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KEGG Pathways and Additional Information from BLAST

Created: 2011-03-29 11:16:17 Last updated: 2011-03-30 16:09:01

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

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Workflow Components

Authors (2)

Titles (2)

Descriptions (3)

Dependencies (0)

Inputs (1)

Name	Description
dgr

Processors (12)

Name	Type	Description
String_to_list	beanshell	Script String [] lines = in1.split("\n"); List list = new ArrayList(); for (int i =0;i
Get_EMBL_ids	workflow
NCBIGitoKeggPathways	workflow
Get_Uniprot_Data	workflow
get_identifiers_from_uniprot	beanshell	Script String [] lines = parsed_uniprot.split("\n"); List list = new ArrayList(); for (String line: lines) { if (line.startsWith(identifier_name)) { list.add(line.substring(3,line.length()).trim()); } } out1 = list;
AC_identifier	stringconstant	Value AC
GO_identifier	stringconstant	Value GO
Gene_Ontology_Results	workflow
InterPro_Results	workflow
InterPro_domain	stringconstant	Value InterPro
Untitledworkflow14	workflow
domain_name_value	stringconstant	Value MEDLINE

Beanshells (14)

Name	Inputs	Outputs
String_to_list	in1	out1
get_identifiers_from_uniprot	parsed_uniprot identifier_name	out1
remove_Nulls	input	output
extract_kegg_ids	input	output
remove_nulls_2	input	output
add_uniprot_to_string	input	output
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
to_Lower_Case_2	in1	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
to_Lower_Case_2	in1	out1
extract_embl_from_blast	unique_identifiers	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
to_Lower_Case_2	in1	out1
parse_embl_id	input	output

Outputs (8)

Name	Description
parsed_data
NCBIGitoKeggPathways_KEGGID
NCBIGitoKeggPathways_pathway_descriptions
NCBIGitoKeggPathways_pathway_by_genes
NCBIGitoKeggPathways_image
GO_output
InterPro_Results
MEDLINE

Datalinks (20)

Source	Sink
Get_EMBL_ids:gi_numbers	String_to_list:in1
dgr	Get_EMBL_ids:thresholded_blast
get_identifiers_from_uniprot:out1	NCBIGitoKeggPathways:uniprot_accs
String_to_list:out1	Get_Uniprot_Data:SearchTerm
Get_Uniprot_Data:parsed_data	get_identifiers_from_uniprot:parsed_uniprot
AC_identifier:value	get_identifiers_from_uniprot:identifier_name
GO_identifier:value	Gene_Ontology_Results:domain_name
Get_Uniprot_Data:parsed_data	Gene_Ontology_Results:parsed_uniprot
InterPro_domain:value	InterPro_Results:domain_name
Get_Uniprot_Data:parsed_data	InterPro_Results:parsed_uniprot
domain_name_value:value	Untitledworkflow14:domain_name
Get_Uniprot_Data:parsed_data	Untitledworkflow14:parsed_uniprot
Get_Uniprot_Data:parsed_data	parsed_data
NCBIGitoKeggPathways:KEGGID	NCBIGitoKeggPathways_KEGGID
NCBIGitoKeggPathways:pathway_descriptions	NCBIGitoKeggPathways_pathway_descriptions
NCBIGitoKeggPathways:pathway_by_genes	NCBIGitoKeggPathways_pathway_by_genes
NCBIGitoKeggPathways:image	NCBIGitoKeggPathways_image
Gene_Ontology_Results:EB_Eye_Results	GO_output
InterPro_Results:EB_Eye_Results	InterPro_Results
Untitledworkflow14:EB_Eye_Results	MEDLINE

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Morgan Taschuk

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

(People/Groups)

Morgan Taschuk

Information Attributions (1)

(Workflows/Files)

extract_uniprot_embl_gi.xml

Information Tags (6)

Uploader tags

BLAST
|
GO
|
interpro
|
medline
|
pathway
|
uniprot

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Information Shared with Groups (1)

A Team

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None

Information Favourited By (0)

No one

Information Statistics

2503 viewings

1576 downloads

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Citations (0)

None

Version History

In chronological order:

KEGG Pathways and Additional Information

Created by Morgan Taschuk on Tuesday 29 March 2011 11:16:17 (UTC)

Last edited by Morgan Taschuk on Tuesday 29 March 2011 11:57:36 (UTC)
KEGG Pathways and Additional Information from BLAST

Created by Morgan Taschuk on Wednesday 30 March 2011 14:49:06 (UTC)

Last edited by Morgan Taschuk on Wednesday 30 March 2011 16:09:01 (UTC)

Revision comment:

Replaced the Gene Ontology and PubMed services and formatted the output. Also, the KEGG pathways display the given enzymes in Pink.

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KEGG Pathways and Additional Information from BLAST

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