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Phenotype to pubmed

Workflow Entry: Phenotype to pubmed

Created at: 05/07/10 @ 14:07:33 Last updated: 11/01/11 @ 12:07:22

Version 3 (latest) (of 3)

Version created on: 11/01/11 @ 12:06:51 by: Paul Fisher | Revision comments Expand

Last edited on: 11/01/11 @ 12:07:22 by: Paul Fisher

Title: Phenotype to pubmed

Type: Taverna 2

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Description

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

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (1)

Name	Description
Phenotype_search_term

Processors (16)

Name	Type	Description
xpath	stringconstant
run_eSearch	wsdl
min_date	stringconstant
extractPMID	localworker
remove_Nulls	beanshell
concat_abstract_ids	beanshell
max_return	stringconstant
pubmed_database	stringconstant
merge_phenotype_abstracts	beanshell
merge_abstracts	localworker
max_date	stringconstant
parametersXML_eSearch	xmlsplitter
merge_abstract_ids	localworker
merge_dates	localworker
Fetch_Abstracts	workflow
clean_text	workflow

Beanshells (4)

Name	Inputs	Outputs
remove_Nulls	input	output
concat_abstract_ids	id abstract_text date_text	output
merge_phenotype_abstracts	phenotype abstracts	output
stringToBytes	string	bytes

Outputs (1)

Name	Description
phenotype_abstracts

Datalinks (20)

Source	Sink
parametersXML_eSearch:output	run_eSearch:parameters
xpath:value	extractPMID:xpath
run_eSearch:parameters	extractPMID:xml-text
merge_phenotype_abstracts:output	remove_Nulls:input
extractPMID:nodelist	concat_abstract_ids:id
merge_abstracts:concatenated	concat_abstract_ids:abstract_text
merge_dates:concatenated	concat_abstract_ids:date_text
merge_abstract_ids:concatenated	merge_phenotype_abstracts:abstracts
Phenotype_search_term	merge_phenotype_abstracts:phenotype
Fetch_Abstracts:abstracts	merge_abstracts:stringlist
max_return:value	parametersXML_eSearch:RetMax
Phenotype_search_term	parametersXML_eSearch:term
pubmed_database:value	parametersXML_eSearch:db
max_date:value	parametersXML_eSearch:maxdate
min_date:value	parametersXML_eSearch:mindate
concat_abstract_ids:output	merge_abstract_ids:stringlist
Fetch_Abstracts:pubmed_dates	merge_dates:stringlist
extractPMID:nodelist	Fetch_Abstracts:pubmed_ids
remove_Nulls:output	clean_text:input
clean_text:cleaned_text	phenotype_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 (18)

Original Uploader tags

abstracts
|
african trypanosomiasis
|
disease
|
efetch
|
entrez
|
esearch
|
loci
|
ncbi
|
phenotype
|
pubmed
|
qtl
|
quanitative
|
sleeping sickness
|
term
|
text
|
text mining
|
text mining; term extraction; entity recognition
|
trait

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Information Shared with Groups (1)

PhD Supplementary Information

Information Featured In Packs (1)

Text Mining Workflows

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Information Ratings (0)

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0.0 / 5

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Information Attributed By (1)

(Workflows/Files)

Item doesn't exist anymore

Information Favourited By (1)

Philip Y.

Information Statistics

231 viewings

421 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - Phenotype to Pubmed

Created on: Monday 05 July 2010 @ 14:07:33 (GMT)

Created by: Paul Fisher

Last edited on: Wednesday 08 December 2010 @ 11:51:26 (GMT)

Last edited by: Paul Fisher

Revision comments:

None

Previous Versions:
[2] - Phenotype to pubmed

Created on: Wednesday 08 December 2010 @ 11:52:00 (GMT)

Created by: Paul Fisher

Last edited on: Wednesday 08 December 2010 @ 11:52:27 (GMT)

Last edited by: Paul Fisher

Revision comments:

Updated workflow to make it more compact

Latest Version:
[3] - Phenotype to pubmed

Created on: Tuesday 11 January 2011 @ 12:06:51 (GMT)

Created by: Paul Fisher

Last edited on: Tuesday 11 January 2011 @ 12:07:22 (GMT)

Last edited by: Paul Fisher

Revision comments:

added nestwed workflow to remove non-ascii characters from text

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Tags (30):

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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...

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Viewed: 64 times | Downloaded: 19 times

Tags (36):