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Pathway to Pubmed

Workflow Entry: Pathway to Pubmed

Created at: 08/12/10 @ 11:47:10 Last updated: 11/01/11 @ 12:00:16

Version 2 (latest) (of 2)

Version created on: 11/01/11 @ 11:59:53 by: Paul Fisher | Revision comments Expand

Last edited on: 11/01/11 @ 12:00:16 by: Paul Fisher

Title: Pathway to Pubmed

Type: Taverna 2

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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/1711/download?version=2
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (1)

Name	Description
pathway_descriptions

Processors (9)

Name	Type	Description
split_search_terms	localworker
pathway_and_abstract	beanshell
remove_nulls	beanshell
merge_outputs_2	localworker
regex	stringconstant
extract_terms	beanshell
add_MeSH_to_string	beanshell
Search_PubMed	workflow
clean_text	workflow

Beanshells (6)

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

Outputs (1)

Name	Description
pathway_abstracts

Datalinks (11)

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	extract_terms:input
extract_terms:output	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 Original Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (13)

Original Uploader tags

abstracts
|
concept
|
data-driven
|
genotype
|
Kegg Pathways
|
KeggID
|
pathway
|
pathway-driven
|
pathways
|
phenotype
|
text
|
text mining
|
text mining; term extraction; entity recognition

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Information Shared with Groups (2)

Information Featured In Packs (1)

Text Mining Workflows

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Information Ratings (0)

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Information Attributed By (2)

(Workflows/Files)

Information Favourited By (0)

No one

Information Statistics

149 viewings

330 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Pathway to Pubmed

Created on: Wednesday 08 December 2010 @ 11:47:10 (GMT)

Created by: Paul Fisher

Revision comments:

None

Latest Version:
[2] - Pathway to Pubmed

Created on: Tuesday 11 January 2011 @ 11:59:53 (GMT)

Created by: Paul Fisher

Last edited on: Tuesday 11 January 2011 @ 12:00:16 (GMT)

Last edited by: Paul Fisher

Revision comments:

- added nested workflow to remove non-ascii characters

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Other workflows that use similar services (26)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Original Uploader

Paul Fisher

Gene to Pubmed (v4)

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

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

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 43 times | Downloaded: 23 times

Tags (30):

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

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Download (v4)

Taverna 2

Original Uploader

Paul Fisher

Pathway and Gene to Pubmed (v2)

Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 64 times | Downloaded: 19 times

Tags (36):