ELIXIR – Infrastructure for biologicaldata

Jiri Vondrasek, IOCB AS CRHead of ELIXIR CZ

What is “INFRASTRUCTURE“?..something you don‘t have to „maintain“ or „take care of“ but you can use it!

Examples of European-wide Infrastructures in Life-Sciences:

INSTRUCTBIOIMAGINGINFRAFRONTIERSOPENSCREENEATRISBBMRB……….

Life Sciences – Data Types

Data growth at EMBL-EBISource: Charles E. Cook et al. Nucl. Acids Res. 2018;46:D21-D29

Data growth in the life sciences• Computer speed and storage capacity is

doubling every 18 months and this rate is steady (Moore’s law)

• The amount of life science data doubles every 12 months and the growth rate is predicted to continue

Data resources in life sciences

The Nucleic Acids Research online Database Collection: http://www.oxfordjournals.org/nar/database/a/

~1800molecular biologydata resources

Examples of genomics based projects across ELIXIR members

Health care and genomics based national initiative projects, regional projects have not been included

..well, am I using ELIXIR Infrastructure?

Clustering of ELIXIR CZ Areas of Expertises – Clustering of the Infrastructure

Structural BioinformaticsData Management

Human DataPlant GenomicsGenomicsCompute

ProteomicsChemical Biology

New ELIXIR Communities

How can I make use of ELIXIR?

Bioinformatics services

https://elixir-europe.org/services

ELIXIR Services

● Databases ○ Deposition○ Knowledge-bases

● Software tools ● Interoperability ● Compute ● Training courses ● Data management

Bioinformatics Tools

• Need to analyse your data but don’t know what tool to use?

• Bio.tools is a registry of life science tools and services

• Search by:• Data type• Web tool or programming

language• Input/output file format• & more…

• You can add your own tools

Integration with OpenEBench

Publication details

Links to ELIXIR Training portal, TeSS

https://bio.tools

Finding resources and databases

www.elixir-europe.org/core-data-resources

• ELIXIR Core Data Resources

• Set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data.

• Decided by an international collaborative effort

Finding resources and databases

https://elixir-europe.org/platforms/data/elixir-deposition-databases

• Need to deposit your data for publication but don’t know where the best place for it is?

• The ELIXIR Deposition Database listwill steer you in the correct direction

Finding resources and databases

• ELIXIR’s Recommended Interoperability Resources.

• These are resources that:

• Establish connections between resources

• Acquire and expose metadata of different resources

• Create the infrastructure needed to build integratable data collections

• They will help you translate your data across databases or resources or find the best standards for your data.

Training

• Need to find training courses or materials?

• ELIXIR’s TeSS Platform enables you to search, share & package training resources, training materials and events

• Led by ELIXIR UK

Search for events held near you...

https://tess.elixir-europe.org

Job and PhD vacancies

• Search for jobs in academia and industry

• Vacancies in:

• Bioinformatics

• Data science

• Software development

• Upload roles for increased exposure.

• Anyone can upload jobs to the page.

• Roles advertised across the ELIXIR Node websites.

https://elixir-europe.org/about-us/vacancies

• Listed as a global research infrastructure in the G7 GSO’s roadmap

• ELIXIR - Australia collaboration strategy being drafted

• Discussions initiated with Canada, South Africa, USA

• ELIXIR::GA4GH strategic partnership

• Additional projects with H3ABioNet and GBIF

• Long-standing collaboration with the OECD

Integrating into an international context

ELIXIR CZ Activity in Interoperability and Data Management

Services/activities:• Interoperability best practices promotion.

• Data Stewardship support to the data producers.

• Ontologies, minimum information standards, vocabularies.

• Bring Your Own Data (BYOD) Workshops –FAIRification of Data.

Mission: Implement principles for Findable, Accessible, Interoperable and Reusable Data

http://elixir-cz.fairdata.solutions

https://ds-wizard.org

The wizard is intended as the basis for helping with creating data management plans.

ELIXIR CZ Resources, Services ,Tools

http://elixir-czech.cz/services

Additional contributions:

- AAI selected as a comissioned service

- Chemical biology resources –IDSM

- 3D Bioinfo Community

- Hardware resources dedicated

according user community needs

- Data Management tools

Thank you for your attention