2016-04-21 BioExcel Usecase Open PHACTS
- 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.
- 4. 4 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
- 6. 6 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/
- 7. 7 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
- 8. 8 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