Open PHACTS a sustainable platform for drug discovery using linked data

1. Open PHACTS – experience of
sustainability MIOSS 2016
nick@openphactsfoundation.org
Openphacts.org

2. Open PHACTS Mission:
Integrate Multiple Research
Biomedical Data Resources
Into A Single Open & Free
Access Point
…and make it sustainable in the long term

5. WHAT WE THOUGHT
… or how we thought the world was

6. Literature
PubChem
Genbank
Patents
Databases
Downloads
Data Analysis Data Integration Firewalled Databases
How do pharma companies use public data?

7. How do pharma companies use public data?
Pfizer
AZ
Roche
n

8. P12047
X31045
GB:29384
Andy Law's Third Law
“The number of unique identifiers assigned to an individual is
never less than the number of Institutions involved in the study”
http://bioinformatics.roslin.ac.uk/lawslaws/

9. WHAT WE DID

10. ChEMBL DrugBank
Gene
Ontology
Wikipathways
UniProt
ChemSpider
UMLS
ConceptWiki
ChEBI
TrialTrove
GVKBio
GeneGo
TR
Integrity
“Find me compounds
that inhibit targets in
NFkB pathway
assayed in only
functional assays with
a potency <1 μM”
“What is the
selectivity profile of
known p38 inhibitors?”
“Let me compare
MW, logP and PSA
for known
oxidoreductase
inhibitors”
DisGeNet
neXtProt
ChEMBL
Target Class
ENZYME
FDA adverse
events
SureChEMBL

11. @gray_alasdair Big Data Integration 11

12. Nanopub
Db
VoID
Data Cache
(Virtuoso Triple Store)
Semantic Workflow Engine
Linked Data API (RDF/XML, TTL, JSON)
Domain
Specific
Services
Identity
Resolution
Service
Chemistry
Registration
Normalisation
& Q/C
Identifier
Management
Service
Indexing
CorePlatform
P12374
EC2.43.4
CS4532
“Adenosine
receptor 2a”
VoID
Db
Nanopub
Db
VoID
Db
VoID
Nanopub
VoID
Public Content Commercial
Public Ontologies
User
Annotations
Apps

13. Mappings: Raw
Mappings (Raw)
25,087,328

14. “CUTTING THE GORDIAN KNOT”
What are the problems with licensing we had to address?
– To make the data and software generated by the project usable and reusable
– Multiplicity of unclear or non-standard licenses on original data sources
• ‘Public’ can mean use but not redistribute, use in commercial environment,
• Legal position on use and reuse extremely unclear
• Different issues than just linking to data
– What is the legal status of integrated collections of the above, and of derived knowledge?
– Appropriate software license selection
– Legal clarity for EFPIA and end users
– Approaches for commercial data integration, EFPIA in-house data
AIM: to enable maximum possible dissemination and usability of the integrated data and
architecture generated by the project - with approaches that will be applicable in other
data integration projects
Licensing Challenges

15. Dataset Downloaded Version Licence Triples
Bio Assay Ontology CC-By 10,360
CALOHA 8 Apr 2015 2014-01-22 CC-By-ND 14,552
ChEBI 4 Mar 2015 125 CC-By-SA 1,012,056
ChEMBL 18 Feb 2015 20.0 CC-By-SA 445,732,880
ConceptWiki 12 Dec 2013 CC-By-SA 4,331,760
DisGeNET 31 Mar 2015 2.1.0 ODbL 15,011,136
Disease Ontology 2015-05-21 CC-By 188,062
DrugBank 19 Feb 2015 4.1 Non-commercial 4,028,767
ENZYME 2015_11 CC-By-ND 61,467
FDA Adverse Events 9 Jul 2012 CC0 13,557,070
Example Data Licenses

16. Handling
private data
securely in
the cloud

17. WHERE DID THAT GET US?

18. DELIVERY UPDATE
Regular data updates as the core data refreshes
API updates aligned to new business questions and
changes
Workstreams to add further new data – see later
New release May 2016 2.1
– SureChEMBL and Pathways update
Further updates planned for summer 2016

19. Usage
>500 million queries

20. Public
Data
Open PHACTS Evolution - Platform
Public
Data
Private
Data
Public
Data
VM VM
Public
Data
Commercial
Data
• Security Audited
Hosted platform
• Platform sustainability

21. Open PHACTS Expanding EcoSystem
Further
Apps
Explorer

23. Workshops
Researchathons
Further planned

24. WHAT IT FEELS LIKE NOW
… or how it really is

25. Sustaining Impact
“Software is free like
puppies are free -
they both need
money for
maintenance”
…and more resource
for future
development

26. Kick-Starting Sustainability
Collaboration
Grants
Industry
Open PHACTS APIUsers
Apps
API

28. Open PHACTS Foundation Routes to Access
Access Route Open API
services
Unlimited API
services
Unlimited API,
RDF and Link
sets
Open PHACTS
Virtual Machine
Full OPF
Member ✓ ✓ ✓ ✓
Licensor/
Reseller*
✓ ✓ ✓
Licensor (Own
Use)
✓ ✓ ✓
High volume
API Licensor
✓ ✓
Open Access
API Consumer
✓
Open Data Non-
commercial
✓ **
*3rd parties must have own agreement with OPF
** talk to us for collaborative proposals – non commercial use

29. Open PHACTS Foundation
engaged in the following projects
……

30. Come and collaborate
New projects
Improve our code and
services
Open Innovation
projects
Webinars
New ideas for data
services and
workflows

31. info@openphactsfoundation.org @Open_PHACTS
Open PHACTS Practical Semantics
Acknowledgements
GlaxoSmithKline – Coordinator
Universität Wien – Managing entity
Technical University of Denmark
University of Hamburg, Center for
Bioinformatics
BioSolveIT GmBH
Consorci Mar Parc de Salut de Barcelona
Leiden University Medical Centre
Royal Society of Chemistry
Vrije Universiteit Amsterdam
Novartis
Merck Serono
H. Lundbeck A/S
Eli Lilly
Netherlands Bioinformatics Centre
Swiss Institute of Bioinformatics
ConnectedDiscovery
EMBL-European Bioinformatics Institute
Janssen Esteve Almirall
OpenLink Scibite
The Open PHACTS Foundation
Spanish National Cancer Research Centre
University of Manchester
Maastricht University
Aqnowledge
University of Santiago de Compostela
Rheinische Friedrich-Wilhelms-Universität
Bonn
AstraZeneca
Pfizer

32. Questions/Discussions
Moving from Project to Foundation – What
are the expectations?
How best to show the value of platform/API?
What would you expect from sustainability?
What can we do differently?
How to best get contributors involved?
Thanks