ELIXIR: data for molecular biology and points of entry for marine scientists
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1 ELIXIR: data for molecular biology and points of entry for marine scientists Guy Cochrane, EMBL-EBI EuroMarine 2018 General Assembly meeting January
2 Scales of molecular biology data Credits: Applied Biosystems Oxford Nanopore Technologies Source: Charles E. Cook et al. Nucl. Acids Res. 2016;44:D20-D26 Source:
3 Data resources in life science Data resources in the life sciences 1800 Diverse Plentiful Dispersed databases Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in MY Galperin, GR Cochrane Nucleic Acids Research, 2011
4 ELIXIR Membership
5 ELIXIR: European infrastructure for biological information Data infrastructure for Europe s life-science research: Data Interoperability Tools Compute Marine metagenomics Crop and forest plants Human data Rare diseases
6 ELIXIR Services Data deposition: ENA, EGA, PDBe, EuropePMC, Data management: Genome annotation Data management plans Added value data: UniProt, Ensembl, OrphaNet, Data Interoperability: BioSharing, identifiers.org and OLS Compute: Secure data transfer, cloud computing, AAI Bioinformatics tools: Bio.tools Industry: Innovation and SME programme Bespoke collaborations Training: TeSS, Data Carpentry, elearning
7 Core Data Resources a data infrastructure Scientific focus and quality of science Curation level, benchmarking Community served by the resource Web statistics Quality of service Uptime, user support and training Legal and funding infrastructure Institutional support, use policy Impact and translational stories Foundational role Initial set of Core Data Resources ArrayExpress ChEBI ChEMBL EGA ENA Ensembl Ensembl Genomes Europe PMC Human Protein Atlas The IMEx Consortium (IntAct and MINT) InterPro PDBe PRIDE STRING db UniProt Durinx C, McEntyre J, Appel R et al. Identifying ELIXIR Core Data Resources F1000Research 2016, 5(ELIXIR):2422
8 Core resource example: European Nucleotide Archive (ENA) Globally comprehensive scientific record and European node of INSDC A broad platform for the management, sharing, integration and dissemination of sequence data Established in the early 1980s, extended for new technologies and applications Connectivity with broader EMBL-EBI resources Sequence data foundation Sustained within EMBL-EBI under EMBL funding with additional support from EC, UK Research councils, Wellcome Trust, etc. Substantial scale: 1 submission every 6 minutes, 1.3 petabase pairs across 1.5 million taxa, 2,000-5,000 active data providers, global consumer userbase Rich submission, discovery and retrieval software, tools and services
9 Use Case: Marine metagenomics Mission: develop sustainable metagenomics infrastructure to enhance research and innovation Actions: Develop standards for the marine domain Develop databases specific to marine metagenomics Implement tools and pipelines for metagenomics analysis Develop search engine for interrogation of marine metagenomics datasets Develop and deliver training for end users Nils P. Willassen, NO & Rob Finn, EBI
10 Tara Oceans Tara Oceans expeditions: expeditions: facts and facts figures and figures 35,000 samples Scientists on the expedition helped collect, pack and ship around 35,000 samples of plankton and water datasets One of the richest molecular sample collections in the public domain - freely available to everyone. 11,535 gigabytes Size of the Tara datasets in the European Nucleotide Archive as of May This represents 12,581 gigabases - roughly equivalent to 135 fully sequenced human genomes. Unlimited Potential to discover new things about life in the world s oceans. Tara data: 40 million genes Largest-ever DNA sequencing effort for ocean science. Genetic sequences collected could represent tens of thousands of new species and ecosystem interactions. Considering the size of the world s oceans, there is much, much more to discover.
11 EMBRIC European Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy Objectives Coherent chains of high quality services across RIs Strengthen connection between science and industry Defragment communities TNA - 15 February 2018 opening of the 2 nd call ( Consortium Led by UPMC Bernard Kloareg 27 partners INFRADEV-4 RI cluster call
12 Online Configurator Form EMBRIC Configurator Marine data consultancy: the EMBRIC Configurator CCMAR MBA SZN Do you have marine data, metadata and/or samples with a biomolecular focus? Do you need help with management, analysis and sharing of your data?? Omics Samples Standards The Configurator provides free data management consultancy to assist marine scientists with their (data) needs around biotechnology and biomolecular work. The Configurator offers help on: data management data QC & curation standards & compliance data analysis cloud compute sustainability and much more! Do you have doubts about whether the Configurator consultancy suits your needs? Get in touch and we will get back to you: annalisa@ebi.ac.uk Recommendations and tools External case consultant advice Call presentation and Final case report For more information visit: Case officer and configurator team This project has received funding from the European Union s Horizon 2020 research and innovation programme under grant agreement No Guidance on data management 22 registered consultants 2 ongoing cases 4 complete cases Call for: More consultants More cases
13 EMBRIC Configurator examples Sustainability: Long-term operation of domain-specific data resource on fish species Data dissemination: Pseudo-nitzschia multistriata genomics, transcriptomics and gene expression Data access: Small molecule activities with respect to strains and genes
14 Acknowledgements ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number EMBRIC has received funding from the European Union s Horizon 2020 research and innovation programme under grant agreement No
15 Talk to us Annalisa Milano Data Coordination Biocurator Jeena Rajan Sequence Data Biocurator Guy Cochrane Team Leader
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