Pathway to Pubmed

Created: 2013-09-03 22:25:15

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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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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
pathway_descriptions

Processors (8)

Name	Type	Description
split_search_terms	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
pathway_and_abstract	beanshell	Script String[] split = abstracts.split("\n"); String pathway_name = pathway; Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); nonEmpty.add(trimmed); } String output = ">> " + pathway_name + "\n"; for (int i = 0; i < nonEmpty.size(); i++) { output = output + (String) (nonEmpty.elementAt(i) + "\n"); }
remove_nulls	beanshell	Script String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++){ if (!(split[i].equals(""))) { nonEmpty.add(split[i].trim()); } } String[] non_empty = new String[nonEmpty.size()]; for (int i = 0; i < non_empty.length; i ++) { non_empty[i] = nonEmpty.elementAt(i); } String output = ""; for (int i = 0; i < non_empty.length; i++) { output = output + (String) (non_empty[i] + "\n"); }
merge_outputs_2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
regex	stringconstant	Value \n
add_MeSH_to_string	beanshell	Script String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); nonEmpty.add(trimmed); } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + (String) (nonEmpty.elementAt(i) + " AND \"Metabolic Networks and Pathways\"[MeSH Terms]" + "\n"); }
Search_PubMed	workflow
clean_text	workflow

Beanshells (5)

Name	Inputs	Outputs
pathway_and_abstract	pathway abstracts	output
remove_nulls	input	output
add_MeSH_to_string	input	output
stringToBytes	string	bytes
concat_abstract_ids	id abstract_text date_text	output

Outputs (1)

Name	Description
pathway_abstracts

Datalinks (10)

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

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Aleksandra Pawlik

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

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Pathway to Pubmed

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Information Shared with Groups (1)

Bonn-September 2013

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Information Statistics

1266 viewings

947 downloads

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Citations (0)

None

Version History

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Pathway to Pubmed

Created by Aleksandra Pawlik on Tuesday 03 September 2013 22:25:14 (UTC)

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This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMe...

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Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms Gene to Pubmed

Pathway to Pubmed

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