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Cow-Human Ortholog Pathways and Gene annotations for QTL Phenotype

Created: 2007-10-03 18:36:00 Last updated: 2009-12-03 16:16:31

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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 and sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

Example input:

chromosome_name: 17

start_position: 58127155

end_position: 68127155

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Workflow Components

Inputs (3)

Name	Description
chromosome
start_position
end_position

Processors (38)

Name	Type	Description
regex_2	stringconstant
kegg_pathway_release	stringconstant
species	stringconstant
add_ncbi_to_string	beanshell
remove_pathway_nulls	beanshell
split_gene_ids	beanshell
REMOVE_NULLS_2	beanshell
remove_pathway_nulls_2	beanshell
remove_desc_gaps	beanshell
add_uniprot_to_string	beanshell
remove_Nulls	beanshell
split_for_duplicates	local
merge_pathway_desc	local
merge_gene_desc	local
merge_uniprot_ids	local
merge_pathway_list_1	local
remove_duplicate_kegg_genes	local
concat_kegg_genes	local
merge_entrez_genes	local
merge_genes_pathways_3	local
remove_uniprot_duplicates	local
merge_reports	local
merge_genes_pathways_2	local
merge_kegg_references	local
remove_entrez_duplicates	local
merge_pathway_list_2	local
merge_genes_pathways	local
binfo	arbitrarywsdl
gene_descriptions	arbitrarywsdl
Kegg_gene_ids_2	arbitrarywsdl
Kegg_gene_ids	arbitrarywsdl
btaurus_gene_ensembl	biomart	Bos taurus genes (Btau_2.0)
compara_btau_hsap_orthologs	biomart	Bos taurus (Btau_2.0)\|Homo sapiens (NCBI36)\|Orthologues
hsapiens_gene_ensembl	biomart	Homo sapiens genes (NCBI36)
create_report	beanshell
GetPathways	workflow	This workflow removes any null values from a list of strings
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species
remove_nulls_3	beanshell

Beanshells (12)

Name	Inputs	Outputs
concat_gene_pathway_ids	pathway_ids gene_id	output
concat_ids	input	output
add_ncbi_to_string	input	output
remove_pathway_nulls	input	output
split_gene_ids	input	output
REMOVE_NULLS_2	input	output
remove_pathway_nulls_2	input	output
remove_desc_gaps	input	output
add_uniprot_to_string	input	output
remove_Nulls	input	output
create_report	ensembl_gene_id chromosome_name end_position start_position ensembl_transcript_id external_gene_id	result
remove_nulls_3	input	output

Outputs (8)

Name	Description
merged_pathways
gene_descriptions
pathway_descriptions
ensembl_database_release
kegg_pathway_release
report
kegg_external_gene_reference
pathway_ids

Links (52)

Source	Sink
GetPathways:pathway_desc	merge_pathway_desc:stringlist
GetPathways:pathway_genes	merge_genes_pathways:stringlist
GetPathways:pathway_ids	merge_pathway_list_1:stringlist
Kegg_gene_ids:return	concat_kegg_genes:string1
Kegg_gene_ids_2:return	concat_kegg_genes:string2
REMOVE_NULLS_2:output	add_uniprot_to_string:input
add_ncbi_to_string:output	Kegg_gene_ids_2:string
add_uniprot_to_string:output	Kegg_gene_ids:string
chromosome	btaurus_gene_ensembl:btaurus_gene_ensembl.chromosome_name_filter
end_position	btaurus_gene_ensembl:btaurus_gene_ensembl.end_filter
kegg_pathway_release:value	binfo:db
merge_entrez_genes:concatenated	remove_Nulls:input
merge_genes_pathways:concatenated	merge_genes_pathways_2:stringlist
merge_genes_pathways_2:concatenated	merge_genes_pathways_3:stringlist
merge_pathway_desc:concatenated	remove_pathway_nulls:input
merge_pathway_list_1:concatenated	merge_pathway_list_2:stringlist
merge_pathway_list_2:concatenated	remove_pathway_nulls_2:input
merge_uniprot_ids:concatenated	REMOVE_NULLS_2:input
regex_2:value	split_for_duplicates:regex
remove_Nulls:output	add_ncbi_to_string:input
remove_duplicate_kegg_genes:strippedlist	merge_kegg_references:stringlist
start_position	btaurus_gene_ensembl:btaurus_gene_ensembl.start_filter
btaurus_gene_ensembl:btaurus_gene_ensembl.chromosome_name	create_report:chromosome_name
btaurus_gene_ensembl:btaurus_gene_ensembl.end_position	create_report:end_position
btaurus_gene_ensembl:btaurus_gene_ensembl.ensembl_gene_id	compara_btau_hsap_orthologs:compara_btau_hsap_orthologs.btau_ensembl_gene_id_filter
btaurus_gene_ensembl:btaurus_gene_ensembl.ensembl_gene_id	create_report:ensembl_gene_id
btaurus_gene_ensembl:btaurus_gene_ensembl.ensembl_transcript_id	create_report:ensembl_transcript_id
btaurus_gene_ensembl:btaurus_gene_ensembl.external_gene_id	create_report:external_gene_id
btaurus_gene_ensembl:btaurus_gene_ensembl.start_position	create_report:start_position
compara_btau_hsap_orthologs:compara_btau_hsap_orthologs.hsap_gene_stable_id	hsapiens_gene_ensembl:hsapiens_gene_ensembl.ensembl_gene_id_filter
concat_kegg_genes:output	split_for_duplicates:string
create_report:result	merge_reports:stringlist
gene_descriptions:return	merge_gene_desc:stringlist
merge_gene_desc:concatenated	remove_nulls_3:input
remove_duplicate_kegg_genes:strippedlist	split_gene_ids:input
remove_entrez_duplicates:strippedlist	merge_entrez_genes:stringlist
binfo:return	kegg_pathway_release
getcurrentdatabase:output	ensembl_database_release
hsapiens_gene_ensembl:hsapiens_gene_ensembl.entrezgene	remove_entrez_duplicates:stringlist
hsapiens_gene_ensembl:hsapiens_gene_ensembl.uniprot_swissprot_accession	remove_uniprot_duplicates:stringlist
merge_genes_pathways_3:concatenated	merged_pathways
merge_kegg_references:concatenated	kegg_external_gene_reference
merge_reports:concatenated	report
remove_desc_gaps:output	gene_descriptions
remove_nulls_3:output	gene_descriptions
remove_uniprot_duplicates:strippedlist	merge_uniprot_ids:stringlist
species:value	getcurrentdatabase:species
split_for_duplicates:split	remove_duplicate_kegg_genes:stringlist
split_gene_ids:output	GetPathways:gene_ids
split_gene_ids:output	gene_descriptions:string
remove_pathway_nulls:output	pathway_descriptions
remove_pathway_nulls_2:output	pathway_ids

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Taverna 1

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Paul Fisher

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Version History

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Pathways and Gene annotations for QTL Phenotype

Created by Paul Fisher on Wednesday 03 October 2007 18:36:00 (UTC)
Cow-Human Ortholog Pathways and Gene annotations for QTL Phenotype

Created by Paul Fisher on Wednesday 03 October 2007 18:36:00 (UTC)

Last edited by Paul Fisher on Thursday 03 December 2009 16:16:33 (UTC)

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Stian Soiland-Reyes	Friday 20 June 2008 15:13:40 (UTC)
	Do you have some kind of description and sample input data for this workflow..? :-)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. 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. The Entrez and UniGene identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway d...

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