This workflow uses one or more services that are deprecated as of 31st December 2012 (almost 12 years ago), and may no longer function. Show details...

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

Created: 2009-11-03 04:29:15 Last updated: 2009-11-03 04:29:19

Download Workflow

This rdfiser query those four federated search services EB-Eye, KEGG LinkDB, NCBI Entrez and UniProt knowledgebase. RDF triples are returned for the founded documents and 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 = pdb4

query = hk1

query = hexokinase

query = paget disease

Preview

Download as scalable diagram (SVG)

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/936/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (1)

Name	Description
query

Processors (7)

Name	Type	Description
Nested_workflow	workflow
Nested_workflow2	workflow
Nested_workflow3	workflow
Nested_workflow4	workflow
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
Merge_String_List_to_a_String2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();

Beanshells (16)

Name	Inputs	Outputs
parse_ebeye_list	namespace	ntriples
ebeye_ntriples		ntriples
build_search_ntriple	namespace query id	ntriple bmuri
build_search_ntriple	namespace query count	ntriple
build_bfind_query	kegg_namespace search	search_query
extract_bmuri	stringlist namespace search	bmuris count_ntriple
build_search_ntriple	bmuri search namespace	search_ntriple
build_ncbi_ntriples	id	ntriples
ncbi_ntriples		ntriples
ncbi_search_by_namespace	term db field retstart retmax mindate maxdate rettype	outputText
Beanshell	query namespace id	bmuri ntriple
ncbi_search_by_namespace	term db field retstart retmax mindate maxdate rettype	outputText
build_search_count_ntriples	query namespace count	ntriple
build_uniprot_search_url	string1 string2	output
build_bmuri	string1 string2	output
build_ntriples	stringlist namespace search	count_ntriples search_ntriples

Outputs (3)

Name	Description
search_all_ntriples
search_all_count_ntriples
search_all_count_bmuris

Datalinks (19)

Source	Sink
query	Nested_workflow:query
query	Nested_workflow2:query
query	Nested_workflow3:query
query	Nested_workflow4:query
Nested_workflow4:count_ntriples	Merge_String_List_to_a_String:stringlist
Nested_workflow3:count_ntriples	Merge_String_List_to_a_String:stringlist
Nested_workflow2:count_ntriples	Merge_String_List_to_a_String:stringlist
Nested_workflow:count_ntriples	Merge_String_List_to_a_String:stringlist
Nested_workflow4:ntriples	Merge_String_List_to_a_String2:stringlist
Nested_workflow3:ntriples	Merge_String_List_to_a_String2:stringlist
Nested_workflow2:ntriples	Merge_String_List_to_a_String2:stringlist
Nested_workflow:ntriples	Merge_String_List_to_a_String2:stringlist
Nested_workflow4:uniprot_search_all_bmuris	Flatten_List:inputlist
Nested_workflow:ebeye_search_all_bmuris	Flatten_List:inputlist
Nested_workflow2:kegg_search_all_bmuris	Flatten_List:inputlist
Nested_workflow2:kegg_search_all_bmuris	Flatten_List:inputlist
Merge_String_List_to_a_String2:concatenated	search_all_ntriples
Merge_String_List_to_a_String:concatenated	search_all_count_ntriples
Flatten_List:outputlist	search_all_count_bmuris

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Francois Belleau

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

(People/Groups)

Francois Belleau

Information Attributions (0)

(Workflows/Files)

None

Information Tags (8)

Uploader tags

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

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 Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

3346 viewings

2012 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

What is (...) from EB-eye, KEGG, NCBI and UniProt ?

Created by Francois Belleau on Friday 30 October 2009 05:53:29 (UTC)

Last edited by Francois Belleau on Friday 30 October 2009 06:01:17 (UTC)
What is [query] from NCBI, EBI, UniProt and KEGG ?

Created by Francois Belleau on Tuesday 03 November 2009 04:29:15 (UTC)

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 (96)

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

Taverna 2

Uploader

Morgan Taschuk

KEGG Pathways and Additional Information f... (2)

Download

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

Created: 2011-03-29 | Last updated: 2011-03-30

Credits: Morgan Taschuk

Attributions: extract_uniprot_embl_gi.xml

Taverna 2

Uploader

Morgan Taschuk

Drug Re-Purposing Workflow (6)

Download

The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene...

Created: 2011-03-25 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

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

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Script

Script

Script

Reviews (0)

Comments (0)

Other workflows that use similar services (96)