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International Data Exchange and Data Representation Standards for Proteomics

Objective

Over the last few years the field of proteomics has evolved into a prolific data producer. As a result, various databases that collect and redistribute the acquired data have been established. While data format standards for quantitative proteomics have now been defined and implemented with significant contribution from the recently completed EU ProDaC grant, standards for quantitative proteomics are still lacking.
This simultaneous creation of multiple repositories and databases, and lack of standards for quantitative proteomics result in a fragmentation of data, and cause confusion for data submitters and users alike.
Based on consortium expertise in the operation of large scale proteomics repositories (PRIDE, PeptideAtlas, Tranche, Peptidome) we aim to implement the next step, regular data exchange between major international proteomics resources. In parallel, we will further develop standards (mzQuantML) for the dynamic field of quantitative mass spectrometry.
The main objectives of ProteomExchange are user-oriented: (i) to provide a single point of data submission to the user; (ii) to ensure data availability in all of the different member databases; (iii) to use community standard formats to represent the data, so it becomes accessible to all regardless of data origin; (iv) to provide added value through different views on the same data, from repositories to derived search tools.
With an international consortium and support from large scale data producers (ISAS (Germany), U. Cambridge (UK), Karolinska Institute (Sweden)), industry (Pfizer, Philips, Waters), and journals (Nature Biotechnology, MCP, JPR), we here propose a Coordination Action project to solidify an emerging informal collaboration between major repositories into a production-quality data deposition and dissemination consortium on par with the systems so successfully employed by three-dimensional structure databases and nucleotide sequence databases, amongst others.

Field of science

  • /natural sciences/computer and information sciences/databases
  • /natural sciences/computer and information sciences/data science/data exchange
  • /natural sciences/biological sciences/biochemistry/biomolecules/proteins/proteomics
  • /natural sciences/chemical sciences/analytical chemistry/mass spectrometry

Call for proposal

FP7-HEALTH-2010-single-stage
See other projects for this call

Funding Scheme

CSA-CA - Coordination (or networking) actions

Coordinator

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Address
Meyerhofstrasse 1
69117 Heidelberg
Germany
Activity type
Research Organisations
EU contribution
€ 502 457
Administrative Contact
Tom Ratcliff (Mr.)

Participants (12)

THE UNIVERSITY OF LIVERPOOL
United Kingdom
EU contribution
€ 204 028
Address
Brownlow Hill 765 Foundation Building
L69 7ZX Liverpool
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Jenny Lawson (Ms.)
VIB VZW
Belgium
EU contribution
€ 187 249
Address
Rijvisschestraat 120
9052 Zwijnaarde - Gent
Activity type
Research Organisations
Administrative Contact
Rik Audenaert (Mr.)
EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Switzerland
EU contribution
€ 94 160
Address
Raemistrasse 101
8092 Zuerich
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Rudolf Aebersold (Prof.)
Institute for Systems Biology
United States
EU contribution
€ 137 302
Address
North 34Th Street 1441
98103-8904 Seattle
Activity type
Research Organisations
Administrative Contact
Trudy Adkins (Ms.)
UNIVERSITY OF MICHIGAN THE REGENTS OF THE UNIVERSITY OF MICHIGAN
United States
EU contribution
€ 68 377
Address
South Street 3003 1068
46109 1274 Ann Arbor
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Christine Koch (Ms.)
INTEGROMICS SL ITG
Spain
EU contribution
€ 186 728
Address
Avenida De Innovacion Granada Parque Tecnologia Ciencas De La Salud 1 Bic
18100 Armilla -Granada
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Isabel Cuesta Rojo (Dr.)
RUHR-UNIVERSITAET BOCHUM
Germany
EU contribution
€ 222 560
Address
Universitaetsstrasse 150
44801 Bochum
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Rhena Beckmann-Fuchs (Ms.)
SIB INSTITUT SUISSE DE BIOINFORMATIQUE
Switzerland
EU contribution
€ 143 629
Address
Rue Michel Servet 1 Cmu
1206 Geneve
Activity type
Research Organisations
Administrative Contact
Jocelyne Bocquet (Ms.)
GENEVA BIOINFORMATICS (GENEBIO) SA
Switzerland
EU contribution
€ 67 559
Address
Avenue De Champel 25
1206 Geneve
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Pierre-Alain Binz (Dr.)
WILEY-VCH VERLAG GMBH & CO KGAA
Germany
EU contribution
€ 36 380
Address
Boschstrasse 12
69469 Weinheim
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Hans-Joachim Kraus (Dr.)
AGENCIA ESTATAL CONSEJO SUPERIOR DEINVESTIGACIONES CIENTIFICAS
Spain
EU contribution
€ 60 000
Address
Calle Serrano 117
28006 Madrid
Activity type
Research Organisations
Administrative Contact
Eusebio Jiménez Arroyo (Mr.)
SCIENTIFIC NETWORK MANAGEMENT SL
Spain
EU contribution
€ 15 533
Address
Calle Ateneu 17
08960 Sant Just Desvern Barcelona
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Pascal Kahlem (Dr.)