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Kegg pathway diagrams (missing part 3)

Workflow Entry: Kegg pathway diagrams (missing part 3)

Created at: 19/03/10 @ 15:40:02 Last updated: 19/03/10 @ 15:40:26

Version 2 (latest) (of 2)

Version created on: 19/03/10 @ 15:40:02 by: Gregg Iceton | Revision comments Expand

Last edited on: 19/03/10 @ 15:40:29 by: Gregg Iceton

Title: Kegg pathway diagrams (missing part 3)

Type: Taverna 2

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Description

Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of my efforts wanted to work so far.

Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.

for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

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Workflow Components

Authors (1)

Titles (2)

Descriptions (3)

Inputs (11)

Name	Description
Species	The three letter species code KEGG The three letter species code used by KEGG
bg_color	The background colour for the boxes containing enzymes. The background colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.
fg_color	The text colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.
path_proteins
drugs_file
DBSavePath
Sequence1	Full path to FastA file containg nucleotide genome sequence (NB this would be supplied by part 1 however due to an oversight only the genome sequence from one EMBL file is generated)
Sequence2	Full path to FastA file containg nucleotide genome sequence (NB this would be supplied by part 1 however due to an oversight only the genome sequence from one EMBL file is generated)
source_file_path	EMBL file name for source (file must be in EMBL folder within path specificed in DBSavePath e.g. D:\Drutex\EMBL\)
target_file_path	EMBL file name for target (file must be in EMBL folder within path specificed in DBSavePath e.g. D:\Drutex\EMBL\)
blast_bin_dir	File path to folder which contains FormatDB.exe

Processors (50)

Name	Type	Description
Workflow89	workflow
Get_Image_From_URL_2	localworker
color_pathway_by_objects	wsdl	See the Service entry for this web service.
get_enzymes_by_gene	wsdl	See the Service entry for this web service.
get_genes_by_enzyme	wsdl	See the Service entry for this web service.
get_pathways_by_genes	wsdl	See the Service entry for this web service.
Flatten_List	localworker
Flatten_List_2	localworker
Remove_String_Duplicates	localworker
Beanshell	beanshell
Flatten_List_3	localworker
Flatten_List_4	localworker
Flatten_List_5	localworker
Flatten_List_6	localworker
Flatten_List_7	localworker
Flatten_List_8	localworker
Nested_workflow	workflow
Flatten_List_9	localworker
Flatten_List_2_2	localworker
Flatten_List_3_2	localworker
Filter_list_of_strings_extracting_match_to_a_regex	localworker
Group	stringconstant
Regex	stringconstant
Beanshell_2	beanshell
Flatten_List_10	localworker
runMGCAT	localworker
MGCAT_Path	stringconstant
Working_Dir	stringconstant
Read_Text_File	localworker
Split_string_into_string_list_by_regular_expression	localworker
Regex1	stringconstant
Filter_List_of_Strings_by_regex	localworker
Regex2	stringconstant
Regex3	stringconstant
Write_Text_File	localworker
Concatenate_strings	localworker
Group_2	stringconstant
INI_File	stringconstant
Read_Text_File_2	localworker
Split_string_into_string_list_by_regular_expression_2	localworker
Regex1_2	stringconstant
Filter_list_of_strings_extracting_match_to_a_regex_2	localworker
Group1	stringconstant
regex2	stringconstant
Thresholder	beanshell
Ask	localworker
Message	stringconstant
Title	stringconstant
INI_Path	stringconstant
Beanshell_3	beanshell

Beanshells (7)

Name	Inputs	Outputs
Beanshell	bg_color fg_color genes_list	bg_colors fg_colors
Beanshell_2	in0	n
Thresholder	seqSim reqSim	cont
Beanshell_3	base_dir target_file_path source_file_path progpath	database_dir
create_formatdb_cmdArgs	fastAFileName DBSavePath	cmdArgsList
Beanshell	blastOutPath eValTol DBSaveLocation	complete
create_blastall_cmdArgs	sequenceFileName DBSaveLocation regex group	cmdArgsList

Outputs (8)

Name	Description
KeggPathwayIDs	A list of the pathways found.
keggimageurl	The URLs of the images produced for the KeggImage output The URLs of the images produced for the KeggImage output.
keggGeneNames	A list of the gene ids, that was given as input with the species code concatenated.
coloured_images	List of pathway diagram with enzyme boxes coloured in specified colours
enzyme_list	List of enzyme id retrieve from Kegg using get_enzymes_by_gene
genes_list	List of ids that are enzymes
Output
test

Datalinks (71)

Source	Sink
Species	Workflow89:part1
Filter_list_of_strings_extracting_match_to_a_regex:filteredlist	Workflow89:part2
color_pathway_by_objects:return	Get_Image_From_URL_2:url
Flatten_List_6:outputlist	color_pathway_by_objects:bg_color_list
Flatten_List_8:outputlist	color_pathway_by_objects:fg_color_list
Remove_String_Duplicates:strippedlist	color_pathway_by_objects:object_id_list
Flatten_List_10:outputlist	color_pathway_by_objects:pathway_id
Workflow89:string	get_enzymes_by_gene:genes_id
Species	get_genes_by_enzyme:org
Flatten_List:outputlist	get_genes_by_enzyme:enzyme_id
Beanshell_2:n	get_pathways_by_genes:genes_id_list
get_enzymes_by_gene:return	Flatten_List:inputlist
get_genes_by_enzyme:return	Flatten_List_2:inputlist
Flatten_List_2:outputlist	Remove_String_Duplicates:stringlist
Remove_String_Duplicates:strippedlist	Beanshell:genes_list
bg_color	Beanshell:bg_color
fg_color	Beanshell:fg_color
Beanshell:bg_colors	Flatten_List_3:inputlist
Beanshell:fg_colors	Flatten_List_4:inputlist
Flatten_List_3:outputlist	Flatten_List_5:inputlist
Flatten_List_5:outputlist	Flatten_List_6:inputlist
Flatten_List_4:outputlist	Flatten_List_7:inputlist
Flatten_List_7:outputlist	Flatten_List_8:inputlist
drugs_file	Nested_workflow:drugs_file
path_proteins	Nested_workflow:path_proteins
DBSavePath	Nested_workflow:DBSavePath
Nested_workflow:output	Flatten_List_9:inputlist
Flatten_List_9:outputlist	Flatten_List_2_2:inputlist
Flatten_List_2_2:outputlist	Flatten_List_3_2:inputlist
Flatten_List_3_2:outputlist	Filter_list_of_strings_extracting_match_to_a_regex:stringlist
Group:value	Filter_list_of_strings_extracting_match_to_a_regex:group
Regex:value	Filter_list_of_strings_extracting_match_to_a_regex:regex
Workflow89:string	Beanshell_2:in0
get_pathways_by_genes:return	Flatten_List_10:inputlist
MGCAT_Path:value	runMGCAT:command
Working_Dir:value	runMGCAT:workingdir
INI_File:value	runMGCAT:args
INI_Path:value	Read_Text_File:fileurl
Read_Text_File:filecontents	Split_string_into_string_list_by_regular_expression:string
Regex1:value	Split_string_into_string_list_by_regular_expression:regex
Split_string_into_string_list_by_regular_expression:split	Filter_List_of_Strings_by_regex:stringlist
Regex2:value	Filter_List_of_Strings_by_regex:regex1
Regex3:value	Filter_List_of_Strings_by_regex:regex2
Sequence2	Filter_List_of_Strings_by_regex:file2
Group_2:value	Filter_List_of_Strings_by_regex:group
Sequence1	Filter_List_of_Strings_by_regex:file
Concatenate_strings:output	Write_Text_File:filecontents
INI_Path:value	Write_Text_File:outputFile
Filter_List_of_Strings_by_regex:filteredlist	Concatenate_strings:stringlist
Working_Dir:value	Read_Text_File_2:fileurl
Read_Text_File_2:filecontents	Split_string_into_string_list_by_regular_expression_2:string
Regex1_2:value	Split_string_into_string_list_by_regular_expression_2:regex
Split_string_into_string_list_by_regular_expression_2:split	Filter_list_of_strings_extracting_match_to_a_regex_2:stringlist
Group1:value	Filter_list_of_strings_extracting_match_to_a_regex_2:group
regex2:value	Filter_list_of_strings_extracting_match_to_a_regex_2:regex
Filter_list_of_strings_extracting_match_to_a_regex_2:filteredlist	Thresholder:seqSim
Ask:answer	Thresholder:reqSim
Message:value	Ask:message
Title:value	Ask:title
target_file_path	Beanshell_3:target_file_path
source_file_path	Beanshell_3:source_file_path
blast_bin_dir	Beanshell_3:progpath
DBSavePath	Beanshell_3:base_dir
Flatten_List_10:outputlist	KeggPathwayIDs
color_pathway_by_objects:return	keggimageurl
Workflow89:string	keggGeneNames
Get_Image_From_URL_2:image	coloured_images
Flatten_List:outputlist	enzyme_list
Remove_String_Duplicates:strippedlist	genes_list
Filter_list_of_strings_extracting_match_to_a_regex:filteredlist	Output
Beanshell_3:database_dir	test

Coordinations (9)

Controller	Target
Concatenate_strings	Write_Text_File
runMGCAT	Read_Text_File_2
Filter_List_of_Strings_by_regex	Concatenate_strings
Write_Text_File	Working_Dir
Beanshell_3	Read_Text_File
Write_Text_File	INI_File
Thresholder	Nested_workflow
Write_Text_File	runMGCAT
Write_Text_File	MGCAT_Path

Information Workflow Type

Taverna 2

Information Original Uploader

Gregg Iceton

Information License

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Information Credits (1)

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Gregg Iceton

Information Attributions (0)

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Information Shared with Groups (1)

Steyn Pharmaceuticals Ltd Unplanned Genetic Experiments (SPLUGE)

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Information Favourited By (0)

No one

Information Statistics

339 viewings

445 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - Blast proteins, select high similarity hits and display those which are enzymes on KEGG image

Created on: Friday 19 March 2010 @ 14:33:00 (GMT)

Created by: Gregg Iceton

Last edited on: Friday 19 March 2010 @ 14:34:33 (GMT)

Last edited by: Gregg Iceton

Revision comments:

None

Latest Version:
[2] - Kegg pathway diagrams (missing part 3)

Created on: Friday 19 March 2010 @ 15:40:02 (GMT)

Created by: Gregg Iceton

Last edited on: Friday 19 March 2010 @ 15:40:29 (GMT)

Last edited by: Gregg Iceton

Revision comments:

None

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Taverna 2

Original Uploader

Katy Wolstencroft

NCBI Gi to Kegg Pathway Descriptions (v2)

Created: 12/01/12 @ 09:46:31 | Last updated: 12/01/12 @ 14:54:37

Credits: Katy Wolstencroft

Attributions: NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database.

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

Viewed: 6 times | Downloaded: 8 times

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