Status (New/Update): Update
A group name should be reasonably descriptive or identifiable. Additionally, the group must define an acronym (maximum of 8 printable ASCII characters) to reference the group in the PSI directories, mailing lists, and general documents. The name and acronym must not conflict with any other PSI name and acronym.
HUPO PSI Proteomics Informatics Standards Working Group (PSI-PI WG)
Chair (with affiliation and current email address):
Juan Antonio Vizcaíno – EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK (firstname.lastname@example.org)
Co-Chairs (1 or 2) (with affiliation and current email address):
Andy Jones, University of Liverpool, UK (email@example.com)
Martin Eisenacher – Medizinisches Proteom Center, Ruhr-Universität Bochum, Germany (firstname.lastname@example.org)
Other officers (optional) (with affiliation and current email address):
Editor(s): Gerhard Mayer - Medizinisches Proteom Center, Ruhr-Universität Bochum, Germany (email@example.com)
Minimal Reporting Requirements Coordinator(s): Pierre-Alain Binz, CHUV – Centre Hospitalier Universitaire Vaudois, Lausanne Switzerland (firstname.lastname@example.org)
Ontology Coordinator(s): Gerhard Mayer - Medizinisches Proteom Center, Ruhr-Universität Bochum, Germany (email@example.com)
Web site Maintainer(s): Da Qi, University of Liverpool, UK (firstname.lastname@example.org)
2.Description and objectives
Focus and Purpose
The PSI-PI working group is composed of academic, government, and industry researchers, software developers, journal representatives, and instrument manufacturers. The main goal of the PSI-PI working group is to define community data formats and associated controlled vocabulary (CV) terms, facilitating data exchange and archiving of the downstream results of proteomics analysis by mass spectrometry (MS), including the identification and quantification of peptides and proteins by software, and the output of integrative analysis of proteomics data with other omics technologies (e.g. proteogenomics analysis).
Current projects of the PSI-PI working group are:
- Ongoing maintenance and enhancement of the mzIdentML and mzTab data formats for proteomics workflows.
- Development of software and adaptation of existing ones to support mzIdentML version 1.2.
- This includes the maintenance and further development of the PSI-MS CV, jointly with the PSI-MS WG (Mass Spectrometry Working Group), and the new XLMOD CV, including cross-linker reagents.
- Development of software to support the proteogenomics standard formats (proBed and proBAM).
- Development of ProXI (the Proteomics eXpression Interface) as a standard Application Programming Interface for accessing different proteomics data types through ProteomeXchange resources.
- Work together with the Metabolomics Standards Initiative (MSI) to extend mzTab to improve the support for MS metabolomics approaches (mzTab-M).
- Work together with the PSI-MS WG to define a set of common metadata and CV for spectral libraries and spectral archives.
Goal 1: Adapt and further develop existing open source software to support mzIdentML version 1.2, promoting its adoption.
Goal 2: Development of ProXI, as a standard interface to access different types of data types through ProteomeXchange resources.
Goal 3: Develop software to support the recently finalised two formats designed for proteogenomics approaches, proBed and proBAM.
Goal 4: Co-lead the development and adaptation of mzTab for metabolomics (mzTab-M), in collaboration with the Metabolomics Standards Initiative (MSI).
Goal 5: Further development and maintenance of the recently created XLMOD CV for cross-linker reagents.
Goal 6: Coordinate efforts in the maintenance and further development of open source software that support the data standards developed by the WG.
Goal 7: Work together with the PSI-Mass Spectrometry Group to define a set of common metadata and controlled vocabulary for spectral libraries and archives.
Website: http://www.psidev.info/groups/proteomics-informatics (and links therein)
Collaborative software development environment: http://github.com/HUPO-PSI