About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
Gene to Pubmed

Workflow Entry: Gene to Pubmed

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

Version 4 (latest) (of 4)

Version created on: 10/02/11 @ 16:00:56 by: Paul Fisher | Revision comments Expand

Last edited on: 10/02/11 @ 16:01:41 by: Paul Fisher

Title: Gene to Pubmed

Type: Taverna 2

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

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.

Download

Download Workflow File/Package (T2FLOW)

Download Workflow as a Galaxy tool

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/1842/download?version=4
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (2)

Name	Description
gene_names
Phenotype_search_term

Processors (63)

Name	Type	Description
regex	stringconstant
remove_nulls	beanshell
gene_and_abstract	beanshell
split_search_terms	localworker
merge_outputs_2	localworker
Search_PubMed	workflow
clean_text	workflow
regular_expression	stringconstant
Remove_duplicate_genes	localworker
split_gene_names	localworker
remove_Nulls_2	beanshell
Merge_string_list_to_string	localworker
xpath	stringconstant
run_eSearch	wsdl
min_date	stringconstant
extractPMID	localworker
remove_Nulls_4	beanshell
concat_abstract_ids	beanshell
max_return_phenotype	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_3	workflow
Encode_byte_to_base64	localworker
merge_strings_2	localworker
regex_3	stringconstant
xpath_2	stringconstant
extract_abstracts	beanshell
merge_search_and_terms	beanshell
extract_Terms_2	localworker
merge_strings	localworker
remove_Nulls_5	beanshell
Remove_duplicate_strings_2	localworker
split_by_regex	localworker
clean_text_4	soaplab
pubmed_database_2	stringconstant
xpath_3	stringconstant
count	stringconstant
xpath_count	stringconstant
eSearch_database	stringconstant
regular_expression_2	stringconstant
extract_terms_3	beanshell
merge_term_count	beanshell
split_extracted_terms	localworker
merge_pubmed_count	localworker
merge_extracted	localworker
merge_list	localworker
extractCount_2	localworker
extractCount	localworker
parametersXML_1	xmlsplitter
run_eInfo	wsdl
run_eSearch_2	wsdl
run_eSearch_request	xmlsplitter
GENE_RankPhenotypeTerms	workflow
max_return_gene	stringconstant
generateTerminology	wsdl
generateTerminology_input	xmlsplitter
applicationCode_value	stringconstant

Beanshells (16)

Name	Inputs	Outputs
remove_nulls	input	output
gene_and_abstract	pathway abstracts	output
remove_Nulls_2	input	output
remove_Nulls_4	input	output
concat_abstract_ids	id abstract_text date_text	output
merge_phenotype_abstracts	phenotype abstracts	output
extract_abstracts	input	output output_search
merge_search_and_terms	terms search_term	output
remove_Nulls_5	input	output
extract_terms_3	input	output
merge_term_count	term count	output
stringToBytes	string	bytes
format_rankings	ranked_terms	title_term_rankings
remove_Nulls	input	output
stringToBytes	string	bytes
concat_abstract_ids	id abstract_text date_text	output

Outputs (7)

Name	Description
gene_abstracts
phenotype_abstracts
phenotype_terms
phenotype_term_counts
pubmed_abstract_number
gene_cosine
gene_term_enrichment_scores

Datalinks (83)

Source	Sink
gene_and_abstract:output	remove_nulls:input
Search_PubMed:concat_data	gene_and_abstract:abstracts
split_search_terms:split	gene_and_abstract:pathway
regex:value	split_search_terms:regex
remove_Nulls_2:output	split_search_terms:string
clean_text:cleaned_text	merge_outputs_2:stringlist
split_search_terms:split	Search_PubMed:search_term
min_date:value	Search_PubMed:min_date
max_date:value	Search_PubMed:max_date
max_return_gene:value	Search_PubMed:max_return
remove_nulls:output	clean_text:input
split_gene_names:split	Remove_duplicate_genes:stringlist
gene_names	split_gene_names:string
regular_expression:value	split_gene_names:regex
Merge_string_list_to_string:concatenated	remove_Nulls_2:input
Remove_duplicate_genes:strippedlist	Merge_string_list_to_string:stringlist
parametersXML_eSearch:output	run_eSearch:parameters
xpath:value	extractPMID:xpath
run_eSearch:parameters	extractPMID:xml-text
merge_phenotype_abstracts:output	remove_Nulls_4: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_phenotype:value	parametersXML_eSearch:RetMax
pubmed_database:value	parametersXML_eSearch:db
max_date:value	parametersXML_eSearch:maxdate
min_date:value	parametersXML_eSearch:mindate
Phenotype_search_term	parametersXML_eSearch:term
concat_abstract_ids:output	merge_abstract_ids:stringlist
Fetch_Abstracts:pubmed_dates	merge_dates:stringlist
extractPMID:nodelist	Fetch_Abstracts:pubmed_ids
remove_Nulls_4:output	clean_text_3:input
clean_text_3:cleaned_text	Encode_byte_to_base64:bytes
merge_strings:concatenated	merge_strings_2:stringlist
clean_text_4:output	extract_abstracts:input
merge_strings_2:concatenated	merge_search_and_terms:terms
extract_abstracts:output_search	merge_search_and_terms:search_term
xpath_2:value	extract_Terms_2:xpath
generateTerminology:parameters	extract_Terms_2:xml-text
Remove_duplicate_strings_2:strippedlist	merge_strings:stringlist
merge_search_and_terms:output	remove_Nulls_5:input
extract_Terms_2:nodelist	Remove_duplicate_strings_2:stringlist
regex_3:value	split_by_regex:regex
extract_abstracts:output	split_by_regex:string
Encode_byte_to_base64:base64	clean_text_4:file_direct_data
remove_Nulls_5:output	extract_terms_3:input
split_extracted_terms:split	merge_term_count:term
merge_extracted:concatenated	merge_term_count:count
extract_terms_3:output	split_extracted_terms:string
regular_expression_2:value	split_extracted_terms:regex
extractCount:nodelist	merge_pubmed_count:stringlist
extractCount_2:nodelist	merge_extracted:stringlist
merge_term_count:output	merge_list:stringlist
xpath_3:value	extractCount_2:xpath
run_eSearch_2:result	extractCount_2:xml-text
xpath_count:value	extractCount:xpath
run_eInfo:result	extractCount:xml-text
pubmed_database_2:value	parametersXML_1:db
parametersXML_1:output	run_eInfo:request
run_eSearch_request:output	run_eSearch_2:request
eSearch_database:value	run_eSearch_request:db
count:value	run_eSearch_request:rettype
split_extracted_terms:split	run_eSearch_request:term
min_date:value	run_eSearch_request:mindate
max_date:value	run_eSearch_request:maxdate
merge_pubmed_count:concatenated	GENE_RankPhenotypeTerms:pubmed_abstract_number
merge_list:concatenated	GENE_RankPhenotypeTerms:phenotype_term_counts
merge_outputs_2:concatenated	GENE_RankPhenotypeTerms:query_abstracts
clean_text_3:cleaned_text	GENE_RankPhenotypeTerms:phenotype_abstracts
remove_Nulls_5:output	GENE_RankPhenotypeTerms:phenotype_terms
generateTerminology_input:output	generateTerminology:parameters
split_by_regex:split	generateTerminology_input:texts
applicationCode_value:value	generateTerminology_input:applicationCode
merge_outputs_2:concatenated	gene_abstracts
clean_text_3:cleaned_text	phenotype_abstracts
remove_Nulls_5:output	phenotype_terms
merge_list:concatenated	phenotype_term_counts
merge_pubmed_count:concatenated	pubmed_abstract_number
GENE_RankPhenotypeTerms:cosine_vector_scores	gene_cosine
GENE_RankPhenotypeTerms:concept_rankings	gene_term_enrichment_scores

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 (7)

(Workflows/Files)

Information Tags (30)

Original Uploader tags

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

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (1)

(Workflows/Files)

Pathway and Gene to Pubmed

Information Favourited By (0)

No one

Information Statistics

208 viewings

303 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Gene to Pubmed

Created on: Tuesday 08 February 2011 @ 13:04:06 (GMT)

Created by: Paul Fisher

Revision comments:

None

Previous Versions:
[2] - Gene to Pubmed

Created on: Tuesday 08 February 2011 @ 13:06:21 (GMT)

Created by: Paul Fisher

Last edited on: Tuesday 08 February 2011 @ 13:07:08 (GMT)

Last edited by: Paul Fisher

Revision comments:

Created output ports for pathway cosine and concept rankings

[3] - Gene to Pubmed

Created on: Tuesday 08 February 2011 @ 13:10:57 (GMT)

Created by: Paul Fisher

Last edited on: Tuesday 08 February 2011 @ 13:12:01 (GMT)

Last edited by: Paul Fisher

Revision comments:

Description of workflow updated - in Taverna

Latest Version:
[4] - Gene to Pubmed

Created on: Thursday 10 February 2011 @ 16:00:56 (GMT)

Created by: Paul Fisher

Last edited on: Thursday 10 February 2011 @ 16:01:41 (GMT)

Last edited by: Paul Fisher

Revision comments:

changed the term extraction service to point to new URL

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (30)

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

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):