This workflow uses one or more services that
are deprecated as of 31st December 2012
(almost 12 years ago), and may no longer function.
Show details...
Affected service WSDL:
- http://soap.genome.jp/KEGG.wsdl
Details:
KEGG will be moving from a WSDL/SOAP interface to REST. Details of the new REST services can be found here.
Working examples that use the new REST service can be viewed here, here and here.
BioMart_hsapiens_gene_ensembl_variation_Noom_Edit_06_01_2552
Created: 2009-01-06 04:00:51
Last updated: 2009-01-06 04:01:53
No description has been set
Preview
Run
Run this Workflow in the Taverna Workbench...
Workflow Components
Inputs (1)
| Name |
Description |
| rsID |
rs1043502
rs10799658 |
Processors (15)
| Name |
Type |
Description |
| Flatten_Entrez_ID |
local |
|
| REG_Merge_by_C |
stringconstant |
|
| REG_Split_by_C |
stringconstant |
|
| Flatten_list |
local |
|
| Split_EnsemblID |
local |
|
| Remove_dup_ID |
local |
|
| Flatten_Ensembl_report |
local |
|
| Merge_EnsemblID |
local |
|
| Nested_GO_Update |
workflow |
|
| Nested_hsapiens_snp |
workflow |
|
| Nested_Motif |
workflow |
get_motifs_by_gene(string:genes_id, string:db)
Search motifs in the specified gene. The value of 'db' can be 'pfam' for Pfam, 'pspt' for PROSITE pattern, 'pspf' for PROSITE profile or 'all' for all the above.
Return value:
ArrayOfMotifResult
Example:
# Returns the all pfam motifs in the E. coli gene 'b0002'
get_motifs_by_gene('eco:b0002', 'pfam') |
| Nested_EnsemblGeneInformation |
workflow |
|
| Nested_Pathway |
workflow |
|
| Nested_OMIM |
workflow |
Input as the entrez gene ID from NCBI and the out put is the OMIM ID and the OMIM description |
| Nested_Entrez |
workflow |
|
Beanshells (11)
| Name |
Description |
Inputs |
Outputs |
| Make_GO_Report |
|
Bio_ID
Bio_Type
Ensembl_ID
|
report
|
| Merge_infomation |
|
snpID
chr_name
ensemblID
chrom_start
allele
chrom_stand
ensembl_type
validated
peptide_shift
|
hsapien
|
| Create_Motif_Information |
|
motif_id
definition
genes_id
start_position
end_position
score
|
motif_info
|
| Make_hsapiens_report |
|
geneEnsembl_id
gene_des
gene_chr
gene_start
gene_stop
gene_stand
gene_name
entrezGeneID
band
|
ensemblInfo
|
| concat_id_with_URL |
|
id
|
url
|
| Lister |
|
word
|
output
|
| trim_replace |
|
in
|
out
|
| prepare_id_result |
|
id
result
|
id_result
|
| substring |
|
in
|
out
|
| remove_null |
|
in
|
out
|
| Beanshell_scripting_host |
|
entrezid
omimid
|
out
|
Outputs (11)
| Name |
Description |
| Gene_Information |
|
| SNP_Information |
|
| Unique_Ensembl_ID |
|
| Unique_Entrez_ID |
|
| Pathway_Image |
|
| Pathways |
|
| Pathways_Description |
|
| GO_Information_Update |
|
| OMIM_Phenotype |
|
| Mofit_Information |
|
| Entrez_Information |
|
Links (26)
| Source |
Sink |
| Flatten_Entrez_ID:outputlist |
Nested_Motif:Entrez_GeneID |
| Flatten_Entrez_ID:outputlist |
Nested_Pathway:Gene_Id |
| Flatten_list:outputlist |
Merge_EnsemblID:stringlist |
| Merge_EnsemblID:concatenated |
Split_EnsemblID:string |
| Nested_EnsemblGeneInformation:EnsemblGene_Information |
Flatten_Ensembl_report:inputlist |
| Nested_EnsemblGeneInformation:Unique_EntrezID |
Nested_Entrez:Entrez_ID |
| Nested_EnsemblGeneInformation:Unique_EntrezID |
Nested_OMIM:entrezID |
| Nested_Entrez:GeneInformation |
Entrez_Information |
| Nested_GO_Update:GO_Information |
GO_Information_Update |
| Nested_OMIM:OMIM_Phenotype |
OMIM_Phenotype |
| Nested_Pathway:ID_with_PathwayDescriptions |
Pathways_Description |
| Nested_hsapiens_snp:ensemblID |
Flatten_list:inputlist |
| REG_Merge_by_C:value |
Merge_EnsemblID:seperator |
| REG_Split_by_C:value |
Split_EnsemblID:regex |
| Remove_dup_ID:strippedlist |
Nested_EnsemblGeneInformation:ensembleID |
| rsID |
Nested_hsapiens_snp:rsID_in |
| Nested_EnsemblGeneInformation:Unique_EntrezID |
Flatten_Entrez_ID:inputlist |
| Split_EnsemblID:split |
Remove_dup_ID:stringlist |
| Flatten_Ensembl_report:outputlist |
Gene_Information |
| Flatten_Entrez_ID:outputlist |
Unique_Entrez_ID |
| Remove_dup_ID:strippedlist |
Nested_GO_Update:ensemblID |
| Nested_Motif:Motif_Information |
Mofit_Information |
| Nested_Pathway:Pathway_Image |
Pathway_Image |
| Nested_Pathway:Pathways |
Pathways |
| Nested_hsapiens_snp:SNP_Information |
SNP_Information |
| Remove_dup_ID:strippedlist |
Unique_Ensembl_ID |
Uploader
License
All versions of this Workflow are
licensed under:
Version 1
(of 1)
Credits (1)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (0)
None
Featured In Packs (0)
None
Log in to add to one of your Packs
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Statistics
Other workflows that use similar services
(120)
Only the first 2 workflows that use similar services are shown. View all workflows that use these services.
Download Workflow
]
Reviews
(0)
Kasikrit
No comments yet
Log in to make a comment