BioData.pt|ELIXIR PT: A Biological Data e -Infrastructure for Research and Innovation

1. BioData.pt|ELIXIR PT: A Biological Data e -Infrastructure for Research and Innovation Ricardo Leite, Ana Portugal Melo, CireniaBaldrich, Daniel Faria, Daniel Neves, João Cardoso Jornadas FCCN – 7 Maio 2019

2. Who is BioData?

3. Who is BioData@IGC? Filipa Almeida - Project Manager João Garcia - System’s Administrator Daniel Neves - User Support Officer/Tools Developer Ricardo Leite - Genomics and Bioinformatics Expert João Sousa - Compute Platform Coordinator Ana Portugal Melo - Executive Director CireniaBaldrich - Software Developer Daniel Faria - Interoperability Expert Pedro Fernandes - Training Coordinator Miguel Cardoso - Training Assistant Beatriz Lima - Galaxy Trainee Henrique Costa - Shiny-R Trainee BioData.pt|ELIXIR PT

4. What is ELIXIR ? Intergovernmental organization: founded in 2014, 23 members over 180 research organisations. Brings together life science resources: databases, software tools, training materials, cloud storage and supercomputers. Aims to coordinate resources so that they form a single infrastructure, making it easier for scientists to find and share data, exchange expertise, and agree on best practices. https://www.elixir-europe.org BioData.pt|ELIXIR PT

5. BioData.ptThe Portuguese Node of ELIXIR BioData.pt|ELIXIR PT

6. Platforms | Communities | Services GTPB https://www.elixir-europe.org/services BioData.pt|ELIXIR PT BioData.pt|ELIXIR PT

7. Platforms| Communities | Services • A sustainable infrastructure for storing, coordinating and distributing human data • Standardised tools to discover and access human data • Local-EGAs for metadata sharing (European Genome-phenome Archive) • Regulating access to sensitive data • Long-term management policies for human data • Ensures that human data in ELIXIR services is handled within the appropriate legal and ethical framework https://www.elixir-europe.org/communities/human-data BioData.pt|ELIXIR PT

8. Data Management in the Life Sciences João Cardoso BioData.pt|ELIXIR PT

9. Platforms | Communities | Services Problem: • Life science research produces hugequantities of data. • It is crucial to make them Findable, Accessible, Interoperable and Reusable (FAIR) • This data can be sensitive or classified. • Data management of this data is a complex task that requires expert knowledge. BioData.pt|ELIXIR PT

10. Platforms | Communities | Services Moving towards: • The Data Management Plan (DMP)is a document describing: • Techniques • Methods • Policies with the goal of enabling good data management practices. • Funding bodies such as the EC, NSF and FCT already require that funding grant applications be accompanied by a DMP. BioData.pt|ELIXIR PT

11. Platforms | Communities | Services Services: • Biodata.pt assists its communitiesin regard to Data Management by: • Providing information andtraining on Data Managementpractices. • Creating a functional digital repository. • Providing assistance in the creation and usage of DMPs. • Creating a collection of DMP templates. BioData.pt|ELIXIR PT

12. Standards for Managing Plant Phenotype Data Daniel Faria BioData.pt|ELIXIR PT

13. Platforms | Communities | Services Plant Sciences: • Core ELIXIR community • Co-lead by BioData.pt and ELIXIR-FR • IGC, iBET and ITQB • Focus on tree species BioData.pt|ELIXIR PT

14. Platforms | Communities | Services Data Submission Structure? Format? Data Storage & Indexing Access? Interoperability: FAIR Data Retrieval Interface? BioData.pt|ELIXIR PT

15. Platforms | Communities | Services • Minimum Information About Plant Phenotyping Experiments Solution: Data Submission • 11 sections; 83 fields • Submission: spreadsheet; ISA-tab; interface (WIP) BioData.pt|ELIXIR PT

16. Platforms | Communities | Services Solution: Data Storage & Indexing • (Plant) Breeding API • PT end-point (https://brapi.biodata.pt/) • 51 tables; 255 fields • 4 datasets; 3 species "result": { "accessionNumber": "A000001", "acquisitionDate": "2019-01-01", "breedingMethodDbId": "crossing", "commonCropName": "cork oak", "countryOfOriginCode": "Portugal", "genus": "Quercus", "species": "suber", "germplasmName": "Quercus suber PTX011", "instituteName": "ITQB", "pedigree": "A000001/A000002", "seedSource": "A000001/A000002" [...] BioData.pt|ELIXIR PT

17. The Cork Oak Genome Portal Community Showcase BioData.pt|ELIXIR PT

18. Platforms | Communities | Services Problem: HL8 Cork oak tree selected for genome sequencing.Lia Rodrigues ? BioData.pt|ELIXIR PT

19. Platforms | Communities | Services Solution: BioData.pt|ELIXIR PT

20. Platforms | Communities | Services BioData.pt|ELIXIR PT

21. Platforms | Communities | Services BioData.pt|ELIXIR PT

22. Empowering Researchers with User-Friendly Applications BioData.pt|ELIXIR PT

23. Platforms | Communities | Services Problem: How to scale-up support to a growing amount of data being generated, a broader user community? Illumina NextSeq 500 10x Genomics Chromium Controller BioData.pt|ELIXIR PT

24. Platforms | Communities | Services Solution: Give researchers the tools to be more independent in their analyses and to better control their own data. Open source web applications with a focus on: • Accessibility • Documentation • Reproducibility Use cases: • Differential expression analysis of RNA-seq data • Analysis of single cell RNA-seq BioData.pt|ELIXIR PT

25. Platforms | Communities | Services BioData.pt|ELIXIR PT

26. Platforms | Communities | Services BioData.pt|ELIXIR PT

27. Thank you! E-mail: info@biodata.pt www.biodata.pt