1. EBI Proteomics Services Team – Standards, Data, and Tools for Proteomics Henning Hermjakob European Bioinformatics Institute SME forum 2009 Vienna

2. Annotation Context UniProt Proteins Archive PRIDE Mass Spec IntAct Interactions Reactome Pathways Integration and dissemination EnVision DAS

3. The Proteomics Identifications Database (PRIDE) Centralized, standards compliant, public data repository for proteomics identifications Open source Open data 50,287,408 spectra 2,555,194 protein identifications Detailed annotation of meta-data Jones, P, et al: PRIDE: new developments and new datasets. Nucleic Acids Res. 2008 Jan;36(Database issue):D878-83. http://www.ebi.ac.uk/pride

4. PRIDE data content

5. pride-support@ebi.ac.uk http://www.ebi.ac.uk/pride PRIDE web interface – overview

6. pride-support@ebi.ac.uk http://www.ebi.ac.uk/pride PRIDE web interface – experiment and protein

7. pride-support@ebi.ac.uk http://www.ebi.ac.uk/pride PRIDE web interface – mass spectra

8. pride-support@ebi.ac.uk http://www.ebi.ac.uk/pride PRIDE web interface – project comparison

9. pride-support@ebi.ac.uk http://www.ebi.ac.uk/pride PRIDE BioMart

10. pride-support@ebi.ac.uk http://www.ebi.ac.uk/pride The spectacular bit: across-BioMart queries! Question: “Which proteins, identified in PRIDE experiment 2, are involved in nucleotide metabolism” PRIDE Reactome

11. The IntAct Molecular Interaction Database Centralized, standards compliant, public data repository for protein interactions Open source Open data 200.000 binary interaction reports S. Kerrien, et al: IntAct – Open Source Resource for Molecular Interaction Data. Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5. Orchard, S. et al: The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug;25(8):894-8. http://www.ebi.ac.uk/intact

12. The IntAct Molecular Interaction Database

20. Reactome Human pathway knowledgebase Manually curated Open source, open data Collaboration between EBI, OCRI and NYU Online since 2003 Matthews L, et al: Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2008 Nov 3. http://www.ebi.ac.uk/pride

21. Pathways 870 Reactions2900 Proteins2900 Complexes2250 References4200 Reactome content

22. authors summary species GO term other species Pathway description

23. Pathway participants UniProt Ensembl MIM KEGG ChEBI Compound Entrez Gene Hapmap UCSC RefSeq PubChem

24. SkyPainter ‘Painting’ the reaction map with user- supplied data, e.g. over- and under- expressed genes from a microarray analysis Animation for time series experiments Overrepresentation analysis, e.g. disease candidate genes concentrated to a pathway

25. #IDvalue1 P202482.381255 P146352.078063 Q010941.358003 P083191.274531 O950671.251352 P120041.031162 P303051.654142 P161041.274092 P339921.560363 P352491.185243 O949132.410139 Q134151.085086 Q150541.148979 P303072.270973 O754960.796653 P497360.998988 Q132432.634955 P506131.466119 O754191.853295 P303040.863513 O960170.889464 P383981.068929 P067301.789461 P159270.89531 P300380.655572 P515301.060222 P171741.611088 P352500.58771 … Usable identifiers: UniProt RefSeq Ensembl MIM Entrez Gene KEGG COMPOUND ChEBI Affymetrix GO SkyPainter

26. SkyPainter coloring according to the numeric values provided

27. SkyPainter Overrepresentation analysis

28. The Team EU: –ProDaC (to 03/2009) –ProteomeBinders –BioSapiens –Felics –LipidomicNet –APO-SYS –PSIMEx (since 03/2009) EMBL Wellcome Trust NIH The Funding

29. ?

30. Lab B Private Data in PRIDE “Collaboration” Comparison Reviewer Lab A Lab C PRIDE private mode Publicly available data Private mode allows data analysis within a collaboration PRIDE tools are already accessible in private mode, in particular experiment comparison (alpha) On manuscript submission, reviewers can access the data in standard format

31. Lab B Private Data “Collaboration” Reviewer Lab A Lab C PRIDE private mode Publicly available data Private mode allows data analysis within a collaboration PRIDE tools are already accessible in private mode, in particular experiment comparison (alpha) On manuscript submission, reviewers can access the data in standard format On manuscript publication, the data becomes public