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