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Pathways and Gene annotations for QTL Phenotype annotated

Created: 2007-10-30 13:04:02 Last updated: 2007-12-04 11:18:33

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Workflow Components

Inputs (0)

Processors (52)

Name	Type	Description
add_uniprot_to_string	beanshell
regex_2	stringconstant
split_gene_ids	beanshell
remove_Nulls	beanshell
Split_for_ncbi_pathways	local
kegg_pathway_release	stringconstant
species	stringconstant
remove_duplicate_pathways	local
split_pathways	local
concat_pathway_lists	local
remove_pathway_nulls	beanshell
merge_probesets	local
comma	stringconstant
comma_sep_probesets	local
split_probesets	local
add_string_to_probesets	beanshell
remove_nulls_4	beanshell
create_report	beanshell
merge_reports	local
remove_entrez_duplicates	local
remove_uniprot_duplicates	local
remove_duplicate_kegg_genes	local
Split_for_swissprot_pathways	local
add_ncbi_to_string	beanshell
merge_ncbi_pathways	local
merge_gene_desc	local
mmusculus_gene_ensembl	biomart	Mus musculus genes (NCBIM36)
ColumnType	stringconstant
Profile	stringconstant
genes_in_qtl	biomart	Mus musculus genes (NCBIM36)
split_ncbi_gene_ids	beanshell
merge_uniprot_ids	local
split_for_duplicates	local
merge_genes_and_pathways	local
merge_entrez_genes	local
Merge_string_list_to_string3	local
REMOVE_NULLS_2	beanshell
Merge_string_list_to_string	local
concat_kegg_genes	local
merge_uniprot_pathways	local
gene_descriptions	arbitrarywsdl
Kegg_gene_ids	arbitrarywsdl
maxdBrowse_query	arbitrarywsdl	The query function
Kegg_gene_ids_2	arbitrarywsdl
binfo	arbitrarywsdl
chromosome	stringconstant
start_position	stringconstant
end_position	stringconstant
MeasurementIDs	stringconstant
Uniprot_pathways	workflow
NCBI_pathways	workflow
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species

Beanshells (10)

Name	Inputs	Outputs
add_uniprot_to_string	input	output
split_gene_ids	input	output
remove_Nulls	input	output
remove_pathway_nulls	input	output
add_string_to_probesets	input	output
remove_nulls_4	input	output
create_report	ensemblGeneId entrezGeneId externalGeneId chromoName geneStart geneEnd ensemblTranscriptId uniprotAcc affy_Mouse430_2 affy_Mouse430a_2	result
add_ncbi_to_string	input	output
split_ncbi_gene_ids	input	output
REMOVE_NULLS_2	input	output

Outputs (8)

Name	Description
swissprot_merged_pathways
merged_ncbi_pathwyas
gene_descriptions
pathway_descriptions
ensembl_database_release
kegg_pathway_release
report
probeset_expressions

Links (72)

Source	Sink
ColumnType:value	maxdBrowse_query:ColumnType
Kegg_gene_ids:return	split_gene_ids:input
Kegg_gene_ids_2:return	split_ncbi_gene_ids:input
MeasurementIDs:value	maxdBrowse_query:MeasurementIDs
Merge_string_list_to_string:concatenated	Merge_string_list_to_string3:stringlist
NCBI_pathways:pathway_descriptions	merge_ncbi_pathways:stringlist
NCBI_pathways:pathway_genes	Merge_string_list_to_string:stringlist
Profile:value	maxdBrowse_query:profile
REMOVE_NULLS_2:output	add_uniprot_to_string:input
Split_for_ncbi_pathways:split	NCBI_pathways:gene_ids
Split_for_swissprot_pathways:split	Uniprot_pathways:gene_ids
Uniprot_pathways:pathway_desc	merge_uniprot_pathways:stringlist
Uniprot_pathways:pathway_genes	merge_genes_and_pathways:stringlist
add_ncbi_to_string:output	Kegg_gene_ids_2:string
add_string_to_probesets:output	split_probesets:string
add_uniprot_to_string:output	Kegg_gene_ids:string
chromosome:value	genes_in_qtl:mmusculus_gene_ensembl.chromosome_name_filter
comma:value	comma_sep_probesets:seperator
comma_sep_probesets:concatenated	maxdBrowse_query:GeneNames
concat_kegg_genes:output	split_for_duplicates:string
concat_pathway_lists:output	remove_pathway_nulls:input
create_report:result	merge_reports:stringlist
end_position:value	genes_in_qtl:mmusculus_gene_ensembl.end_filter
gene_descriptions:return	merge_gene_desc:stringlist
genes_in_qtl:mmusculus_gene_ensembl.ensembl_gene_id	mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_gene_id_filter
kegg_pathway_release:value	binfo:db
merge_entrez_genes:concatenated	remove_Nulls:input
merge_ncbi_pathways:concatenated	concat_pathway_lists:string1
merge_probesets:concatenated	remove_nulls_4:input
merge_uniprot_ids:concatenated	REMOVE_NULLS_2:input
merge_uniprot_pathways:concatenated	concat_pathway_lists:string2
mmusculus_gene_ensembl:mmusculus_gene_ensembl.affy_mouse430_2	create_report:affy_Mouse430_2
mmusculus_gene_ensembl:mmusculus_gene_ensembl.affy_mouse430_2	merge_probesets:stringlist
mmusculus_gene_ensembl:mmusculus_gene_ensembl.affy_mouse_430a_2	create_report:affy_Mouse430a_2
mmusculus_gene_ensembl:mmusculus_gene_ensembl.chromosome_name	create_report:chromoName
mmusculus_gene_ensembl:mmusculus_gene_ensembl.end_position	create_report:geneEnd
mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_gene_id	create_report:ensemblGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.ensembl_transcript_id	create_report:ensemblTranscriptId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.entrezgene	create_report:entrezGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.entrezgene	remove_entrez_duplicates:stringlist
mmusculus_gene_ensembl:mmusculus_gene_ensembl.external_gene_id	create_report:externalGeneId
mmusculus_gene_ensembl:mmusculus_gene_ensembl.start_position	create_report:geneStart
mmusculus_gene_ensembl:mmusculus_gene_ensembl.uniprot_swissprot_accession	create_report:uniprotAcc
mmusculus_gene_ensembl:mmusculus_gene_ensembl.uniprot_swissprot_accession	remove_uniprot_duplicates:stringlist
regex_2:value	Split_for_ncbi_pathways:regex
regex_2:value	Split_for_swissprot_pathways:regex
regex_2:value	split_for_duplicates:regex
regex_2:value	split_pathways:regex
regex_2:value	split_probesets:regex
remove_Nulls:output	add_ncbi_to_string:input
remove_duplicate_kegg_genes:strippedlist	gene_descriptions:string
remove_entrez_duplicates:strippedlist	merge_entrez_genes:stringlist
remove_nulls_4:output	add_string_to_probesets:input
remove_pathway_nulls:output	split_pathways:string
Merge_string_list_to_string3:concatenated	merged_ncbi_pathwyas
binfo:return	kegg_pathway_release
getcurrentdatabase:output	ensembl_database_release
maxdBrowse_query:return	probeset_expressions
merge_gene_desc:concatenated	gene_descriptions
merge_genes_and_pathways:concatenated	swissprot_merged_pathways
merge_reports:concatenated	report
remove_duplicate_pathways:strippedlist	pathway_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	Split_for_swissprot_pathways:string
split_gene_ids:output	concat_kegg_genes:string1
split_ncbi_gene_ids:output	Split_for_ncbi_pathways:string
split_ncbi_gene_ids:output	concat_kegg_genes:string2
split_pathways:split	remove_duplicate_pathways:stringlist
split_probesets:split	comma_sep_probesets:stringlist
start_position:value	genes_in_qtl:mmusculus_gene_ensembl.start_filter

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Information Workflow Type

Taverna 1

Information Uploader

Stian Soiland-Reyes

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Stian Soiland-Reyes

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Pathways and Gene annotations for QTL Phenotype annotated

Created by Stian Soiland-Reyes on Tuesday 30 October 2007 13:04:02 (UTC)

Last edited by Stian Soiland-Reyes on Tuesday 04 December 2007 11:18:33 (UTC)

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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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