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PubMed Search

Workflow Entry: PubMed Search

Created at: 03/02/11 @ 15:24:57 Last updated: 03/02/11 @ 15:25:32

Version 1 (of 1)

Version created on: 03/02/11 @ 15:24:56 by: Paul Fisher | Revision comments Expand

Last edited on: 03/02/11 @ 15:25:32 by: Paul Fisher

Title: PubMed Search

Type: Taverna 2

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Description

This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

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http://www.myexperiment.org/workflows/1833/download?version=1
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Workflow Components

Authors (1)

Titles (2)

Descriptions (2)

Inputs (4)

Name	Description
search_term
end_date
start_date
maximum_articles

Processors (10)

Name	Type	Description
merge_dates	localworker
merge_abstracts	localworker
merge_abstract_ids	localworker
pubmed_database	stringconstant
extractPMID	localworker
xpath	stringconstant
run_eSearch	wsdl
parametersXML_eFecth	xmlsplitter
Retrive_abstracts	workflow
concat_abstract_ids	beanshell

Beanshells (1)

Name	Description	Inputs	Outputs
concat_abstract_ids		id abstract_text date_text	output

Outputs (1)

Name	Description
concat_data

Datalinks (16)

Source	Sink
Retrive_abstracts:date	merge_dates:stringlist
Retrive_abstracts:abstract	merge_abstracts:stringlist
concat_abstract_ids:output	merge_abstract_ids:stringlist
xpath:value	extractPMID:xpath
run_eSearch:parameters	extractPMID:xml-text
parametersXML_eFecth:output	run_eSearch:parameters
pubmed_database:value	parametersXML_eFecth:db
search_term	parametersXML_eFecth:term
end_date	parametersXML_eFecth:maxdate
start_date	parametersXML_eFecth:mindate
maximum_articles	parametersXML_eFecth:RetMax
extractPMID:nodelist	Retrive_abstracts:pubmed_ids
merge_dates:concatenated	concat_abstract_ids:date_text
extractPMID:nodelist	concat_abstract_ids:id
merge_abstracts:concatenated	concat_abstract_ids:abstract_text
merge_abstract_ids:concatenated	concat_data

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 (4)

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Information Shared with Groups (0)

None

Information Featured In Packs (0)

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Information Ratings (0)

Current:

0.0 / 5

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Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (1)

Philip Y.

Information Statistics

168 viewings

325 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - PubMed Search

Created on: Thursday 03 February 2011 @ 15:24:56 (GMT)

Created by: Paul Fisher

Last edited on: Thursday 03 February 2011 @ 15:25:32 (GMT)

Last edited by: Paul Fisher

Revision comments:

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This Workflow only has one version.

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Other workflows that use similar services (27)

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
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enrichment
|
entity recognition
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evidence
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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
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phenotype
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pubmed
|
qtl
|
ranking
|
re-use
|
term
|
term extraction
|
terms
|
text
|
text mining
|
text mining; term extraction; entity recognition
|
trichuris muris

View

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):