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What is [query] from NCBI, EBI, UniProt and KEGG ?

Workflow Entry: What is [query] from NCBI, EBI, UniProt and KEGG ?

Created at: 03/11/09 @ 04:29:15 Last updated: 03/11/09 @ 04:29:19

| License | Credits (1) | Attributions (0) | Tags (8) | Featured in Packs (0) | Ratings (0) | Attributed By (0) | Favourited By (0) |
| Citations (0) | Version History | Reviews (0) | Comments (0) |

Information

Version 2 (latest) (of 2)

Version created on: 03/11/09 @ 04:29:15 by: Francois Belleau | Revision comments Expand

Title: What is [query] from NCBI, EBI, UniProt and KEGG ?

Type: Taverna 2

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Description

test values:

query = paget disease query = pdb4 query = hk1 query = h1n1

This rdfiser query those four federated search services EB-Eye, KEGG LinkDB, NCBI Entrez and UniProt knowledgebase. RDF triples are returned for search statistics with Bio2RDF normalised URIs.

This workflow should be used responsibly because it can generate high load at the provider resources.

test values:

query = paget disease query = pdb4 query = hk1 query = h1n1

query = paget disease query = pdb4 query = hk1 query = h1n1

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http://www.myexperiment.org/workflows/936/download?version=2
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Workflow Components

Information

Authors (1)

Information

Titles (1)

Information

Descriptions (3)

Inputs (1)

Processors (4)

Beanshells (13)

Name	Description	Inputs	Outputs
build_ncbi_ntriples		id	ntriples
ncbi_ntriples			ntriples
ncbi_search_by_namespace		term db field retstart retmax mindate maxdate rettype	outputText
build_search_count_ntriples		query namespace count	ntriple
parse_ebeye_list		namespace	ntriples
ebeye_ntriples			ntriples
build_search_ntriple		namespace query count	ntriple
build_uniprot_search_url		string1 string2	output
Split_string_into_string_list_by_regular_expression		string regex	split count
build_count_ntriples		namespace search count	count_ntriples
build_bfind_query		kegg_namespace search	search_query
Split_string_into_string_list_by_regular_expression		string regex	split count
build_count_ntriples		count namespace search	count_ntriples

Outputs (4)

Datalinks (8)

Coordinations (3)

Information Workflow Type

Information Original Uploader

1443?size=60x60

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 (8)

Original Uploader tags

bio2rdf
|
cognoscope
|
eb-eye
|
kegg
|
ncbi
|
rdfiser
|
search
|
uniprot

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Information Ratings (0)

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Information Attributed By (0)

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None

Information Favourited By (0)

No one

Information Statistics

709 viewings

624 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - What is (...) from EB-eye, KEGG, NCBI and UniProt ?

Created on: Friday 30 October 2009 @ 05:53:29 (GMT)

Created by: Francois Belleau

Last edited on: Friday 30 October 2009 @ 06:01:17 (GMT)

Last edited by: Francois Belleau

Revision comments:

None

Latest Version:
[2] - What is [query] from NCBI, EBI, UniProt and KEGG ?

Created on: Tuesday 03 November 2009 @ 04:29:15 (GMT)

Created by: Francois Belleau

Revision comments:

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Taverna 2

Original Uploader

1443?size=60x60

Francois Belleau

Triplify namespace list from global search services from EBI, KEGG, NCBI and UniProt [myexperiment:search_services_namespace2rdf] (v1)

Created: 30/11/09 @ 21:38:23 | Last updated: 30/11/09 @ 21:44:57

Credits: Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

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

Viewed: 22 times | Downloaded: 13 times

Tags (7):

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Taverna 2

Original Uploader

Morgan Taschuk

KEGG Pathways and Additional Information from BLAST (v2)

Created: 29/03/11 @ 11:16:17 | Last updated: 30/03/11 @ 16:09:01

Credits: Morgan Taschuk

Attributions: extract_uniprot_embl_gi.xml

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

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

Viewed: 45 times | Downloaded: 20 times

Tags (6):

BLAST
|
GO
|
interpro
|
medline
|
pathway
|
uniprot

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Download (v2)

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/workflows/936

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