1. BioData.pt|ELIXIR PT: A Biological Data e -Infrastructure for Research and Innovation
Ricardo Leite, Ana Portugal Melo, Cirenia Baldrich, 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
Cirenia Baldrich - 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.
BioData.pt|ELIXIR PT

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

6. Platforms | Communities | Services
GTPB
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
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 huge quantities 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
Biodata.pt assists its communities in regard to Data Management by:
Providing information and training on Data Management practices.
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
Interoperability:
Data Submission
Structure? Format?
Data Storage & Indexing
Access?
FAIR
Data Retrieval
Interface?
BioData.pt|ELIXIR PT

15. Platforms | Communities | Services
Solution: Data Submission
Minimum Information About Plant Phenotyping Experiments
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 (
51 tables; 255 fields
4 datasets; 3 species
"result": {
"accessionNumber": "A000001",
"acquisitionDate": " ",
"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
The Cork Oak Genome Portal
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!