2:stringlist	remove_nulls:output
Search_PubMed:Pathway_search_term	split_search_terms:split
pathway_and_abstract:pathway	split_search_terms:split