The ELIXIR Deposition Databases Rachel Drysdale Data Platform

The ELIXIR Deposition Databases Rachel Drysdale Data Platform Coordinator 21 st March 2018 www. elixir-europe. org

ELIXIR is an intergovernmental research infrastructure that coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access services that are vital for their research. medicine agriculture bioindustries 2 environment These resources include databases, software tools, interoperability services, training materials and cloud storage.

https: //www. elixir-europe. org/

Building a sustainable infrastructure for biological information across Europe

Life science research relies on data resources…… both Diverse and Numerous “The NAR online Molecular Biology Database Collection has been updated……. bringing the current [2018] total to 1737 databases. ” https: //academic. oup. com/nar/article/46/D 1/4781210

Building a sustainable infrastructure for biological information across Europe

https: //f 1000 research. com/articles/5 -2422/v 2

What are ELIXIR Core Data Resources? • A set of data resources that are of fundamental importance to the broad life science community and the long-term preservation of biological data • They provide complete collections of generic value to life science, and show high levels of usage, scientific quality and service https: //f 1000 research. com/articles/5 -2422/v 2

A carefully chosen set of indicators, reflecting the multiple facets of bioinformatics resources Legal & funding infrastructure Scientifi Quality c impact 1. Scientific focus and quality of science Community Scientific Impact focus 2. Community served 3. Quality of service 4. Legal and funding infrastructure and governance 5. Impact and translational stories Indicators that support decision making https: //f 1000 research. com/articles/5 -2422/v 2

A carefully chosen set of indicators, reflecting the multiple facets of bioinformatics resources Legal & funding infrastructure Scientifi Quality c impact 1. Scientific focus and quality of science Community Scientific Impact focus 2. Community served 3. Quality of service 4. Legal and funding infrastructure and governance *open data* Indicators that support decision making 5. Impact and translational stories https: //f 1000 research. com/articles/5 -2422/v 2

Licensing to support remixing and reuse: Open Science • Open terms of use: • CC 0 • CC-BY-SA http: //opendefinition. org/licenses/

Building a sustainable infrastructure for biological information across Europe ELIXIR Network & Expertise ELIXIR Services ELIXIR Core Data Resources

https: //www. elixir-europe. org/news/core-data-resources

Emerging requirement: Deposition Databases • To respond to needs of funders and journals regarding data management policies, and data access requirements • Life scientists not only need to • Find the information that is essential to their research, but also • Safely deposit and share their precious research results • ELIXIR Deposition Databases • are part of an ELIXIR Node portfolio of services • accept deposition of experimental data from an international community of researchers beyond the funding envelope of the database itself • In addition ….

ELIXIR Deposition Databases – Emerging need • The ELIXIR Deposition Databases meet the technical quality and governance criteria expected of ELIXIR Core Data Resources. • May be at an earlier stage of development, meeting an emerging scientific requirement, or maybe narrower in scope. • Some, but not all, of the ELIXIR Deposition Databases also appear in the ELIXIR Core Data Resources list. https: //www. elixir-europe. org/platforms/data/elixir-deposition-databases

Current set of ELIXIR Deposition Databases: Array. Express Bio. Models Bio. Samples Biostudies EGA EMDB ENA EVA Int. Act Metabo. Lights PDBe PRIDE https: //www. elixir-europe. org/platforms/data/elixir-deposition-databases

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

Building a sustainable infrastructure for biological information across Europe ELIXIR Network & Expertise ELIXIR Services ELIXIR Core Data Resources ELIXIR Deposition Databases

To provide guidance about repositories for publishing open data in the life sciences

https: //erc. europa. eu/sites/default/files/document/file/ERC_info_document-Open_Research_Data_and_Data_Management_Plans. pdf

Questions? rachel. drysdale@elixir-europe. org

u o Y k n Tha Durinx, e in t is r h Entyre, C c M o J f o ok, Heinz o C k c u on behalf h ysdale, C z, Daniel e p o Rachel Dr L o ig r, Rodr ub Kim, y H e Stockinge e J , ry Barlow a M , asteiger, a G ir h e t e b Teix a s katesh, Eli n e V lomberg B d s in v la ik N Ara d daschi an e R le o ic N ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559.

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

ELIXIR funding Nodes funded by national agencies Hub funded jointly by ELIXIR member states Hub & Nodes - Joint applications to EU funding

1. Scientific focus and quality of science Measuring what? Inherent scientific quality of the resource, its uniqueness and comprehensiveness Indicators: a. Archives vs knowledge bases b. Scope statement: scientific coverage and comprehensiveness c. International dimension d. Staff effort: including curation effort Scientific focus

2. Community served Community Measuring what? Usage of the resource Indicators: a. Overall usage: access via web browser and other methods b. Potential usage c. Usage in research as measured through citation in the literature: the resource name, data of a resource d. Dependency of other resources

3. Quality of service Quality Measuring what? Service levels and reliability Indicators: a. Use of persistent and unique identifiers b. Data throughput: number of entries, depositions c. Technical performance: uptime, response time d. Use of community-recognized standards for (meta)data e. Links to documentation of provenance f. Data availability - access services and formats g. Customer service: helpdesk, user feedback, training activities

4. Legal and funding infrastructure, and governance Legal & funding infrastructure Measuring what? Soundness of the legal, funding and governance structure guaranteeing its long-term stability Indicators: a. Scientific Advisory Board b. Legal framework supporting Open Science c. Privacy policy d. Ethics policy e. Sustainable support and funding

5. Impact and translational stories Measuring what? Is the resource meeting its objective of fulfilling a specific need of the scientific community Indicators: a. Counterfactual analysis b. Accelerating science c. Translational data Impact

Benchmarking FAIR against our indicators Core Data Resource Indicators FAIR Principles 2 Community 1 Science a b c d a b c 3 Service d a b c d 4 Governance e f g a b c d 5 Impact e a b c Findable: F 1 F 2 F 3 F 4 Accessible: A 1 A 1. 2 A 2 Interoperable: I 1 I 2 I 3 Re-usable: R 1 R 1. 2 R 1. 3 • Core resources are • Findable • Accessable • Interoperable • Reusable • Core resources address scientific need, community and impact • Core resource indicators support decisions on value