How to run and maintain a popular biological data repository?
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Dr. Juan Antonio Vizcaíno discusses the operation and sustainability of the PRIDE proteomics data repository, emphasizing the importance of robust infrastructure and skilled personnel. He highlights strategies for promoting the repository, stressing active communication with the scientific community and the necessity of user-friendly data management tools. Finally, he outlines the financial challenges of maintaining PRIDE and the need for collaboration within the research ecosystem to ensure long-term viability.
How to run and maintain a popular biological data repository?
- 1. How to run and maintain a popular biological data repository? Dr. Juan Antonio Vizcaíno EMBL-European Bioinformatics Institute Hinxton, Cambridge, UK E-mail: juan@ebi.ac.uk
- 2. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Data resources at EMBL-EBI Genes, genomes & variation ArrayExpress Expression Atlas PRIDE InterPro Pfam UniProt ChEMBL ChEBI Molecular structures Protein Data Bank in Europe Electron Microscopy Data Bank European Nucleotide Archive European Variation Archive European Genome-phenome Archive Gene & protein expression Protein sequences, families & motifs Chemical biology Reactions, interactions & pathways IntAct Reactome MetaboLights Systems BioModels Enzyme Portal BioSamples Ensembl Ensembl Genomes GWAS Catalog Metagenomics portal Europe PubMed Central Gene Ontology Experimental Factor Ontology Literature & ontologies
- 3. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 • PRIDE stores mass spectrometry (MS)-based proteomics data: • Peptide and protein expression data (identification and quantification) • Post-translational modifications • Mass spectra (raw data and peak lists) • Technical and biological metadata • Any other related information • Full support for tandem MS approaches • Any type of data can be stored. • Since July 2017, an ELIXIR core resource. PRIDE (PRoteomics IDEntifications) Archive http://www.ebi.ac.uk/pride/archive Martens et al., Proteomics, 2005 Vizcaíno et al., NAR, 2016
- 4. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 A data repository is a service to the scientific community
- 5. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Infrastructure and personnel are the key (1) Computing infrastructure is very expensive to maintain. (We are very lucky to be at the EBI).
- 6. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Stats (3): Data growth in EBI resources
- 7. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Infrastructure and personnel are the key (2) Expert staff members are essential (like in any other business): - It is not easy to get good people with the needed skills - Complementary skills are essential - Managing people as a team is challenging
- 8. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 At an early stage • Promote your resource as much as possible and demonstrate that you can provide an essential service in a reliable way • Interaction with scientific journals was essential for PRIDE. • Scientists are busy people • Journals and funders requirements are pushing for open data • Develop user-friendly tools. Submitting and accessing data must be very easy. • Demonstrate that the team does and enables good science • Publications, conferences/workshops.
- 9. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 At a more advanced stage • Keep active communication with some wet labs, and with the community as a whole (finding the right balance) • New ideas come often from a simple chat • Conferences and workshops • Training courses • Work actively together with your collaborators/competitors to look for synergies: • ProteomeXchange
- 10. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 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 raw data deposition since July 2015 • Goal: Development of a framework to allow standard data submission and dissemination pipelines between the main existing proteomics repositories. http://www.proteomexchange.org New in 2016 Vizcaíno et al., Nat Biotechnol, 2014 Deutsch et al., NAR, 2017
- 11. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 At a more advanced stage • Keep active communication with some wet labs, and with the community as a whole (finding the right balance) • New ideas come often from a simple chat • Conferences and workshops • Training courses • Work actively together with your collaborators/competitors to look for synergies: • ProteomeXchange • An International Consortium is better than a single resource (perception, funding, etc)
- 12. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Running PRIDE every day -> Sustainability • Keep our clients happy! • (People usually only says something when something is not working!) • Make things as easy as possible in terms of software development: • Long-term maintainability is key • Good software practises, e.g. documentation • Community-based data standards are essential
- 13. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Taken from Biocomicals, http://biocomicals.blogspot.com
- 14. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 •Develops data standards for proteomics •Both data representation and annotation standards •Involves data producers, database providers, software producers, publishers, everyone who wants to be involved… •Active Workgroups: MI, MS, PI, Mod and the new QC •Inter-group activities: MIAPE and Controlled Vocabularies •Started in 2002, so some experience already… •One annual meeting in March-April, regular phone calls •Close interaction with the metabolomics community (MSI) http://www.psidev.info HUPO Proteomics Standards Initiative
- 15. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Running PRIDE every day -> Sustainability • Keep our clients happy! • (People usually only say something when something is not working!) • Make things as easy as possible in terms of software development: • Long-term maintainability is key • Good software practises, e.g. documentation • Community-based data standards are essential. • Open source tools, open data. • Find the right balance between maintenance/doing new things.
- 16. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Running PRIDE every day -> Sustainability (2)• Running a resource like PRIDE is expensive: • Constantly looking for funding • Take opportunities to collaborate, looking for synergies: • a) with other resources: • UniProt • Genomics resources (e.g. Ensembl) • Metabolomics resources • b) with other researchers in the field.
- 17. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017 Aknowledgements: People Attila Csordas Tobias Ternent Mathias Walzer Gerhard Mayer (de.NBI) Johannes Griss Yasset Perez-Riverol Manuel Bernal-Llinares Andrew Jarnuczak Former team members, especially Rui Wang, Florian Reisinger, Noemi del Toro, Jose A. Dianes & Henning Hermjakob Acknowledgements: The PRIDE Team All data submitters !!! @pride_ebi @proteomexchange
- 18. Juan A. Vizcaíno juan@ebi.ac.uk Danish Bioinformatics Conference Odense, 23 August 2017