1 introduction to_the_ebi_(katrina_pavelin)

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The EMBL-EBI is a non-profit bioinformatics research and service institute that is part of the European Molecular Biology Laboratory. It has over 1500 staff from more than 60 nationalities working across its five branches. EMBL-EBI provides freely available data and bioinformatics services to support scientific research and discovery. Its mission is to advance biology through both basic investigator-driven bioinformatics research and by providing advanced training and cutting-edge technologies to scientists and industry.

Technology Education

The European Bioinformatics Institute

EMBL-EBI
Katrina Pavelin
Scientific Outreach Officer
Services | Research | Training | Industry
katrina@ebi.ac.uk

What is EMBL-EBI?

• Bioinformatics Research & Service Institute
• Non-profit organisation
• Part of the European Molecular Biology Laboratory

EMBL-EBI

The five branches of EMBL
Heidelberg Hamburg Hinxton

• Basic research in Structural biology Bioinformatics
molecular biology
• Administration Grenoble Monterotondo
• EMBO

• 1500 staff
• >60 nationalities
Structural biology Mouse biology

EMBL-EBI

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
• To coordinate biological data provision across Europe

EMBL-EBI

What is bioinformatics?
• The science of storing,
retrieving and Growth of raw storage
analysing large at EMBL-EBI (in terabytes)
amounts of biological 12000

information 10000

8000
• An interdisciplinary

Disks (TB)
6000
science, involving
4000
biologists, computer
scientists and 2000

mathematicians 0

• At the heart of modern Year

biology

EMBL-EBI

Services
www.ebi.ac.uk/services

EMBL-EBI

Services | Research | Training | Industry

Databases: molecules to systems Literature and ontologies
Genomes UKPMC, CiteXplore, GO
Ensembl
Ensembl Genomes Protein families,
EGA motifs and domains
Metagenomics InterPro
portal Functional
genomics
Macromolecular
ArrayExpress
Nucleotide sequence structure
Expression Atlas
ENA PDBe

Protein activity
IntAct, PRIDE Pathways
Reactome
Protein Sequences
UniProt

Chemical entities
ChEBI
Systems
Chemogenomics BioModels
ChEMBL BioSamples

EMBL-EBI

EBI’s search service
Access from the
EBI’s homepage

Species selector
allows for easy
comparison

Data organised
according to:
• gene Explore data,
• expression return easily to
• protein your results
• structure
• literature

EMBL-EBI

Research
www.ebi.ac.uk/groups

EMBL-EBI

Services | Research | Training | Industry

Key facts about research at EMBL-EBI
• A unique
environment for
bioinformatics
research
• Nine dedicated
research groups
• Services teams also
carry out R&D
• Research and
services are mutually
supportive

EMBL-EBI

Training
www.ebi.ac.uk/training

EMBL-EBI

Services | Research | Training | Industry

Pre- and postdocs at EMBL-EBI

• EMBL International PhD Programme
• Postdoctoral fellowships:
• EIPOD – EMBL-sponsored interdisciplinary fellowships
• ESPOD – EBI–Sanger combined experimental and
computational fellowships

EMBL-EBI

NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!

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Event: Plant and Animal Genomes Conference 2012 Speaker: Cath Brooksbank Train online (www.ebi.ac.uk/training/online/) is a free, web-based learning resource for life scientists. Train online helps you make the most of the huge amount of biological data that EMBL-EBI makes publicly available for the research community. Using a combination of tutorials, guided examples, exercises and quizzes, Train online guides you towards becoming a confident user of open-access data resources. This training portal is there for you to learn in your own time and at your own pace, anywhere in the world. You do not need previous experience in bioinformatics to benefit from our courses. This presentation will provide a short introduction to the courses currently available in Train online, which will include a demonstration of the resource. After the demonstration, the speaker will welcome questions about Train online and any suggestions that you may have for future courses.

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Ontologies and Semantic Web technologies play an important role in the life sciences to help make data more interoperable and reusable. There are now many publicly available ontologies that enable biologists to describe everything from gene function through to animal physiology and disease. Various efforts such as the Open Biomedical Ontologies (OBO) foundry provide central registries for biomedical ontologies and ensure they remain interoperable through a set of common shared development principles. At EMBL-EBI we contribute to the development of biomedical ontologies and make extensive use of them in the annotation of public datasets. Biological data typically comes with rich and often complex metadata, so the ontologies provide a standard way to capture “what the data is about” and gives us hooks to connect to more data about similar things. These ontology annotations have been put to good use in a number of large-scale data integration efforts and there’s an increasing recognition of the need for ontologies in making data FAIR (Findable, Accessible, Interoperable and Reusable). EMBL-EBI build a number of integrative data platforms where ontologies are at the core of our domain models. One example is the Open Targets platform, where data about disease from 18 different databases can be aggregated and grouped based on therapeutic areas in the ontology and used to identify potential drug targets. The ontologies team at EMBL-EBI provide a suite of services that are aimed at making ontologies more accessible for both humans and machines. We work with scientific data curators and software developers to integrate ontologies and semantics into both the data generation and data presentation workflows. We provide: – An ontology lookup service (OLS) that provides search and visualisation services to over 200+ ontologies – Services for automating the annotation of metadata and learning from previous annotations (Zooma) – An ontology mapping and alignment service (OXO) – Tools for working with metadata and ontologies in spreadsheets (Webulous) – Software for enriching documents in search engines to support “semantic” query expansion I’ll present how we are using these services at EMBL-EBI to scale up the semantic annotation of metadata. I’ll talk about our open source technology stack and describe how we utilise a polyglot persistence approach (graph databases, triples stores, document stores etc) to optimize how we deliver ontologies and semantics to our users.

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SureChEMBL is a new resource provided by the European Bioinformatics Institute (EMBL-EBI) that annotates, extracts and indexes chemistry from full text patent documents by means of continuous, automated text and image mining. SureChEMBL is perhaps the only open, freely available, live patent chemistry resource available, in a field that has been traditionally commercial. Since its launch last September, the SureChEMBL interface provides sophisticated keyword and chemistry-based querying and exporting functionality against a corpus of more than 16 million compounds extracted from 13 million patent documents. Both the interface and the underlying data pipeline leverage extensively ChemAxon technologies for name to structure conversion, as well as compound standardisation, registration and searching. In addition to providing an overview of the system, recent developments and improvements will be described. These include the introduction of various data interexchange and exporting options, such as flat files and a data feed client. Furthermore, our future plans for the SureChEMBL system will be outlined. To date, such plans include complementing the chemical annotations with biological ones, covering genes, proteins, diseases and indications. Furthermore, we are planning to further enrich the chemical annotations with a relevance score, indicating their importance in the patent document.

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1 introduction to_the_ebi_(katrina_pavelin)

1. The European Bioinformatics Institute EMBL-EBI Katrina Pavelin Scientific Outreach Officer Services | Research | Training | Industry katrina@ebi.ac.uk

2. What is EMBL-EBI? • Bioinformatics Research & Service Institute • Non-profit organisation • Part of the European Molecular Biology Laboratory EMBL-EBI

3. The five branches of EMBL Heidelberg Hamburg Hinxton • Basic research in Structural biology Bioinformatics molecular biology • Administration Grenoble Monterotondo • EMBO • 1500 staff • >60 nationalities Structural biology Mouse biology EMBL-EBI

4. 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 • To coordinate biological data provision across Europe EMBL-EBI

5. What is bioinformatics? • The science of storing, retrieving and Growth of raw storage analysing large at EMBL-EBI (in terabytes) amounts of biological 12000 information 10000 8000 • An interdisciplinary Disks (TB) 6000 science, involving 4000 biologists, computer scientists and 2000 mathematicians 0 • At the heart of modern Year biology EMBL-EBI

6. Services www.ebi.ac.uk/services EMBL-EBI Services | Research | Training | Industry

7. Databases: molecules to systems Literature and ontologies Genomes UKPMC, CiteXplore, GO Ensembl Ensembl Genomes Protein families, EGA motifs and domains Metagenomics InterPro portal Functional genomics Macromolecular ArrayExpress Nucleotide sequence structure Expression Atlas ENA PDBe Protein activity IntAct, PRIDE Pathways Reactome Protein Sequences UniProt Chemical entities ChEBI Systems Chemogenomics BioModels ChEMBL BioSamples EMBL-EBI

8. EBI’s search service Access from the EBI’s homepage Species selector allows for easy comparison Data organised according to: • gene Explore data, • expression return easily to • protein your results • structure • literature EMBL-EBI

9. Research www.ebi.ac.uk/groups EMBL-EBI Services | Research | Training | Industry

10. Key facts about research at EMBL-EBI • A unique environment for bioinformatics research • Nine dedicated research groups • Services teams also carry out R&D • Research and services are mutually supportive EMBL-EBI

11. Training www.ebi.ac.uk/training EMBL-EBI Services | Research | Training | Industry

12. Pre- and postdocs at EMBL-EBI • EMBL International PhD Programme • Postdoctoral fellowships: • EIPOD – EMBL-sponsored interdisciplinary fellowships • ESPOD – EBI–Sanger combined experimental and computational fellowships EMBL-EBI

13. EMBL-EBI

14. 1 4 EMBL-EBI

15. Thank you! EMBL-EBI

1 introduction to_the_ebi_(katrina_pavelin)

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