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ProteomeXchange update
1) ProteomeXchange is a global database containing proteomics data from several repositories including PRIDE, MassIVE, and jPOST. 2) A new member, iProX, joined in 2017 and contains over 60 terabytes of data from China. 3) Usage of ProteomeXchange data is increasing, with PRIDE downloads growing from 50 terabytes in 2013 to over 295 terabytes in 2017.
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ProteomeXchange update
- 1. ProteomeXchange update Dr. JuanAntonio Vizcaíno (on behalf of all ProteomeXchange partners) EMBL-European Bioinformatics Institute Hinxton, Cambridge, UK
- 2. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Overview • Introduction • Some usage statistics • Guidelines: Handling of reprocessed datasets • New prospective member: Panorama Public • Miscellaneous
- 3. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 ProteomeXchange: A Global, distributed proteomics database PASSEL (SRM data) PRIDE (MS/MS data) MassIVE (MS/MS data) Raw ID/Q Meta jPOST (MS/MS data) Mandatory data deposition http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014 Deutsch et al., NAR, 2017 • Framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories.
- 4. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 ProteomeXchange: A Global, distributed proteomics database PASSEL (SRM data) PRIDE (MS/MS data) MassIVE (MS/MS data) Raw ID/Q Meta jPOST (MS/MS data) Mandatory data deposition http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014 Deutsch et al., NAR, 2017 iProX (MS/MS data) • Framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories. New in 2017
- 5. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 VIP Load balance server 1 nginx keepalived CentOS Load balance server 2 nginx keepalived CentOS Application server 1 SpringMVC MyBatis tomcat java CentOS Application server 2 SpringMVC MyBatis tomcat java CentOS Database server (Master) CentOS MySql Database server (slave) CentOS MySql Data storage server 2 nginx CentOS Data storage server 1 nginx keepalived CentOS aspera Data storage server 3 nginx keepalived CentOS aspera iProX- the integrated proteome resources in China Cloud platform architecture with High Availability http://www.iprox.org
- 6. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Deployment of iProX Beijing Hunan Shanghai • BPRC & NCPSB (Beijing): Main location of deployment and the only submission site • Three Offsite data backups • CNIC (Beijing, north China) • SCBIT(Shanghai, east China) • NSCC(Hunan, south China) • All four sites will provide downloading service at the same time coordinated by the load balancer. • By the end of March 2018, 374 datasets are submitted, with a total amount of 60 TB
- 7. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 ProteomeXchange: A Global, distributed proteomics database PASSEL (SRM data) PRIDE (MS/MS data) MassIVE (MS/MS data) Raw ID/Q Meta jPOST (MS/MS data) Mandatory data deposition http://www.proteomexchange.org Vizcaíno et al., Nat Biotechnol, 2014 Deutsch et al., NAR, 2017 iProX (MS/MS data) • Framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories. New in 2017
- 8. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 https://jpostdb.org/ Repository is going well. Database part is just open. Re-analysis part is under development. Funding is just renewed for next 5 years! JPOST status
- 9. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 ProteomeCentral: Portal for all PX datasets http://proteomecentral.proteomexchange.org/cgi/GetDataset
- 10. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Public datasets from different omics: OmicsDI http://www.omicsdi.org/ • Aims to integrate of ‘omics’ datasets (proteomics, transcriptomics, metabolomics and genomics at present). PRIDE MassIVE jPOST PASSEL GPMDB ArrayExpress Expression Atlas MetaboLights Metabolomics Workbench GNPS EGA …and others Perez-Riverol et al., Nat Biotechnol, 2017
- 11. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Overview • Introduction • Some usage statistics • Guidelines: Handling of reprocessed datasets • New prospective member: Panorama Public • Miscellaneous
- 12. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Data content per resource (PXD identifiers) 84.9% 11.5% 1.8% 1.5% 0.3%
- 13. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 PRIDE data submissions and data growth > 2,400 datasets submitted in 2017 In March 2018 we have reached for the first time 300 submitted datasets Datasets submitted per month Datasets submitted per year
- 14. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Data re-use in proteomics is increasing Data download volume for PRIDE Archive in 2017: 295 TB 0 50 100 150 200 250 300 350 2013 2014 2015 2016 2017 Downloads in TBs
- 15. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Overview • Introduction • Some usage statistics • Guidelines: Handling of reprocessed datasets • New prospective member: Panorama Public • Miscellaneous
- 16. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Guidelines developed
- 17. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Guidelines developed • Initial implementation in MassIVE
- 18. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Other guidelines developed during the last year • Retraction of datasets (“Re-calling”) • Support for alternative location of datasets (alternative URLs) • Try to get external datasets into PX (e.g. CPTAC)
- 19. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Overview • Introduction • Some usage statistics • Guidelines: Handling of reprocessed datasets • New prospective member: Panorama Public • Miscellaneous
- 20. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Panorama Public • Panorama Public is designed for sharing data generated through Skyline-based targeted proteomics workflows such as SRM and PRM or targeted DDA and DIA. • Led by Brendan MacLean & Mike MacCoss group • Processed results are stored in the Skyline XML format • Interested to join ProteomeXchange as a repository for targeted proteomics workflows.
- 21. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Panorama Public https://panoramaweb.org/
- 22. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Overview • Introduction • Some usage statistics • Guidelines: Handling of reprocessed datasets • New prospective member: Panorama Public • Miscellaneous
- 23. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 PRIDE has become and ELIXIR core data resource • ELIXIR coordinates, integrates and sustains bioinformatics resources across Europe and enables users in academia and industry to access services that are vital for their research • First list of core resources announced on July 2017. • PRIDE included in the initial list. https://www.elixir-europe.org/platforms/data/core-data-resources
- 24. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 • The goal of the ELIXIR proteomics community is to develop and maintain sustainable proteomics tools and data resources • An essential part of the development will also be the ‘FAIRification’ of the resources (i.e. making the resources FAIR) • Integrate proteomics bioinformatics activities in ELIXIR PRIDE as a “pillar” of the ELIXIR Proteomics Community
- 25. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Main plans for meeting • General update • Panorama Public application to join PX • Do we need more formalised guidelines for several topics? • Short Report about GDPR guidelines • Two related projects (NIH “data standards” grant): • Universal Spectrum Identifier (USI) • PROXI
- 26. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018 Aknowledgements: People Yasset Perez-Riverol Attila Csordas Tobias Ternent Gerhard Mayer (de.NBI) Andrew Jarnuczak Mathias Walzer Suresh Hewapathirana Jingwen Bai Former team members, especially: Henning Hermjakob Acknowledgements: All ProteomeXchange partners All data submitters !!! Eric Deutsch Zhi Sun David Campbell Nuno Bandeira Mingxun Wang Jeremy Carver Yasushi Ishihama Shin Kawano Follow new datasets @proteomexchange Yunping Zhu Masheng Li
- 27. Juan A. Vizcaíno juan@ebi.ac.uk PSIMeeting 2018 Heidelberg, 18 April 2018