About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
EBI PICR, find cross-references for protein accessions

Workflow Entry: EBI PICR, find cross-references for protein accessions

Created at: 18/05/11 @ 09:36:26 Last updated: 29/05/11 @ 17:35:20

Version 2 (latest) (of 2)

Version created on: 29/05/11 @ 17:35:18 by: Rafael C. Jimenez | Revision comments Expand

Title: EBI PICR, find cross-references for protein accessions

Type: Taverna 2

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

Download

Download Workflow File/Package (T2FLOW)

Download Workflow as a Galaxy tool

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/2126/download?version=2
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (4)

Name	Description
Protein_accessions	Input a list (comma-separated values) of protein accessions
searchDatabases	Which databases do you want the cross-references for? You can add more than one. You can get a list of databases available in PICR using the method "getMappedDatabaseNames" from the same PICR service or looking at this document http://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do
onlyActive	Do you just want accession that are active (no-deprecated)? … write down "true" or "false". If you do not specify this parameter the workflow will not work.
taxonId	Create a new value and leave it empty if you do not want to filter by specie. Chose a Taxa Id if you want to limit by specie … http://www.uniprot.org/taxonomy/?query=*

Processors (8)

Name	Type	Description
getUPIForAccession	wsdl	See the Service entry for this web service.
getUPIForAccession_input	xmlsplitter
getUPIForAccession_output	xmlsplitter
getUPIForAccession_getUPIForAccessionReturn	xmlsplitter
getUPIForAccessionReturn_identicalCrossReferences	xmlsplitter
build_mapping_table	beanshell
split_string	localworker
regex_value	stringconstant

Beanshells (1)

Name	Description	Inputs	Outputs
build_mapping_table		originalAccs crossReferenceAccs databaseNames taxonIds accessionVersions	results

Outputs (1)

Name	Description
mapping_table

Datalinks (16)

Source	Sink
getUPIForAccession_input:output	getUPIForAccession:parameters
searchDatabases	getUPIForAccession_input:searchDatabases
onlyActive	getUPIForAccession_input:onlyActive
taxonId	getUPIForAccession_input:taxonId
split_string:split	getUPIForAccession_input:accession
getUPIForAccession:parameters	getUPIForAccession_output:input
getUPIForAccession_output:getUPIForAccessionReturn	getUPIForAccession_getUPIForAccessionReturn:input
getUPIForAccession_getUPIForAccessionReturn:identicalCrossReferences	getUPIForAccessionReturn_identicalCrossReferences:input
getUPIForAccessionReturn_identicalCrossReferences:accession	build_mapping_table:crossReferenceAccs
getUPIForAccessionReturn_identicalCrossReferences:databaseName	build_mapping_table:databaseNames
getUPIForAccessionReturn_identicalCrossReferences:accessionVersion	build_mapping_table:accessionVersions
getUPIForAccessionReturn_identicalCrossReferences:taxonId	build_mapping_table:taxonIds
split_string:split	build_mapping_table:originalAccs
regex_value:value	split_string:regex
Protein_accessions	split_string:string
build_mapping_table:results	mapping_table

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Rafael C. Jimenez

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Rafael C. Jimenez

Information Attributions (0)

(Workflows/Files)

None

Information Tags (5)

Original Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (2)

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

96 viewings

256 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - EBI PICR, find cross-references for protein accessions

Created on: Wednesday 18 May 2011 @ 09:36:26 (GMT)

Created by: Rafael C. Jimenez

Revision comments:

None

Latest Version:
[2] - EBI PICR, find cross-references for protein accessions

Created on: Sunday 29 May 2011 @ 17:35:18 (GMT)

Created by: Rafael C. Jimenez

Revision comments:

None

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 (8)

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

Taverna 2

Original Uploader

Rafael C. Jimenez

Get homologous from NCBI homoloGene using one UniProt accession (v1)

Created: 14/10/11 @ 17:26:32 | Last updated: 14/10/11 @ 17:26:28

Credits: Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get homologous from NCBI homoloGene for one UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 18 times | Downloaded: 4 times

Tags (3):