Current projects

1. Pistoia Alliance HELM Project
Setting the Standard for Biomolecular Data Exchange
18th October 2016
Sergio H. Rotstein, Ph.D.

2. ©PistoiaAlliance
G
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One-Minute Introduction
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Small Molecules SequencesBiomolecules
Small Molecule Tools Sequence-Based Tools
The representation language and
toolkit that remediate this gap
:

3. ©PistoiaAlliance
Main Goal: The HELM Ecosystem
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R&D Organizations
Software Vendors
Content ProvidersService Providers
Regulatory Agencies
• BMS
• GSK
• Ionis
• Merck
• Novartis
• Pfizer
• Roche
• ACD/Labs
• Arxspan
• Biochemfusion
• BioMax
• Biovia
• ChemAxon
• NextMove
• PerkinElmer
• Scilligence
• EBI (ChEMBL)
• NCBI (PubChem)
• quattro
• FDA
• (IDMP / ISO 11238)

4. ©PistoiaAlliance
Supporting Goal: Improve “Adoptability”
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• Removal of barriers to adoption
– Completed
• Biomolecular ambiguity representation
– Increased variety of entity complexities supported
• Improved architecture
– More service-oriented
– Easier to integrate into desired infrastructure
– Underway
• Implementation of a web-based HELM editor
– Enables integration into web-only portfolios
– Coalesces functionality of HELM Editor and HELM / Roche
Antibody Editor and supports ambiguity
• Elimination of dependency on commercial libraries
– No licensing required to adopt, modify, etc.
• Public monomer repository
– Currently hosted by Ionis, seeking alternatives

5. ©PistoiaAlliance
What’s Next?
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• Project will finish end of this year or early 2017
• Team is exploring continuity mechanisms
– All input welcome!

6. ©PistoiaAlliance
Acknowledgements
Pfizer Team
• Peter Henstock
• David Klatte
• Christine Lawrence
• Frank Loganzo
• Hongli Li
• Sergio Rotstein
• Simone Sciabola
• Rob Stanton
• Nathan Tumey
• Simon Xi
• Tianhong Zhang
Leadership
• Sergio Rotstein (Pfizer) – Project Lead
• Claire Bellamy (Pistoia Alliance) – Project Manager
Active Team
• Dennis Hanssen (Roche)
• Stefan Klostermann (Roche)
• Roland Knispel (ChemAxon)
• Jeff Milton (Ionis)
• Sven Neumeyer (Novartis)
• Matthias Nolte (BMS)
• Yohann Potier (Novartis)
• Eric Swayze (Ionis)
• Markus Weisser (quattro)
• Tianhong Zhang (Pfizer)
Steering Committee
• Margret Assfalg (Roche)
• Ramesh Durvasula (BMS)
• Leah O'Brien (GSK)
• Sergio Rotstein (Pfizer)
• Eric Swayze (Ionis)
• Chris Waller (Merck)
• John Wise (Pistoia Alliance)
• Quan Yang (Novartis)
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7. ©PistoiaAlliance
www.OpenHelm.org
info@openhelm.org
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8. 18 October, 2016
Chemical Safety Library Project
Sharing Reaction Safety Data Amongst the
Chemistry Community
Pistoia Alliance US Conference, Boston MA, October 18, 2016
Mark Manfredi - BMS

9. ©PistoiaAlliance
Chemical Safety Library (CSL)
Project Rationale

10. ©PistoiaAlliance
Chemical Safety Library (CSL)
Progress
 $$$
 Teams Formed
 Charter
 Data
 Requirements
 RFP
 Vendor Selection
Next Steps
 Tool
 Develop
 Test
 Deploy
 Generate broad
community interest
 Monitor
 Phase 2 options
 Hand off
 Join with academic org
 Develop tool further
 End project

11. ©PistoiaAlliance
How you can get involved!!!

12. info@pistoiaalliance.org @pistoiaalliance www.pistoiaalliance.org
Thank you Pistoia, contributors and all participating team
members!!!

13. October 18, 2016
Ontologies Mapping Project
Pistoia Alliance Conference in Boston
18th October 2016
Martin Romacker (Roche) on behalf of the Project Team

14. ©PistoiaAlliance
The Ontologies Mapping Challenge
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• Ontologies can include hierarchical relationships;
taxonomies; classifications and vocabularies
• They underpin numerous applications such as
semantic search, linked data integration and text
mining
• Ontologies are the “smart glue” of linked data to
semantically enable knowledge management
BUT…
• Many varying ontologies overlap in the same data
domain e.g. disease and phenotype
• Need better practice, tools and services to manage
ontologies and how they map to each other
=> The Ontologies Mapping Project

15. ©PistoiaAlliance
Project Timeline and Deliverables
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1) Ontologies
domain selected
as “test case”
2Q 3Q
2015
4Q
4) Evaluate & select existing
Ontologies Mapping tool(s) 5)
Requirements for an
Ontologies Mapping service
6) Understand the demand for an
Ontologies Mapping service
1Q 2Q
2016
4Q3Q
2) Guidelines for minimal
standards & best practices
3) Requirements for Ontologies
Mapping tool
Funded by GSK, Merck & Co, Novartis, Roche and BIOVIA 3DS

16. ©PistoiaAlliance
Ontologies Guidelines for Best Practice
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Guidelines Positive measures
1. Format Open standards followed
2. URIs Used and persistent
3. Versioning Used with date
4. Documentation High quality and coverage
5. Users Evidence beyond provider
6. Authority locus Clearly defined
7. Maintenance Evidence of currency and sustainability
8. License Clearly defined terms and conditions
9. Content delineation Clear delineation of content
10. Content coverage Acceptable* - tested through relevant sampling
11. Content quality Acceptable* - tested through relevant sampling
12. Textual definitions Acceptable* - tested through relevant sampling
13. Naming conventions Acceptable* - tested through relevant sampling
14. Relations Clear model applied consistently
15. Conserved URIs Cross references to source URIs for external ontologies
*for user requirements

17. ©PistoiaAlliance
Adoption of the Ontologies Guidelines
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• Guidelines are widely applicable to “health check”
any ontology in the Life Sciences and beyond
– A desirable preparation for ontology mapping
• Promote adoption through:-
– Guidelines conform to the FAIR principles
• Findable and Accessible (public wiki)
• Interoperable and Re-usable (aligned to OBO etc.)
– Endorsed by external groups:-
• Interoperable Services at ELIXIR
• Molecular Archival Resources at EMBL-EBI
• Ontologies Mapping Project Community of Interest
– Visibility at conferences/workshops:-
• EMBL-EBI Industry Partners: March 2016
• ISMB 2016: July
• ECCB 2016: September
• Industry Semantic Forum at Roche: September 2016
• OM 2016 and ISWC 2016: October

18. ©PistoiaAlliance
Mapping Tool Requirements: Overview
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User Interface
• Visualisation of
ontological space
• Mapping
Alignment Editor
Framework
• Workflow and
Evaluation
• Ontology Matching
algorithms
API
Ontologies Mapping Tool
Import Mappings
Export Mappings
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1 2
=> Detailed Requirements documentDetailed requirements are available on the OM project public wiki:-
https://pistoiaalliance.atlassian.net/wiki/display/PUB/Ontologies+Mapping+Resources

19. ©PistoiaAlliance
Evaluate Tools, Define Service and
Publicity
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• Evaluation of existing OM tools through an RFI process
– 7 tool providers submitted responses, 4 academic & 3 commercial
– Evaluation found that top academic and commercial tools meet
>80% of our requirements
• Requirements and demand for an OM service
– Includes a draft service level agreement
– On-line questionnaire to determine the demand for an OM service
among the Pistoia Alliance members and Community of Interest
• Consider the options for an OM service, beyond Phase 2
– E.g. An RFP process to evaluate and select a service provider
• Conferences and Publicity
– Sponsor Ontology Matching (OM-2016) at ISWC 2016
– Presentations/posters at high impact conferences and workshops:
e.g. ECCB 2016 (Sept) and ISWC 2016 (Oct)
– Target a wider audience through publication in journals,
newsletters, blogs and other media channels

20. ©PistoiaAlliance
Summary
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1. The Ontologies Mapping (OM) challenge and establishing the project
2. The Ontologies Guidelines for Best Practice and “check list” is
accessible on a public wiki
– Widely applicable to any ontology in the Life Sciences and beyond
– Endorsed by external bodies e.g. ELIXIR and EMBL-EBI
3. Evaluation of existing OM tools through an RFI process
– Two tools (academic and commercial) meet >80% of our requirements
– The tool alignments show similar recall performance in the alignment tasks
4. Requirements and demand for an OM service to complete Phase 2
– Includes a draft Service Level Agreement (SLA)
– On-line questionnaire to determine the demand for a service among the Pistoia
Alliance members and the Community of Interest
5. Consider the options for an OM service, beyond Phase 2
– E.g. An RFP process to evaluate and select a service provider
6. Conferences and Publicity
– Sponsor Ontologies Matching (OM-2016) tasks to align phenotype ontologies
– Presentations and posters at high impact conferences and workshops: EMBL-EBI
workshops; ISMB 2016, ECCB 2016 and ISWC 2016

21. ©PistoiaAlliance
Acknowledgements
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Funders
• BIOVIA 3DS
• GSK
• Merck & Co
• Novartis
• Roche
Pistoia Operations
• Richard Holland
• John Wise
• Carmen Nitsche
• Nick Lynch
Project team
• Ian Harrow (Pistoia Project Manager)
• Martin Romacker (Roche)
• Andrea Splendiani (Novartis)
• Stefan Negru (Merck & Co)
• Peter Woollard (GSK)
• Scott Markel (BIOVIA)
• Martin Koch (Osthus)
• Heiner Oberkampf (Osthus)
• Yasmin Alam-Faruque (Eagle Genomics)
• Erfan Younesi (Bayer)
• James Malone (FactBio)
Community of Interest

22. ©PistoiaAlliance
info@pistoiaalliance.org @pistoiaalliance www.pistoiaalliance.org
Thank you for your attention

23. Pistoia Alliance CSCS Expert
Community
18th October 2016
Domain Lead – Zofia Jordan - GSK
Project manager – Claire Bellamy

24. ©PistoiaAlliance
CSCS Expert Community
Aim
Create an industry-leading Controlled Substance
Compliance Services Expert Community.
Goal of the Expert Community
To improve the understanding and interpretation of
controlled substance legislation around the world.
http://www.cscs-experts.org
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25. ©PistoiaAlliance
CSCS Expert Community
• Zofia Jordan of GSK is community lead
• Members include:
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AZ
Bayer
Binocular Vision
ChemAxon
Dotmatics
Genetech
GSK
KWS
J&J
Merck
Millipore Sigma
Novartis
Roche
Pfizer
Science for solutions
Scitegrity

26. ©PistoiaAlliance
CSCS Expert Community
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Enhancing best practice – monthly meetings
Feasibility Studies
Regulator Watch
Discussion
de-minimis exemption
Guest speakers
Wiki materials
Nagoya protocol
share best practice
Spin off

27. ©PistoiaAlliance
De-minimis exemption
• At present all controlled substances are subject to
the same regulations no matter how small the
sample.
• Many research samples are extremely small,
containing less than 10mmoles, well below any
therapeutic dose.
• The group is putting together a case for small
quantities to be exempted from the regulations.
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CSCS Expert Community

28. ©PistoiaAlliance
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CSCS Expert Community
Regulator watch
• HR 3537
• US customs ACE/ITDS Working Group
• UK Psychoactive Substances Bill
• UK Misuse of Drugs Act (Amendment) Order 2016
Activities
• Alerted members so they contributed to the consultation on HR 3537
• Members involved with ACE/ITDS working group when it was operational.
• Engagement with UK Home Office on psychoactive substances bill.
• Approaches to UK Home Office about the amendment order.

29. ©PistoiaAlliance
CSCS Expert Community
Discussions and External speaker programme
• Harmonised Tariff System coding
• External speaker on a third party system
• Nagoya
• External speaker from Aberdeen University and Abs-int
• This month - Guidelines regulating synthetic double stranded DNA
• External speaker from IGSC
• Coming soon – shipping experts on import/export issues
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30. ©PistoiaAlliance
CSCS Expert Community
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An industry-leading Controlled Substance Compliance
Services Expert Community.
http://www.cscs-experts.org

31. ©PistoiaAlliance
Antibodies in the PDB
Problem Statement: Predictive methods in antibody research are hampered
by the limited number and diversity of antibody crystal structures in the PDB
and accompanying data.
• Can tackle by soliciting post-competitive data and commissioning new
representative examples.
Antibodies

32. ©PistoiaAlliance
Antibodies in the PDB
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• Status
– Business case available on
IP3
– Fundraising has begun
– Publicity
• Participated in EMBL/EBI
Antibody workshop
• Publicized with ACS
Pharma Leaders group
• Presented project at ACS
and BioIT
• Building ties with PDB, D3R
project, SGC
– PM recruitment underway
– 2 companies so far have
pledged to submit
post/non-competitive
samples
• Next steps
– Looking for PM to manage
team and solicit samples
– Fundraise
• $50K invoiced
• Need $160K total; another
$25K to start
• If this is of interest to you:
– Recommend PM
– Join the project team
– Submit post-competitive
samples
– Make a $ pledge
Antibodies