This workflow uses one or more services that are deprecated as of 31st December 2012 (over 9 years ago), and may no longer function. Show details...

NCBI Gi to Kegg Pathways

Created: 2009-06-08 18:39:38 Last updated: 2009-12-14 11:51:20

Download Workflow

This workflow converts a list of NCBI gi numbers and converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings.

Example input for this workflow is as follows (new line separated):
gi:215422388
gi:120407068

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...'
https://myexperiment.org/workflows/786/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
Gi_numbers

Processors (14)

Name	Type	Description
regex	stringconstant
merge_pathways	local
merge_pathways_2	local
merge_descriptions	local
Remove_duplicate_pathways	local
split_by_regex	local
btit1	arbitrarywsdl
get_pathways_by_genes	arbitrarywsdl
btit	arbitrarywsdl
remove_nulls_2	beanshell
remove_Nulls	beanshell
add_ncbi_to_string	beanshell
extract_gene_ids	beanshell
bconv	arbitrarywsdl

Beanshells (4)

Name	Inputs	Outputs
remove_nulls_2	input	output
remove_Nulls	input	output
add_ncbi_to_string	input	output
extract_gene_ids	input	output

Outputs (4)

Name	Description
gene_descriptions
pathway_by_genes
pathway_descriptions
Kegg_strings

Links (18)

Source	Sink
Gi_numbers	add_ncbi_to_string:input
Remove_duplicate_pathways:strippedlist	merge_pathways_2:stringlist
add_ncbi_to_string:output	bconv:string
bconv:return	extract_gene_ids:input
btit:return	merge_descriptions:stringlist
extract_gene_ids:output	btit:string
extract_gene_ids:output	split_by_regex:string
add_ncbi_to_string:output	Kegg_strings
get_pathways_by_genes:return	merge_pathways:stringlist
merge_descriptions:concatenated	remove_Nulls:input
merge_pathways:concatenated	Remove_duplicate_pathways:stringlist
merge_pathways:concatenated	btit1:string
merge_pathways_2:concatenated	remove_nulls_2:input
regex:value	split_by_regex:regex
btit1:return	pathway_descriptions
remove_Nulls:output	gene_descriptions
remove_nulls_2:output	pathway_by_genes
split_by_regex:split	get_pathways_by_genes:genes_id_list

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Paul Fisher

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

(Workflows/Files)

None

Information Tags (6)

Uploader tags

bconv
|
gene
|
genes
|
ncbi
|
pathway
|
pathways

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 (9)

(Workflows/Files)

Item doesn't exist anymore
UnigeneID to KEGG Pathways
Private item
Private item
UnigeneID to KEGG Pathways
NCBI Gi to Kegg Pathway Descriptions
Private item
NCBI Gi to Kegg Pathways
Compare genome, extract proteins which are drug targets, apply to KEGG pathway

Information Favourited By (1)

Ian Laycock

Information Statistics

3573 viewings

2318 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

NCBI Gi to Kegg Pathways

Created by Paul Fisher on Monday 08 June 2009 18:39:38 (UTC)

Last edited by Paul Fisher on Monday 14 December 2009 11:51:22 (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 (93)

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

Taverna 2

Uploader

Paul Fisher

Get Kegg Pathway information (1)

Download

This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: Paul Fisher

Taverna 1

Uploader

Paul Fisher

Cow-Human Ortholog Pathways and Gene annot... (2)

Download

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

Created: 2007-10-03 | Last updated: 2009-12-03