HUPO Proteomics Standards Initiative

The PSI Spring Meeting 2007 took place in Lyon, France, April 23-25, 2007.

Topics

Agenda

Sponsors

Report

The PSI Spring meeting was followed by a ProDac meeting, April 26th.
For more info please contact Michael Eisenacher (martin.eisenacher@ruhr-uni-bochum.de)

Topics

In 2006, the HUPO Proteomics Standards Initiative has reached a major milestone with the submission of manuscripts from several work groups to the Nature Biotechnology journal, where currently six manuscripts are under public review. A major topic for the PSI spring meeting 2007 will be the evaluation and incorporation of comments from this new approach into PSI documents and standards. In detail, the following activities are planned for the different PSI work groups:

• Molecular interactions
• Sample processing
• GEL
• Mass spectrometry
• Proteomics informatics
• Protein modifications
• Controlled vocabularies

Molecular Interactions: Focus on Interactome Quality Assesment and Quality Control

Up to 2006, the Molecular Interactions work group of the PSI has focussed on a standardised representation of Molecular Interactions. However, with the PSI MI 2.5 XML format and the lightweight MITAB format defined, we now consider the work on data representation to be in maintenance mode, and we increasingly aim to extend PSI MI work to other areas of community interest. The focus topic of the PSI MI 2006 autumn meeting in Washington was the adaptation of the PSI format to use in the field of protein binding, and this effort is now well under way.

The focus topic of the spring meeting 2007 in Lyon, France, will be Interactome Quality Assesment and Quality Control, with the following initial discussion seeds:

1. Try to find and agree on a Gold Standard dataset of 200-300 proteins with their proven interactions that may allow us to measure the Accuracy and Precision of the different methods. Accuracy, as the degree of conformity of a measurement to its actual (true) value; Precision, as the degree to which further measurements will show the same or similar results, i.e. reproducibility).
2. To catalogue and evaluate published methods to determine confidence values for individual interactions or interaction data sets.
3. No single method has so far found "broad community acceptance". The aim of this meeting and subsequent work is to explore the potential for a broadly applicable Consensus method to determine confidence scores across experimental methods, species, and organisations.

Please contact Javier de las Rivas (jrivas@usal.es) or Henning Hermjakob (hhe@ebi.ac.uk) for suggested agenda items.

Sample Processing

* Reporting Requirements:
The MIAPE (Minimum Information About a Proteomics Experiment -- see link on the PSI home page) documents for Column Chromatography and Capillary Electrophoresis are now at a reasonable stage of maturity and at this meeting we will examine both in some detail. We will also discuss the role of the PSI in the nascent MIBBI (Minimum Information for Biological and Biomedical Investigations) project; specifically how PSI should go forwards in producing or contributing to reporting requirements for areas shared with other domains, such as the description of the origin of (biological) study material, general sample processing (for example, centrifugation) and general statistics (as distinct from proteoinformatics).

* Format development
The meeting will feature a detailed presentation of the current state of the spML model. We will also, time permitting, develop that model further at the meeting. Again we will discuss cross-domain issues, specifically the applicability of the model to metabolomics.

* Controlled Vocabulary
It is likely that a number of updates will be required to sepCV, which contains terms required for both spML and GelML. This CV will be developed in conjunction with the GEL working group.

Mass spectrometry

The PSI-MS working group defines community data formats and controlled vocabulary terms facilitating data comparison, exchange and verification. PSI-MS is focused on the field of mass spectrometry. The mzData format, capturing mass spectral data, is already supported by a number of MS instrument vendors as well as software developers. It is further evolving in a merge with the ISB mzXML format

1. Merge of mzData and mzXML. The merge of both formats is progressing and requires now refinements, completion and validation. CV has to be completed and some of it homogenized with the rest of the PSI-CV;
2. MIAPE-MS. After about 3 1/2 months public comment period on the Nature Biotechnology website, the comments will be evaluated and the document reanalysed and possibly refined.

GEL

• Gel Electrophoresis

  It is anticipated that the GelML format will have completed or will be close to completing the PSI document process. Any remaining issues with the process will be worked through, such that GelML can be released as a stable version 1. It is likely that a number of updates will be required to sepCV, which contains terms required for GelML. This will be developed in conjunction with the SP working group

  The MIAPE GE document will be stable and therefore no development work will be undertaken.

• Gel Informatics

  The group will work on the MIAPE Gel Informatics document to get it ready for submission to the PSI document process. If there is sufficient interest from format developers at the meeting, we will work on GelInfoML. We would like to encourage vendors of gel image informatics software to attend the meeting and contribute to this process.

Proteomics Informatics

The PSI Proteomics Informatics working group is focused on development of
common data formats for mass spectrometry based proteomics analysis
applications. To this end, previous working groups efforts have focused on
the AnalsysisXML format and a shared ontology specification for search
engines.

The PSI-PI group will be working on finalization of the AnalysisXML schema,
which is quickly reaching consensus, and in tandem developing the search
engine ontology following the PSI ontology best practice guidelines agreed
to at the last meeting.

Protein Modifications

The PSI-MOD work group is charged with constructing a hierarchical CV incorporating information from public resources describing protein modifications (RESID, UniMod and DeltaMass). While PSI-MOD has extensive coverage of public resources, maintaining a comprehensive CV hierarchy of protein modifications requires on-going discussion and refinement. Furthermore, the group should establish procedures to synchronize the information in PSI-MOD and maintain concurrency with the source databases.

Controlled Vocabularies

The PSI Controlled Vocabularies (CVs) work group aims at developing
consensus guidelines for CV creation, maintenance and usage across the
various technology based PSI module. In the incoming meeting the group
will focus on a common mapping strategy to describe the
associations between specific elements of exchange schema and the PSI
CVs or other external ontology resources. Moreover the group will continue the development of a common CV for the overlapping area covered redundantly by the technology specific CVs.

Preliminary Agenda

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Molecular Interactions Track - Agenda details

Registration

Registration is closed.

Logistics

Venue:

The meeting will take place at the Ecole Normale Supérieure (ENS) de Lyon.

Hotels:

As for previous PSI meetings, we ask you to make the reservations by your own. More information about suggested hotels will be made available here.

Special prices on Campanile hotels, valid for reservation before March 1st. Please announce access code « rhône-alpes futur »:

Novotel Lyon Gerland
Single: 136 €
Double : 146 €
Breakfast: 13.50 €
Daily tax: 0.77 €
Place Jean de Verrazane
70 avenue Leclerc
69363 LYON
T : + 33 (0) 4 72 71 11 03
http://fr.federal-hotel.com/hotel_novotel-lyon-gerland-lyon_99382.htm

Hôtel Ibis Lyon Gerland
Weekend : 53 €
Weekdays : 79 €
Breakfast : 7 €
Daily tax : 0.55 €
68 avenue Leclerc
69007 LYON
T : + 33 (0) 4 78 58 30 70
http://www.accorhotels.com/accorhotels/fichehotel/fr/ibi/0778/fiche_hotel.shtml

Local organisation:

Yves Vandenbrouck (CEA, Grenoble)

Murielle Felin (Fondation Rhône-Alpes Futur, Lyon)

Magalie d'Orazio (Fondation Rhône-Alpes Futur, Lyon)

Christine Hoogland (SIB, Geneva)

Pierre-Alain Binz (SIB / GeneBio, Geneva)

Sponsors

Already confirmed sponsors (in alphabetic order):

Organisational partners:

Commissariat à l'Energie Atomique Grenoble, ENS Lyon, Fondation Rhône-Alpes Futur, Swiss Institute of Bioinformatics

If your organisation want to financially contribute to the meeting and help in making it as efficient and fruitful as possible, please contact Pierre-Alain Binz (pierre-alain.binz@isb-sib.ch) or Yves Vandenbrouck (yves.vandenbrouck@cea.fr) for more details.

Signups closed for this event