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

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
https://www.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 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

 

Citations (0)

None


Version History

In chronological order:



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.


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

Uploader

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