BioExcel Use case 6: Open PHACTS - leverating integrated pharmacological datasets for cross-domain queries. Presented at: BioExcel All Hands meeting, Schiphol, 2016-04-21 Source: http://slides.com/soilandreyes/2016-04-21-bioexcel-usecase-openphacts/

1. 1
bioexcel.eu
Open PHACTSOpen PHACTS
BioExcel use case #6BioExcel use case #6
Leveraging integrated pharmacological
datasets for cross-domain queries
Stian Soiland-Reyes, University of Manchester
http://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.eu
EINFRA-5-2015 675728
https://slides.com/soilandreyes/2016-04-21-bioexcel-usecase-openphacts/

2. 2
Centre of Excellence for Computational Biomolecular Research
bioexcel.eu
http://www.openphacts.org/
Bringing togetherBringing together pharmacological data resourcespharmacological data resources
in an integrated, interoperable infrastructurein an integrated, interoperable infrastructure
Data sources integrated and linked together
so that you can easily see the relationships
between compounds, targets, pathways,
diseases and tissues.
, , , ,
, , , ,
, ,
ChEBI ChEMBL ChemSpider ConceptWiki
DisGeNET DrugBank FAERS Gene Ontology
neXtProt SureChEMBL, UniProt WikiPathways

3. 3
Centre of Excellence for Computational Biomolecular Research
bioexcel.eu
doi:10.1371/journal.pone.0115460
Get 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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Centre of Excellence for Computational Biomolecular Research
Workflow gap analysisWorkflow gap analysis
Combining private and public data ➟ Tutorials
Local install of Open PHACT ➟ Docker
Testing and comparing different APIs
Integrate third-party tools ➟ Identifier mappings
API changes ➟ Semantic versioning
Lack of flexibility for:
Workflow language, API URLs, Data sources
bioexcel.eu

5. 5
Centre of Excellence for Computational Biomolecular Research
bioexcel.eu
http://commonwl.org/
Common format for bioinformatics tool execution
Community based standards effort
Choose your own workflow engine
Designed for cluster & cloud environments
Designed 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
Rabix
Arvados
Galaxy
Parallel Recipes
Toil
CancerCollaboratory
Airflow (SciDAP)
cwl2script
Apache Taverna

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Centre of Excellence for Computational Biomolecular Research
bioexcel.eu
Apache Taverna
https://taverna.incubator.apache.org/
https://summerofcode.withgoogle.com/
http://www.commonwl.org/
http://www.openphacts.org/
https://www.docker.com/
Tools and
Data Services Registry
https://bio.tools/

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Centre of Excellence for Computational Biomolecular Research
Work so farWork so far
Apache Taverna:
Initiated CWL and Docker support
Open PHACTS:
Docker install
Data distribution of sources
Sure CHEMBL (patent data)
bioexcel.eu

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Centre of Excellence for Computational Biomolecular Research
Future workFuture work
Docker tool for local/remote Open PHACTS API
CWL tool descriptions (workflow building blocks)
Use case 6 workflow as CWL
Configuration of data sources / API
Open PHACTS platform as EGI VM appliance
bioexcel.eu