1. Home
  2. Workflows
  3. Find compounds pharmacology and align against target sequences

Find compounds pharmacology and align against target sequences

Created: 2013-10-16 14:12:06

Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any.

Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369.

Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors.

Until there is a Local worker to filter out Errors, the best way to view only the results is to manually select "View results" for each output port - after the workflow run has finished. Note that some of the ports have XML outputs.

Information Preview

Medium

Download as scalable diagram (SVG)

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3860/download?version=1
[ More InfoExpand ]


Information Workflow Components

Information Authors (1)
Information Titles (1)
Information Descriptions (1)
Information Dependencies (0)
Inputs (1)
Processors (12)
Beanshells (0)
Outputs (11)
Datalinks (27)
Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

9?size=60x60 Gb Stian Soiland-Reyes

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (2)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

Information Tags (8)

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (1)

(Workflows/Files)

Information Favourited By (0)

No one

Information Statistics

1972 viewings

1386 downloads

[ see breakdown ]

More
 

Citations (0)

None


Version History

In chronological order:

  1. Find compounds pharmacology and align against target sequences

    Created by Stian Soiland-Reyes on Wednesday 16 October 2013 14:12:05 (UTC)



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (14)

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


Taverna 2
Uploader
394?size=60x60 Gb Hamish McWilliam

Workflow EMBL-EBI ClustalW2 (SOAP) (1)

Thumb
Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).

Created: 2010-12-06 | Last updated: 2013-03-28

Attributions: Workflow EBI_ClustalW2

Taverna 2
Uploader
2324?size=60x60 Hectorj2f

Workflow Blast Report from ID (1)

Thumb
This workflow retrieves a fasta sequence or blast report from an id. Firstly, given some inputs (e.g. ids:EDL10223.1, format:fasta, style:default and db:emblcds), it returns the sequence in fasta format associated to those inputs using the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). Next, we obtain a Blast report from this fasta sequence and some others parameters. The final result in that case corresponds with the same fasta sequence introduced...

Created: 2011-04-07 | Last updated: 2011-04-07

Credits: User Hectorj2f

Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
About | Privacy | Publications | Contact / Feedback | Mailing List
Icons: Silk icon set 1.3

Copyright © 2007 – 2018 The University of Manchester and University of Southampton