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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.

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9?size=60x60 Gb Stian Soiland-Reyes

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  1. Find compounds pharmacology and align against target sequences

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



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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...

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Credits: User Hectorj2f

Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
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