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Pathway to Pubmed

Workflow Entry: Pathway to Pubmed

Created at: 02/09/08 @ 20:53:53 Last updated: 08/09/08 @ 15:35:53

Version 1 (of 1)

Version created on: 02/09/08 @ 20:53:53 by: Stian Soiland-Reyes | Revision comments Expand

Last edited on: 08/09/08 @ 15:35:54 by: Stian Soiland-Reyes

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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http://www.myexperiment.org/workflows/388/download?version=1
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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

Beanshells (5)

Name	Inputs	Outputs
concat_abstract_ids	id abstract_text date_text	output
remove_nulls	input	output
pathway_and_abstract	pathway abstracts	output
extract_terms	input	output
add_MeSH_to_string	input	output

Outputs (1)

Name	Description
pathway_abstracts

Links (10)

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

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Stian Soiland-Reyes

Information License

All versions of this Workflow are licensed under:

Information Credits (2)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

ProteinSynonymsToQuery

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Information Favourited By (0)

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Information Statistics

68 viewings

344 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Pathway to Pubmed

Created on: Tuesday 02 September 2008 @ 20:53:53 (GMT)

Created by: Stian Soiland-Reyes

Last edited on: Monday 08 September 2008 @ 15:35:54 (GMT)

Last edited by: Stian Soiland-Reyes

Revision comments:

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This Workflow only has one version.

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Taverna 2

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Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41

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

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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Viewed: 43 times | Downloaded: 23 times

Tags (30):

abstracts
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cosine vector space
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data-driven
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disease
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enrichment
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entity recognition
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evidence
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kegg
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Kegg Pathways
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literature
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loci
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locus
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medline
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microarray
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pathways
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phenotype
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pubmed
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qtl
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ranking
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re-use
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition
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trichuris muris

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Download (v4)

Taverna 2

Original Uploader

Paul Fisher

microRNA to KEGG Pathways and Abstracts (v1)

Created: 17/03/10 @ 10:53:02

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

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):