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Open PHACTSOpen PHACTSBioExcel use case #6BioExcel use case #6

Leveraging integrated pharmacologicaldatasets for cross-domain queries

Stian Soiland-Reyes, University of Manchesterhttp://orcid.org/0000-0001-9842-9718

@soilandreyes

This work is licensed under a .Creative Commons Attribution 4.0 International License

BioExcel All Hands meeting, Schiphol, 2016-04-21

This work has been done as part of the BioExcel CoE ( ),a project funded by the EC H2020 program, contract number

www.bioexcel.euEINFRA-5-2015 675728

https://slides.com/soilandreyes/2016-04-21-bioexcel-usecase-openphacts/

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http://www.openphacts.org/

Bringing together Bringing together pharmacological data resourcespharmacological data resources

in an integrated, interoperable infrastructurein an integrated, interoperable infrastructure

Data sources integrated and linked togetherso that you can easily see the relationships

between compounds, targets, pathways,diseases and tissues.

, , , ,, , , ,

, ,

ChEBI ChEMBL ChemSpider ConceptWikiDisGeNET DrugBank FAERS Gene Ontology

neXtProt SureChEMBL, UniProt WikiPathways

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doi:10.1371/journal.pone.0115460Get approved drugs from a pathway of interest. This use case is based on a KNIME workflow for Open PHACTS (myexperiment.org/workflows/4292) published in PLOS One (doi:10.1371/journal.pone.0115460.g004). This workflow finds approved drugs that have potent activity against any target in the selected pathway, combining data from ChEMBL and DrugBank through the Open PHACTS platform. This workflow was developed for the KNIME workflow system by Emiliano Cuadrado et al.

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Workflow gap analysisWorkflow gap analysisCombining private and public data ➟ Tutorials

Local install of Open PHACT ➟ DockerTesting and comparing different APIs

Integrate third-party tools ➟ Identifier mappingsAPI changes ➟ Semantic versioning

Lack of flexibility for:

Workflow language, API URLs, Data sources

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http://commonwl.org/

Common format for bioinformatics tool executionCommunity based standards effortChoose your own workflow engineDesigned for cluster & cloud environmentsDesigned for containers (e.g. Docker)

Main focus: command line tools

and ongoing discussions for super computer support

Adapted from Peter Amstutz' Broad Institute CWL meetup 2015-11-13

Implementors:cwltool

RabixArvados

GalaxyParallel Recipes

ToilCancerCollaboratory

Airflow (SciDAP)cwl2script

Apache Taverna

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Apache Tavernahttps://taverna.incubator.apache.org/

https://summerofcode.withgoogle.com/http://www.commonwl.org/

http://www.openphacts.org/

https://www.docker.com/

Tools andData Services Registryhttps://bio.tools/

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Work so farWork so farApache Taverna:

Initiated CWL and Docker support

Open PHACTS:Docker install

Data distribution of sourcesSure CHEMBL (patent data)

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Future workFuture workDocker tool for local/remote Open PHACTS API

CWL tool descriptions (workflow building blocks)Use case 6 workflow as CWL

Configuration of data sources / APIOpen PHACTS platform as EGI VM appliance

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