EBI Proteomics Services Team –

Standards, Data, and Tools for Proteomics

Henning HermjakobEuropean Bioinformatics Institute

SME forum 2009Vienna

Annotation

Context

UniProtProteins

Archive PRIDEMass Spec

IntActInteractions

ReactomePathways

Integration and dissemination

EnVision

DAS

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

PRIDE data content

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

PRIDE web interface – overview

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

PRIDE web interface – experiment and protein

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

PRIDE web interface – mass spectra

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

PRIDE web interface – project comparison

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

PRIDE BioMart

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”PRIDEReactome

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

The IntAct Molecular Interaction Database

The IntAct Molecular Interaction Database

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

• Pathways 870

• Reactions 2900

• Proteins 2900

• Complexes 2250

• References 4200

Reactome content

authors

summary

speciesGO term

other species

Pat

hway

desc

riptio

n

Pat

hway

part

icip

ants

UniProtEnsembl

MIMKEGG

ChEBICompound

Entrez Gene

HapmapUCSC

RefSeq

PubChem

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

#ID value1P20248 2.381255P14635 2.078063Q01094 1.358003P08319 1.274531O95067 1.251352P12004 1.031162P30305 1.654142P16104 1.274092P33992 1.560363P35249 1.185243O94913 2.410139Q13415 1.085086Q15054 1.148979P30307 2.270973O75496 0.796653P49736 0.998988Q13243 2.634955P50613 1.466119O75419 1.853295P30304 0.863513O96017 0.889464P38398 1.068929P06730 1.789461P15927 0.89531P30038 0.655572P51530 1.060222P17174 1.611088P35250 0.58771…

Usable identifiers:

•UniProt

•RefSeq

•Ensembl

•MIM

•Entrez Gene

•KEGG COMPOUND

•ChEBI

•Affymetrix

•GO

SkyPainter

SkyPaintercoloring according to the numeric values provided

SkyPainterOverrepresentation analysis

The Team• EU:

– ProDaC (to 03/2009)– ProteomeBinders– BioSapiens– Felics– LipidomicNet– APO-SYS– PSIMEx (since 03/2009)

• EMBL• Wellcome Trust• NIH

The Funding

• ?

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

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