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Open Targets: Mining gene and disease associations for improved drug target identification
Part of EMBL-EBI webinar seriesOctober 18th 2017
The logistics for the next hour
•
• switch to desktop version
• ‘Materials’ section: presentation.pdf
• muted
• Take questions at the end: look for the chat box!
• Evaluation survey
Chat box
Please enter any questions into this box
Address chat to ‘Everyone’
What is the Open Targets Platform?
How to navigate the Platform?
Goals
What is the Open TargetsConsortium?
Outline
• Introduction
• Live demos
• Wrap up
Outline
• Introduction
• Live demos
• Wrap up
Drug discovery path: timeline
Source: doi:10.1038/nrd1470
Lengthy, costly, low success rate, HIGH ATTRITION RATES
Drug discovery: the challenges
Our Vision
A partnership to transform drug discovery through the systematic identification and
prioritisation of targets
Causal links between
targets and disease
Support data driven prioritisation
decision making Share tools
and methods for
target ID
Change attrition rates of industry pipelines
Publish high impact
science, and openly share our
data
World leader for human target discovery
Two major areas of work in Open Targets
Core bioinformatics pipelines
www.opentargets.org/projects
Experimental projects
Integration of available dataWeb interface
REST API Data dumps
Generate new evidenceCRISPR/Cas9
Organoids and IPS cells(cellular models for disease)
Concurrent
Core bioinformatics pipelines
www.opentargets.org/projects
Experimental projects
Concurrent
Two major areas of work in Open Targets
Generate new evidenceCRISPR/Cas9
Organoids and IPS cells(cellular models for disease)
Integration of available dataWeb interface
REST API Data dumps
Open Targets Platform*
• Developed by the Core team at EMBL-EBI
• To allow users to identify target and disease associations
• Improvements driven by you
* First release: December 2015
Experimental Factor Ontology (EFO)
• Ontology: dictionary of relationships between entities
• EFO: way to organise experimental variables (e.g. diseases)
Promotes consistencyIncreases the richness of annotationAllow for easier and automatic integration
controlled vocabulary +
hierarchy (relationship)
Evidence model
Original sources à more being added
Evidence from publicly available data
targetvalidation.org/data_sources
Data integration
Data generation
OncologyImmunology
Neurodegeneration
OpenTargets Platform
Present and Future
Generated as we speak
EVA!
UniProt!
Gene2Phenotype!
GWAS catalog!
Cancer Gene Census!
EVA (somatic)!
IntOGen!
ChEMBL!
Reactome!
Expression Atlas!
Europe PMC!
PhenoDigm!!
Genetic associations!
Somatic mutations!
RNA expression!
Animal models!
Affected pathways!
Text mining!
Drugs!
*1.0!
*1.0!
*1.0!
*1.0!
*0.5!
*1.0!
*1.0!
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*0.2!
*1.0!
*0.2!
*1.0!
Association!
S1 + S2/22 + S3/32 + S4/42 + Si/i2
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Genomics England!
PhEWAS catalog!*1.0!
*1.0!ΣH
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How do we score the associations?
Calculated at 4 levels:
• Evidence• Data source• Data type• Overall
Score: 0 to 1 (max)
weight factor
Aggregation with (harmonic sum)
ΣHNote: Each data set has
its own scoring and ranking scheme
Outline
• Introduction
• Live demos
• Wrap up
Which targets are associated with a disease?
https://www.targetvalidation.org/
Demo 1: Disease centric workflow
*Supported ones: Internet Explorer 11 (and above), Chrome, Firefox and Safari
Choose your favourite internet browser*
What is the evidence for the association between CD86
and multiple sclerosis?
https://www.targetvalidation.org/evidence/ENSG00000114013/EFO_0003885
Demo 2: Evidence for an association
Target profile page
Disease profile page
We have a list of 26 possible targets for IBD (inflammatory
bowel disease).
https://www.targetvalidation.org/batch-search
Demo 3: Several targets at once
Are these targets represented in other diseases?
Which pathways are represented in this set of
targets?
Alternative ways to access the data
Outline
• Introduction
• Live demos
• Wrap up
DataGenera)on
Therapeu)cHypothesis
PublicData
DataIntegra)on
targetvalidation.org
Experimental Projects Bioinformatic Projects
Wrap up
For drug target ID and selection in drug discoveryRank target and disease associations: different sourcesIntegrated information on target and diseases
Intuitive graphical web interface
June 2017 release
26Ktargets
9.1Kdiseases
2.8 Massociations
5.3 Mevidence
Open Targets Platform
We support decision-makingWhich targets are associated with a
disease?
Are there FDA drugs for this association?
…
Can I find out about the mechanisms of the
disease?
How to cite us
http://nar.oxfordjournals.org/content/45/D1/D985.long
http
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narb
reak
thro
ugh.
com
/
Acknowledgements
blog.opentargets.org/
@targetvalidate
www.facebook.com/OpenTargets/
http://tinyurl.com/opentargets-in
Support, dissemination, video tutorials
http://imgur.com/a/JIDCPhttp://imgur.com/a/LKDhp
https://vimeo.com/233638392
Upcoming EMBL-EBI webinarshttp://www.ebi.ac.uk/training/webinars
Chat box
Address chat to ‘Everyone’
Please enter any questions into this box