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

Who is BioData?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Platforms | Communities | Services BioData.pt|ELIXIR PT

Platforms | Communities | Services BioData.pt|ELIXIR PT

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

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

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

Platforms | Communities | Services BioData.pt|ELIXIR PT

Platforms | Communities | Services BioData.pt|ELIXIR PT

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