Proteomics repositories integration using EUDAT resources
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This document discusses plans to integrate proteomics data repositories using resources from the EUDAT data infrastructure. It describes replicating data from the ELIXIR repository PRIDE to EUDAT data centers for backup and access. This will test using EUDAT services like B2SAFE for replication and assigning persistent identifiers (PIDs) to datasets and files. The current status describes installing necessary software at participating sites and initial testing of replication from PRIDE to the Swedish National Bioinformatics Infrastructure data center. Future plans include syncing data changes and exploring data push/pull models between repositories.
Proteomics repositories integration using EUDAT resources
- 1. European Life Sciences Infrastructure for Biological Information www.elixir-europe.org Rafael C Jimenez ELIXIR CTO EDUAT conference, 25 September 2014 Proteomics repositories integration using EUDAT resources
- 2. Data submissions 2 Submissions raw data processed data metadata Data repository Search Integration
- 3. Noble WS, MacCoss MJ (2012) Computational and Statistical Analysis of Protein Mass Spectrometry Data. PLoS Comput Biol 8(1): e1002296. doi:10.1371/journal.pcbi.1002296 http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002296 Overview of shotgun proteomics data production MKKKNIYSIRKLGVG IASVTLGTLLISG GVTPAANAAQHD FYQVLNMPNLNADQ RNGFIQSLK DDPSQSANVKLN 4 Peptide sequences Raw data Process data Metadata
- 4. Data examples 4 Raw data Process data Metadata DNA Human Liver Mitochondria W. Smith … Peptide Mouse Heart Nucleus J. Heinz … LPISASHSSK… TTGTTATCCG… … … …
- 5. Proteomics data in PRIDE 5 ~85% raw data
- 6. ProteomeCentral Metadata / Manuscript Raw Data* Results Journals UniProt/ NeXtProt Peptide Atlas Other DBs Receiving repositories PASSEL (SRM data) PRIDE (MS/MS data) GPMDB Researcher’s results Reprocessed results Raw data* Metadata ProteomeXchange Vizcaíno et al., Nature Biotechnology, 2014 • Framework to enable standard data submission and dissemination pipelines between the main existing proteomics resources.
- 7. 7 Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2013 PRIDE (PRoteomics IDEntifications) database Mass spectrometry
- 8. Origin: 152 USA 108 Germany 67 United Kingdom 53 Switzerland 48 Netherlands 42 China 42 Canada 41 France 36 Spain 33 Belgium 25 Australia 23 Sweden 17 Japan 16 Denmark 13 Norway 12 Finland 12 India 12 Taiwan 10 Italy 9 Republic of Korea 8 Austria 8 Ireland 8 Brazil 7 Singapore 5 Israel 5 Russia … Type: 273 PRIDE complete 501 PRIDE partial 47 PeptideAtlas/PASSEL complete Access: 38.3% PRIDE public 5.3% PASSEL public 56% PRIDE private 0.4% PASSEL private Data volume: Total: >40 TB Number of all files: >120,000 PXD000320-324: ~ 5 TB PXD000065: ~ 1.4TB Top Species studied by at least 8 datasets: 381 Homo sapiens 100 Mus musculus 31 Arabidopsis thaliana 26 Saccharomyces cerevisiae 16 Escherichia coli 14 Rattus norvegicus 12 Mycobacterium tuberculosis 11 Drosophila melanogaster ~ 215 species in total Submissions/year: 2012: 102 2013: 527 2014: 192
- 9. Pilot evolution • Use EUDAT • Replication of ELIXIR data in EUDAT data centers • Delegation of ELIXIR data in EUDAT data centers • Adopt EUDAT • Replication of ELIXIR data in ELIXIR data centers using EUDAT technology 9
- 10. Replication of ELIXIR data in EUDAT data centers 10 Central repository Data storage centers Meta data Raw Data Meta data Results Raw Data
- 11. ProteomeCentral Metadata / Manuscript Raw Data* Results Journals UniProt/ NeXtProt Peptide Atlas Other DBs Receiving repositories GPMDB Researcher’s results Reprocessed results Raw data* Metadata Vizcaíno et al., Nature Biotechnology, 2014 Raw Data* PASSEL (SRM data) PRIDE (MS/MS data) Replication of ELIXIR data in EUDAT data centers
- 12. Delegation of ELIXIR data in EUDAT data centers 12 Central repository Data storage centers Meta data Raw Data Meta data Results Raw Data
- 13. ProteomeCentral Metadata / Manuscript Raw Data* Results Journals UniProt/ NeXtProt Peptide Atlas Other DBs Receiving repositories GPMDB Researcher’s results Reprocessed results Raw data* Metadata Vizcaíno et al., Nature Biotechnology, 2014 Raw Data* PRIDE (MS/MS data) PASSEL (SRM data) Delegation of ELIXIR data in EUDAT data centers
- 14. Replication of ELIXIR data in ELIXIR data centers using EUDAT technology 14 National proteomics centers Meta data Results Raw Data Central repository Meta data Results Raw Data
- 15. Plans 15 National proteomics centers Meta data Results Raw Data Central repository Meta data Results Raw Data Data storage centers Meta data Raw Data 1.- ELXIR replication 2.- EUDAT replication
- 16. Plans 16 National proteomics centers Meta data Results Raw Data Central repository Meta data Results Raw Data Data storage centers Meta data Raw Data 3.- delegation
- 19. File sharing model 19 CSC BILS Site B Site C EUDAT CDIELIXIR B2SAFE B2SAFE B2SAFE B2SAFE PRIDE EMBL-EBI
- 20. Pilot – EUDAT adoption: ELIXIR replication 20 CSC BILS Site B Site C EUDAT CDIELIXIR B2SAFE B2SAFE B2SAFE B2SAFE PRIDE EMBL-EBI Central repositoryNational proteomics centers Meta data Results Raw Data Meta data Results Raw Data
- 21. PIDs 21 ELIXIR community center ELIXIR Data center 1 EUDAT Data center 1 CSCPRIDEBILS
- 22. Status • BILS • Migrating from existing Swestore dCache to iRODS • Testing compatibility with B2SAFE • Latest iRDOS not compatible with B2SAFE? • PRIDE • iRODS service installed • B2SAFE module have been deployed at EMBL-EBI (PRIDE) • Test B2SAFE replication PRIDE -> CSC • DOI for datasets • PID for dataset files • Web service to associate datasets to dataset files 22
- 23. Status In progress • Handle System Registration • Test requests of EPIC/EUDAT identifiers Open questions • BILS local PIDs? • Sync back from PRIDE to BILS for modifications/additions at PRIDE? • Data push or pull model? • Replication of process data requires previous validation 23
- 24. Participants EUDAT/CSC • Jani Heikkinen • Damien Lecarpentier • Johannes Reetz EMBL-EBI/systems • Andy Jenkinson • Steven Newhouse 24 BILS • Mikael Borg • Fredrik Levander • Bengt Persson EMBL-EBI/PRIDE • JuanAntonioVizcaíno • RuiWang • Henning Hermjakob ELIXIR Hub • Rafael C Jimenez
- 25. European LifeSciences Infrastructure for Biological Information www.elixir-europe.org Thank you for your attention
- 26. Delegation of raw data 26 processed data metadata Data repository PID Submissions Search Integration
- 27. 27 National proteomics centers Meta data Results Raw Data Central repository Meta data Results Raw Data Data storage centers Meta data Raw Data National proteomics centers Meta data Results Raw Data Central repository Meta data Results Raw Data Data storage centers Meta data Raw Data
Editor's Notes
- #8: Proteomics is the large-scale study of proteins, particularly their structures and functions Mass spectrometry (MS) is an analytical technique that measures the mass-to-charge (m/z) ratio of charged particles.