Workflow Entry: Find Orthologs for proteins in Ensembl

Created at: 03/10/11 @ 14:33:04 Last updated: 03/10/11 @ 14:33:07

Version 1 (of 1)

Version created on: 03/10/11 @ 14:33:04 by: Rafael C. Jimenez | Revision comments Expand

Title: Find Orthologs for proteins in Ensembl

Type: Taverna 2

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Find Orthologs for proteins in Ensembl using biomart.

Option 1:

Authors (1)

Titles (1)

Descriptions (1)

Inputs (4)

Name	Description
ensemblDataset	Ensembl dataset name corresponding to the specie for protein ID. Look for Ensembl dataset names in http://www.biomart.org/biomart/martservice?type=datasets&mart=ensembl
idReference	The reference database for the protein ID. Three options: ensembl, swissprot or trembl
proteinId	Protein identifier
orthologSpecie	Chose in which specie you want to find the orthologs. i.e human, mouse, rabbit, yeast

Processors (1)

Name	Type	Description
findOrthologs	beanshell

Beanshells (1)

Name	Description	Inputs	Outputs
findOrthologs		proteinId ensemblDataset idReference orthologSpecie	esemblId orthologId summary orthologyType homologSubtype homologPercId homologDs homologDn homologPercIdR1

Outputs (9)

Datalinks (13)

Source	Sink
ensemblDataset	findOrthologs:ensemblDataset
idReference	findOrthologs:idReference
proteinId	findOrthologs:proteinId
orthologSpecie	findOrthologs:orthologSpecie
findOrthologs:esemblId	esemblId
findOrthologs:summary	summary
findOrthologs:orthologId	orthologId
findOrthologs:homologDn	homologDn
findOrthologs:homologDs	homologDs
findOrthologs:homologPercId	homologPercId
findOrthologs:homologSubtype	homologSubtype
findOrthologs:orthologyType	orthologyType
findOrthologs:homologPercIdR1	homologPercIdR1