ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and...
Transcript of ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and...
![Page 1: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/1.jpg)
ELIXIR – Infrastructure for biologicaldata
Jiri Vondrasek, IOCB AS CRHead of ELIXIR CZ
![Page 2: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/2.jpg)
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……….
![Page 3: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/3.jpg)
Life Sciences – Data Types
![Page 4: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/4.jpg)
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
![Page 5: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/5.jpg)
Data resources in life sciences
The Nucleic Acids Research online Database Collection: http://www.oxfordjournals.org/nar/database/a/
~1800molecular biologydata resources
![Page 6: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/6.jpg)
![Page 7: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/7.jpg)
Examples of genomics based projects across ELIXIR members
Health care and genomics based national initiative projects, regional projects have not been included
![Page 8: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/8.jpg)
![Page 9: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/9.jpg)
![Page 10: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/10.jpg)
![Page 11: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/11.jpg)
![Page 12: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/12.jpg)
..well, am I using ELIXIR Infrastructure?
![Page 13: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/13.jpg)
![Page 14: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/14.jpg)
![Page 15: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/15.jpg)
![Page 16: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/16.jpg)
Clustering of ELIXIR CZ Areas of Expertises – Clustering of the Infrastructure
Structural BioinformaticsData Management
Human DataPlant GenomicsGenomicsCompute
ProteomicsChemical Biology
![Page 17: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/17.jpg)
![Page 18: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/18.jpg)
![Page 19: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/19.jpg)
![Page 20: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/20.jpg)
New ELIXIR Communities
![Page 21: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/21.jpg)
![Page 22: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/22.jpg)
How can I make use of ELIXIR?
![Page 23: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/23.jpg)
Bioinformatics services
https://elixir-europe.org/services
ELIXIR Services
● Databases ○ Deposition○ Knowledge-bases
● Software tools ● Interoperability ● Compute ● Training courses ● Data management
![Page 24: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/24.jpg)
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
![Page 25: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/25.jpg)
![Page 26: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/26.jpg)
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
![Page 27: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/27.jpg)
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
![Page 28: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/28.jpg)
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.
![Page 29: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/29.jpg)
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
![Page 30: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/30.jpg)
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
![Page 31: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/31.jpg)
• 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
![Page 32: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/32.jpg)
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
![Page 33: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/33.jpg)
https://ds-wizard.org
The wizard is intended as the basis for helping with creating data management plans.
![Page 34: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/34.jpg)
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
![Page 35: ELIXIR CZ Info Days 2019-lecture-Ceske Budejovice · ELIXIR CZ Activity in Interoperability and Data Management Services/activities: • Interoperability best practices promotion.](https://reader033.fdocuments.net/reader033/viewer/2022042711/5f71b0a371027776bd0ec3c4/html5/thumbnails/35.jpg)
Thank you for your attention