1. 3rd Annual Forum for SMEs: Meeting Overview
Dominic Clark,
Industry Programme Manager,

2. 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 shares its central four mission objectives with EMBL, although focussed on bioinformatics rather than molecular biology. The EBI is at the centre of Europe’s efforts to collect, organise and make all types biological data available and we do this by providing services so researchers can access and make sense of the information, by being active in bioinformatics research, by providing training and by working closely with industry.

3. What Technologies? Bioinformatics resources Literature resources
Cheminformatics resources (ChEBI, CDK)
ChemoGenomics resources (ChEMBL)
Knowledge management technologies and standards …

4. Databases: molecules to systems
Literature and ontologies
CiteXplore, GO
Genomes
Ensembl Ensembl Genomes EGA
Protein families,
motifs and domains
InterPro
Nucleotide sequence
EMBL-Bank
Microarray & gene expression data
ArrayExpress
Protein structure
ePDB
Protein interactions
IntAct
Pathways
Reactome
Proteomes
UniProt, PRIDE
Chemical entities
ChEBI, ChEMBL
The slide shows the core resources at the EBI mapped on to the same arrow to show the range of data you can access through 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

5. Industry is a broad term
Business Focus
Pharmaceuticals/Drug Discovery
Biotechnology companies
Diagnostics
Imaging
Agriculture and Agrochemicals
Livestock breeding
DNA forensics
Microbial genomics
Bioprocessing
The food industry
Size
Large Multinationals
SMEs

6. How do we SMEs, generically?
All EMBL-EBI data resources and services are freely available to industry stakeholders in the same way as they are freely available to members of the academic research community. They can be searched, downloaded in their entirety etc.
Furthermore, SMEs may attend all EMBL-EBI training courses on a similar cost basis as academic researchers. For details of the current list of courses, see:
We organise workshops to which SMEs are invited:
NextGen Sequencing (29th October 2009)

7. How else do we support SMEs?
For SMEs, we provide an annual information forum at various locations within Europe. This is customised to the particular interests of SMEs.
2007: Hinxton, Cambridge, UK.
2008: Berlin.
2009: Vienna!

8. SME Information Workshop
The workshop will provide the opportunity to introduce the tools and data resources that are available and the opportunities for SMEs to use and integrate these resources in order to derive benefit from the existing and developing infrastructure.
The topics of the workshop have been 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, with whom we collaborate.

9. SME Meeting Agenda, 3rd September 2009
Time
Item
12.00
Registration and refreshments
13.00
Welcome (Nina Sallacz, Technology & Innovation, Austria Wirtschaftsservice)
13.10
Meeting Overview (Dominic Clark, EMBL-EBI)
13.20
Overview of EMBL-EBI data resources and services (Dominic Clark, EMBL-EBI)
13.40
EMBL-EBI Proteomics data resources and services (Henning Hermjakob, EMBL-EBI)
14.10
ChEMBL databases and tools: Support of target selection and validation (John Overington, EMBL-EBI)
14.40
EMBL-EBI text mining tools and mapping of targets/pathways to disease (Dietrich Rebholz-Schuhmann, EMBL-EBI)
15.10
COFFEE BREAK
15.40
Using Web services in Your Data Analysis Pipeline (Erik Bongcam-Rudloff, U. Uppsala)
16.10
The FuncNet platform (Andrew Clegg, UCL)
16.40
ENFIN – Data integration with EnVISION (Henning Hermjakob, EMBL-EBI)
17.10
In-silico Workflows for Biomarker and Target Identification. (Bernd Mayer, Emergentec Biodevelopment GmbH, Vienna).
17.40
Met and Unmet Bioinformatics needs in Targeted Metabolomics. (Klaus M Weinberger, Biocrates Life Sciences AG, Innsbruck).
18.10
Close of first day
18.20
Networking Buffet Supper

10. SME Meeting Agenda 4rd September 2009
09.00
Introduction to the second day & overview of ELIXIR Industry Stakeholders report (Dominic Clark, EMBL-EBI)
09.10
EMBL-EBI Literature Services and Applications (Jo McEntyre, Head of Literature Services, EMBL-EBI)
09.40
EMBL-EBI Patent related services (Jennifer McDowell, EMBL-EBI).
10.10
EPO Services and Resources for SMEs and the FELICS project (Stephane Nauche, European Patent Office)
10.30
Patent Information ( The European Patent Office Open Patent Services Nigel Clarke (European Patent Office, Austria)
11.00
COFFEE
11.30
Patent Information: ( Nigel Clarke (European Patent Office, Austria)
12.00
How the EPO searches prior art in Biotech; European Patent Academy and dissemination of knowledge (Titus Vogt, European Patent Office)
12.30
Cheminformatics resources and services at EBI (Paula de Matos, EMBL-EBI).
12.55
Patent and Licensing Management (Angela Siegling)
13.05
Wrap up and discussion (Pascal Kahlem, EMBL-EBI)
13.20
LUNCH and end of meeting

11. Acknowledgements
The workshop is sponsored by a number of EU projects coordinated by EMBL-EBI that are targeted to provide bioinformatics tools and data resources for European research. These include:
ENFIN NoE
EMBRACE NoE
CALBC project
SLING project (formally FELICS)
ELIXIR project
We would like to thank everyone involved in the preparation of the agenda (Pascal Kahlem, Nina Sallacz, Stéphane Nauche, Holly Edwards)
We would like to thank all the speakers.
We are grateful to AWS (Nina Sallacz and colleagues) for their support and for hosting the meeting.

12. Thank You
Any Questions?