1. EMBL-EBI Industry Programme
Jennifer McDowall
Dominic Clark,
Industry Programme Manager,
30th November 2010, Prague

2. Overview Short overview of EMBL-EBI.
Interaction between EMBL-EBI and industrial companies though Industry Programme & SME Forum.
SME Forum: key factors of interest to the smaller sized companies and how interactions are managed.
Industry Programme: drivers behind company involvement and resulting pre-competitive projects.

3. What is EMBL-EBI?
Based on the Wellcome Trust Genome Campus near Cambridge, UK
Part of the European Molecular Biology Laboratory
Non-profit organisation
But first some background about the EBI. The EBI is based on the Wellcome Trust Genome Campus in Hinxton, which is near Cambridge in UK.
We share the campus with the Sanger Institute and the Wellcome Trust Conference Centre.
The EBI is part of the European Molecular Biology Laboratory and as part of that, we’re a non-profit organisation.
The reason that we are based on the WTGC is that once EMBL had decided that it was necessary to establish a separate outstand to focus on data services, the Wellcome Trust was instrumental in the competitive bidding process along with the UK research councils.

4. EMBL member states
Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands,
Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia
EMBL itself is one of a number of treaty organisations – like CERN in Geneva for example.
It is funded through a number of EMBL member states (signatories) including Spain.
Recently, Australia has joined as an associate member.
All of these countries care about support for industry.

5. The five branches of EMBL
EMBL is a basic research institute funded by public research monies from 20 member states.
1400 staff, over 60 nationalities.
Bioinformatics
Hinxton
Structural biology
Hamburg
Basic research in molecular biology
Administration
EMBO
Heidelberg
Structural biology
Grenoble
Monterotondo
In fact there are a total of five EMBL sites each with their own area of specialisation. The EBI is the second largest of the five EMBL sites; there is the main lab and administrative centre in Heidelberg; structural biology labs in Hamburg and Grenoble; mouse biology in Monterotondo, near Rome. There are around 1,400 staff within EMBL and over 400 of those work at the EBI.
Mouse biology

6. EMBL-EBI’s mission
To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress
To contribute to the advancement of biology through basic investigator-driven research in bioinformatics
To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
To help disseminate cutting-edge technologies to industry
EBI has four elements to its mission and is primarily focussed on service delivery.
The EBI is at the centre of Europe’s efforts to collect, organise and make all types of bio-molecular data available to academic and industry users alike.

7. TODAY: EMBL-EBI’s Mission
Services
Disseminate new technologies to industry
Basic Research
In fact all four elements of the mission co-exist in a number of mutually beneficial ways.
Services support users
Research can lead to service development
Training allows users to extract more value from services and data
And Industry support ensures that industry stakeholders are kept aware of the services and have access to training etc.
Advanced Training 7

8. Databases: molecules to systems
Literature and ontologies
CiteXplore, GO
Genomes
Ensembl Ensembl Genomes EGA
Protein families,
motifs and domains
InterPro
Nucleotide sequence
ENA
Functional genomics
ArrayExpress
Protein structure
PDBe
Protein interactions
IntAct
Pathways
Reactome
Proteomes
UniProt, PRIDE
Chemical entities
ChEBI, ChEMBL
The slide shows the core resources at the EBI .
The EBI is the European centre for the collection and dissemination of biological data; we do this in collaboration with other global centres such as NCBI, the Institute of Genetics in Japan, the Swiss Institute of Bioinformatics and Cold Spring Harbor.
Systems
BioModels

9. Database collaborations
Many of the EBI’s data resources are members of international consortia, Some, such as the International Nucleotide Sequence Collaboration, exchange data on a regular basis; others, such as the UniProt Consortium and the GO Consortium, work together to produce a single resource.
Generally there is a move towards coordination and data exchange and EBI meets annually with NCBI to facilitate this process across a range of key data resources.

10. Standards development – international collaborations
Genomics Standards Consortium (GSC)
Genome annotation
Protein sequence
Nucleotide sequence
HUPO- Proteomics
Standards Initiative (PSI)
Protein structure
Microarray and Gene Expression Data (MGED)
Cheminformatics
Pathways
It id of no surprise therefore that we are involved in international standardisation activities for all these areas.
Systems modelling standards
Metabolomics Standards Initiative (MSI)

11. EMBL-EBI’s mission
To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress
To contribute to the advancement of biology through basic investigator-driven research in bioinformatics
To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
To help disseminate cutting-edge technologies to industry
Let’s now focus on the fourth element of the mission statement .. To help disseminate cutting edge technologies to industry. This raised two questions....[next slide]

12. What Technologies? Bioinformatics resources Literature resources
Cheminformatics resources (ChEBI, CDK)
ChemoGenomics resources (ChEMBL)
Knowledge management technologies and standards …
What Technologies?
In fact although we are called the EBI and bioinformatics is central to what we do, we are not limited to bioinformatics, we have [read list]
In the future we anticipate further initiatives in the medical domain

13. Industry is a broad term
Business Focus
Pharmaceuticals/Drug Discovery
Biotechnology companies
Agriculture and Agrochemicals
The food industry
Diagnostics
Imaging
Livestock breeding
DNA forensics
Microbial genomics
Bioprocessing
Size
Large Multinationals
SMEs
Industry itself is also a broad term
And we should not forget that the stakeholder environment ranges from Small companies (fewer than 250 employees and turnover < 40m Euro per year) to large multinationals.

14. Many to many mapping Life sciences Medicine Agriculture
Genomes
Ensembl ,
Genomes,
EGA
Nucleotide sequence
EMBL -
Bank
Gene expression
ArrayExpress
Proteomes
UniProt
, PRIDE
Protein families,
motifs and domains
InterPro
Protein structure
PDBe
Protein interactions
IntAct
Chemical entities
ChEBI
ChEMBL
Pathways
Reactome
Systems
BioModels
Literature and
ontologies
CitExplore
, GO
Life sciences
Medicine
Agriculture
Pharmaceuticals
Biotechnology
Environment
Bio-fuels
Cosmaceuticals
Neutraceuticals
Consumer products
Personal genomes
Etc…
And clearly there is a many to many mapping between the industry sectors and the data resources.

15. How do we support industry, generically?
Data resources & services freely available to industry stakeholders.
Industry stakeholders may attend all EMBL-EBI training courses on a similar cost basis as academic researchers.
(Restrictions apply to course funded by Wellcome Trust, EMBO and FEBS)
So how do we support industry generally?
With a few exceptions (externally funded courses designed for academics) participation is available on the same basis for industry stakeholders as academic stakeholders, Furthermore our courses are typically costed just to cover the overheads (so typically £50 or so per day). This represents exceptionally good value for money I think you will agree.
Please do have a look through the hands on training link and the more general events page.

16. Why an SME Forum? SMEs important for economies of EMBL member states.
Support for Industry is part of the mission of the EMBL-EBI.
Established annual series of information workshops in different European locations hosted by regional agencies in bio-clusters.
For SMEs we have been running an annual SME forum.

17. How do SMEs benefit?
SMEs are often driven by shorter-term expedients than larger companies.
SMEs benefit most from knowledge dissemination meetings focusing on tools & information resources that are:
freely available in the public domain
can add value to their business processes immediately.
Workshops allow SMEs to hear about data resources, tools and services provided freely by EMBL-EBI & collaborators.
This year there is a major additional focus on tools and data provided the European Patent Office (EPO).

18. Annual Forum for SMEs
These meetings have been initially funded from EU projects coordinated by EMBL-EBI.
In 2008, the forum was held in Berlin.
In 2009, the forum was held in Vienna.
In 2010, it was in Munich, co-hosted by Bio-M & EPO.
We have secured funding for a meeting in We are discussing the venue. Thereafter we hope to fund through a new EU grant application.

19. The Forum Topics
Workshop topics specifically selected on the basis of previous interactions with SMEs and include:
chemogenomics, cheminformatics,
proteomics,
text mining, literature services and analysis,
web services
and patent services providing by EMBL-EBI and the European Patent Office.
This year in addition to the presentations, discussion and networking opportunities, there will also be an opportunity for hands-on tutorials at the EPO offices.

20. Mathias Lamparter BioM Biotech Cluster Development GmbH
This is Mathias Lamparter from Bio-M the regional development agency for Munich introducing the talk.
BioM Biotech Cluster Development GmbH

21. Monday 18th October 2010
12.40
Welcome from BioM Prof. Dr. Horst Domdey, Managing Director, BioM Biotech Cluster Development GmbH
12.50
Meeting Overview (Dominic Clark & Pascal Kahlem, EMBL-EBI)
12.55
Overview of EMBL-EBI data resources and services (Dominic Clark, EMBL-EBI)
13.10
EMBL-EBI Proteomics data resources and services (Rafael Jimenez, EMBL-EBI)
13.40
ENFIN – EnVISION and DAS (Rafael Jimenez, EMBL-EBI)
14.10
Cheminformatics resources and services at EBI (Chris Steinbeck, EMBL-EBI).
14.40
COFFEE BREAK

22. Chris Steinbeck, EMBL-EBI
Chris gave a presentation on EBI cheminformatics resources such as ChEBI and the new metabolomics resource that is being developed (MetaboLights)
Head of Cheminformatics and Matabolism

23. Monday 18th October 2010
15.10
Using Web services in Your Data Analysis Pipeline (Erik Bongcam-Rudloff, U. Uppsala)
15.40
Web Services: The Biocatalogue Project (Eric Nzuobontane, EMBL-EBI)
16.10
ChEMBL databases and tools: Support of target selection and validation (John Overington, EMBL-EBI)
16.40
Short Break
17.00
Presentations from Regional Organisation: Introduced by Mathias Lamparter, BioM.
17.15
Knowledge Management for Scientific Intelligence with BioXM, Klaus Heumann, CEO, Biomax Informatics AG, BioMax Informatics AG, (
17.45
Presentation from Dr. Martin Seifert, Vice President Business Development and Consulting, Genomatix Software GmbH.
18.15
Closing Comments, BioM
18.25
Closing Comments (Dominic Clark & Pascal Kahlem, EMBL-EBI)
18.35
Networking Buffet Supper

24. Dr. Martin Seifert, VP Genomatix
We always include local speakers

25. Noël Campling, EPO Director of Know-How introduces the second day.
Here Noel introduces the second day at the EPO offices in Grasserstr.
Features in the picture are [list names and titles]
Representing EBI: Jennifer McDowall, Johanna McEntyre, Dietrich Rebholz-Schuhmann and Dominic Clark

26. Tuesday 19th October 2010, EPO, room 8661 (Grasserstr 2), Munich.
Time
Item
08.45
COFFEE
09.00
Welcome Noël Campling, Director of Know-How, EPO
Introduction to the second day (Dominic Clark, EMBL-EBI)
09.10
EMBL-EBI Literature Services and Applications (Jo McEntyre, Head of Literature Services, EMBL-EBI)
09.40
EMBL-EBI text mining tools and mapping of targets/pathways to disease (Dietrich Rebholz-Schuhmann, EMBL-EBI)
10.10
EMBL-EBI Patent related services (Jennifer McDowall, EMBL-EBI).
10.35

27. Tuesday 19th October 2010, EPO, room 8661 (Grasserstr 2), Munich
11.00
EPO Services, resources for SMEs and the SLING project (Stephane Nauche, European Patent Office)
11.15
EPO information resources and ( (David Evans, European Patent Office, Munich)
11.45
How the EPO searches prior art in Biotech; and dissemination of knowledge (Titus Vogt, European Patent Office)
12.15
Biotech patentability (Titus Vogt, European Patent Office)
13.00
Wrap up of second morning including Panel Q&A – Pascal Kahlem EMBL-EBI..
13.15
Lunch

28. Hands-on Tutorials (in EPO training rooms 1909 & 1910, Bayerstr 115 “Building no. 7”).
14.30
Workshop A: EMBL-EBI resources (Jennifer McDowall, EMBL-EBI)
Workshop B: EPO resources (David Evans)
15.30
Break
15.45
Workshop A: EPO resources (David Evans)
Workshop B: EMBL-EBI resources (Jennifer McDowall, EMBL-EBI)
16.45
Wind down cocktail & feedback discussion
17.30
Close of day

29. Tutorial on using EBI Patent searching services
Finally we organised some hands on training in two parallel sessions – one on EPO services one on EBI services.
And we included some hands on exercises.

30. Tutorial Contents Workshop A: EMBL-EBI resources (Jennifer McDowall)
Workshop B: EPO resources (David Evans)
How to use public patent database espacenet - ep.espacenet.com/
Patent classification codes (IPC & ECLA) for targeted searching
Interpreting search results; how to "read" a patent
Using espacenet to find collaborators and partners
How to monitor a pending application of interest in Register Plus -
How to use INPADOC to check the status of a patent
Here is a brief overview of the EPO resources. I will tell you more about the EBI resources later.

31. Interests of Industry & academics overlap
Important databases according to sector
Important
Useful
Essential
A question that sometime comes up is: does industry care about the same resources as academia. We tested this in our ELIXIR user survey where we asked respondents to classify themselves as Industry or academic
The very high correlation in the ratings shows that generally industry and academic research care about the same resources:
Literature
Protein sequence
Nucleotide sequences and so on

32. Supporting larger companies through the “Industry Programme”
Industry Programme well established (set up in 1996).
Subscription-funded programme for larger companies.
EMBL-EBI provides:
Specialist workshops
Standards-based activities
Pre-competitive research & development opportunities.
The industry programme was established right at the beginning of the EBI
You can download a brochure if interested

33. Scope of Industry Programme
1. Forum for interaction between EBI and industry users
2. Provide training for our commercial users
3. Inform industrial users of EBI’s status and future plans
4. Feed industry requirements into the EBI’s planning (influencing)
5. Provide neutral meeting place for inter-company interactions on bioinformatics
6. Coordinate workshops – expert speakers (academia & industry)
7. Initiate ‘pre-competitive projects’ at EBI with targeted collaborative funding
8. External liaison with other industry initiatives (Standards initiatives, industry organisations)
There are a number of areas to the scope 33

34. 18 Industry Programme members
Astella Pharma
AstraZeneca
Bayer Schering Pharma
Boehringer Ingelheim
Eli Lilly and Company
F. Hoffmann-La Roche
Galderma
GlaxoSmithKline
Johnson &
Johnson Pharmaceutical Research & Development
Merck Serono
Novo Nordisk
Orion Pharma
Pfizer Ltd
Sanofi-Aventis
Nestlé Research Centre
Syngenta
Unilever
“The Industry Programme’s regular meetings foster inter- company interactions as we collaborate on special projects and liaise on other industry initiatives”
Bertram Weiss, Principle Scientist, Target Discovery, Bayer Schering Pharma
Philips Research
There are current 18 members, 2 have joined recently:
Novo Nordisk and Astellas Pharma Inc of Japan
Of the 18, 14 are Pharma companies and 3 agri-food 34 34

35. Quarterly Strategy Meetings
The Industry Programme members meet on a quarterly basis at the EMBL-EBI to:
Discuss current status and future directions of programme
Update on EMBL-EBI’s activities and strategy
Review progress on pre-competitive initiatives
Review outcomes of workshops
Review priorities for future workshops and pre-competitive research areas
Discuss funding for pre-competitive research areas
The quarterly meetings are the business strategy meetings in which we review and prioritise

36. Precompetitive challenges and opportunities
Pharma R&D faces significant challenges, prompting a shift in funding from early to late stage in order to maintain the rate of drug development.
There are many opportunities for precompetitive activities
Target and Target Pharmacology Space
Drug Safety and Efficacy Space
Knowledge Management Space
Pharmaceutical R&D relevant Infrastructure
The key areas for pre-competitive opportunities are shown here. These overlap with some of the pillars of the IMI

37. Workshops 2010 Feb: Joint OBO Foundry & Pistoia Alliance
March: Therapeutic Applications of Computational Biology and Chemistry
May: Cheminformatics in R
June: Computational Drug Repositioning
Sept: Structural Biology & PDBeMotif
Oct: Ontology Engineering workshop
Nov: Toxicology Ontologies Roadmap
Dec: Chemical Structure Resources
Workshops cover a broad range of topics

38. What happens after workshops
Workshops are either for training or knowledge exchange.
Knowledge exchange workshops  identification & documentation of shared needs among companies that are “pre-competitive”:
Development of standards
Support for data resources in the public domain
Public information integration activities
Development of new services
Projects are made publicly available  sharing benefits
At workshops we assess the interest in pre-competitive projects and develop a position paper of industry drivers and project scope.

39. Pre-competitive initiatives
Disease knowledge, targets, safety, infrastructure
The rationale for pre-competitive projects is summarised in this paper in Nature Reviews Drug Discovery from Sept 2009, written by many people at the industry programme. Essentially, it is driven by the need for the pharmaceutical industry to cut costs by avoiding duplication of effort between companies.
Dutch Medicines Day, October13, 2009 39 39

40. In Summary EMBL-EBI is committed to supporting industry
Provide access to resources & training
For SMEs, organise an annual subsidised forum
To subscribe to the mailing list for information, visit
For larger companies, the Industry Programme promotes pre-competitive projects that benefit all our stakeholders