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Triplify search results from KEGG bfind SOAP service [myexperiments:kegg_search2rdf]

Workflow Entry: Triplify search results from KEGG bfind SOAP service [myexperiments:kegg_search2rdf]

Created at: 30/11/09 @ 16:21:05 Last updated: 30/11/09 @ 20:48:50

Version 3 (latest) (of 3)

Version created on: 30/11/09 @ 16:21:05 by: Francois Belleau | Revision comments Expand

Last edited on: 30/11/09 @ 20:48:51 by: Francois Belleau

Title: Triplify search results from KEGG bfind SOAP service [myexperiments:kegg_search2rdf]

Type: Taverna 2

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Description

This workflow use KEGG's SOAP service provided to do a BFIND serch within one of the KEGG's official database. The results are returned in RDF ntriples format.

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http://www.myexperiment.org/workflows/977/download?version=3
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Workflow Components

Authors (1)

Titles (5)

Descriptions (8)

Inputs (2)

Name	Description
query	A full text search query string. example: hki, parkinson disease
kegg_namespace	One of KEGG database name The official list is here : example: path, genes One of KEGG database name The official list is here : http://www.myexperiment.org/workflows/967 example: path, genes

Processors (7)

Name	Type	Description
bfind	wsdl	See the Service entry for this web service.
build_bfind_query	beanshell
Split_string_into_string_list_by_regular_expression	localworker
eol	stringconstant
extract_bmuri	beanshell
Merge_String_List_to_a_String	localworker
build_search_ntriple	beanshell

Beanshells (3)

Name	Inputs	Outputs
build_bfind_query	kegg_namespace search	search_query
extract_bmuri	stringlist namespace search	bmuris count_ntriple
build_search_ntriple	bmuri search namespace	search_ntriple

Outputs (4)

Name	Description
kegg_search_bmuris
kegg_search_ntriples
search_count_ntriples
o1

Datalinks (16)

Source	Sink
build_bfind_query:search_query	bfind:string
query	build_bfind_query:search
kegg_namespace	build_bfind_query:kegg_namespace
bfind:return	Split_string_into_string_list_by_regular_expression:string
eol:value	Split_string_into_string_list_by_regular_expression:regex
Split_string_into_string_list_by_regular_expression:split	extract_bmuri:stringlist
query	extract_bmuri:search
kegg_namespace	extract_bmuri:namespace
build_search_ntriple:search_ntriple	Merge_String_List_to_a_String:stringlist
query	build_search_ntriple:search
kegg_namespace	build_search_ntriple:namespace
extract_bmuri:bmuris	build_search_ntriple:bmuri
extract_bmuri:bmuris	kegg_search_bmuris
Merge_String_List_to_a_String:concatenated	kegg_search_ntriples
extract_bmuri:count_ntriple	search_count_ntriples
build_bfind_query:search_query	o1

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Francois Belleau

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Francois Belleau

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Original Uploader tags

bfind
|
bio2rdf
|
cognoscope
|
kegg
|
search
|
soap

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Information Shared with Groups (0)

None

Information Featured In Packs (0)

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Information Ratings (0)

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Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

480 viewings

600 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Search one of KEGG<s database for a specific txt query [myexperiments:kegg_search2rdf]

Created on: Monday 30 November 2009 @ 16:11:11 (GMT)

Created by: Francois Belleau

Revision comments:

None

Previous Versions:
[2] - Search one of KEGG database for a specific txt query [myexperiments:kegg_search2rdf]

Created on: Monday 30 November 2009 @ 16:11:55 (GMT)

Created by: Francois Belleau

Last edited on: Monday 30 November 2009 @ 16:20:46 (GMT)

Last edited by: Francois Belleau

Revision comments:

None

Latest Version:
[3] - Triplify search results from KEGG bfind SOAP service [myexperiments:kegg_search2rdf]

Created on: Monday 30 November 2009 @ 16:21:05 (GMT)

Created by: Francois Belleau

Last edited on: Monday 30 November 2009 @ 20:48:51 (GMT)

Last edited by: Francois Belleau

Revision comments:

None

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Taverna 1

Original Uploader

Franck Tanoh

bfind (v1)

Created: 29/09/08 @ 13:21:12 | Last updated: 29/09/08 @ 13:23:39

Credits: Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Used for searching entries by keywords. User needs to specify a database from those which are supported by DBGET system before keywords. List of databases available at : http://www.genome.jp/dbget/ Example of input parameter: gb E-cadherin human

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 40 times | Downloaded: 16 times

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