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EBI Meetings
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Proteomics Standards Initiative |
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Mission Statement
The Proteomics Standards Initiative (PSI) aims to define
community standards for data representation in proteomics to
facilitate data comparision, exchange and verification, similar to
the now widely accepted standard for microarray data developed by
the Microarray Gene Expression Data
society (MGED).
The Proteomics Standards Initiative was founded at the HUPO
meeting in Washington, April 28-29, 2002 (see Science 296, 827). As a first step, the PSI will develop standards for two key
areas of proteomics: mass spectrometry and protein-protein
interaction data. |
Protein-Protein interaction
Several well-established databases for protein-protein interaction
data exist, including BIND, DIP, MINT, and the MIPS interaction
tables. However, their data are provided in many different formats and are not synchronised. In addition, many
data producers offer only their data from their own web sites,
again in different formats. The tedious work of combining the data
from different data sources is performed over and over again.
The aim of the PSI is to develop a common data standard that will
allow users to retrieve all relevant data from different sites and
perform comparative analysis of different data sets much more easily than
is currently possible. The standard will define a minimal data model
that allows scientists to provide core data, but refer back to
the original data
source for full information, in particular for complex, fully curated
entries.
As a long-term aim, the standard should allow a synchronisation
of the core data between public protein interaction database
providers, similar to the synchronisation of nucleotide data
between EMBL, GenBank and DDBJ. |
Mass spectrometry
Currently, widely accepted public repositories for mass spectra
do not exist; experimental results are usually compared against a
database of theoretical spectra calculated from protein
databases. It is well known, however, that theoretical and real
spectra for given proteins often differ significantly, in an
unpredictable, but reproducible way.
The aim of the PSI is to evaluate how to improve the identification of
unknown proteins by using a database of experimental spectra of
known peptides. To facilitate the comparison of spectra and their
correct classification, for example according to instrument type, a
standard representation of experimental spectra will be
developed. |
Schedule
19-20 Oct. 2002: PSI meeting in Cambridge, UK
An initial PSI meeting will be held at the European Bioinformatics
Institute near Cambridge, UK, on October 19 and 20. The aim of the
meeting is for both working groups to
- evaluate existing data representations,
- define requirements for a community standard,
- analyse where existing elements, e.g. controlled
vocabularies, can fulfill the requirements
of a community standard, and where new components need to be developed,
- initiate working groups to develop the missing components.
For more information on the first PSI meeting, please see the
following pages:
20 Nov. 2002: Satellite meeting of the First HUPO World Congress
The PSI working groups will have a coordination meeting directly before
the conference to consolidate the first results, and present their
work during the First HUPO World Congress in Paris.
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Contact
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