Proteomics Informatics Standards Working Group Charter

Submitted: 2016-06-10

Template Rev2016b


1.Administrative Section

Status (New/Update): Update

Group Name:

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 Working Group (PSI-PI WG)

 

Chair (with affiliation and current email address):

Andy Jones, University of Liverpool, UK (andrew.jones@liverpool.ac.uk)

 

Co-Chairs (1 or 2) (with affiliation and current email address):

Martin Eisenacher – Medizinisches Proteom Center, Ruhr-Universität Bochum, Germany (martin.eisenacher@rub.de)

Juan Antonio Vizcaíno – EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK (juan@ebi.ac.uk)


Secretary:

Juan Antonio Vizcaíno – EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK (juan@ebi.ac.uk)

 

Other officers (optional) (with affiliation and current email address):

Editor(s): Gerhard Mayer - Medizinisches Proteom Center, Ruhr-Universität Bochum, Germany (gerhard.mayer@rub.de)

Minimal Reporting Requirements Coordinator(s): Pierre-Alain Binz, CHUV – Centre hospitalier universitaire vaudois, Lausanne Switzerland (pierre-alain.binz@chuv.ch)

                                                                                  

Ontology Coordinator(s): Gerhard Mayer - Medizinisches Proteom Center, Ruhr-Universität Bochum, Germany (gerhard.mayer@rub.de)

Web site Maintainer(s): Da Qi, University of Liverpool, UK (ddq@liverpool.ac.uk)

 

Mailing list:

psidev-pi-dev@lists.sourceforge.net

 
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 terms, facilitating data exchange and archiving of the downstream results of proteomics analysis by mass spectrometry, 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, mzQuantML and mzTab formats

    • Including adding support for cross-linking studies, involving also the creation of a controlled vocabulary (CV) for cross-linker reagents;

    • Including the maintenance and further development of the PSI-MS CV, jointly with the PSI-MS WG.

  • Completion of formats for proteogenomics (proBED, ProBAM).

  • Coordinating outreach to the metabolomics standards group for the extension of mzTab.

 

Goals/Milestones

Goal 1: Develop, release and support mzIdentML 1.2.

Goal 2: Assist in the defining, development and release of two complementary formats for the assisting in proteogenomics approaches (the use of proteomics data for annotating genomes), for example storing chromosomal coordinates to which peptides have been mapped, along with scores and metadata. The two formats are proteomics-specific adaptations of genomics formats – BED and BAM, called ProBed and proBAM. 

Goal 3: Standards organizations in metabolomics (MSI; COSMOS) are tasked with developing similar standards to those in use in PSI, particularly for metabolite identification and quantification from mass spectrometry. PSI-PI WG is assisting in the development and adaptation of mzTab for metabolomics.

Goal 4: Development and maintenance of an ontology/CV for cross-linker reagents. 

Goal 5: Coordinate efforts in the maintenance and further development of open source software that support the data standards developed by the WG. 

Goal 6: Align and update the corresponding MIAPE documents with the updates of the mzIdentML, mzQuantML, mzTAB, the covered workflows and make it compatible with external guidelines (for instance the HPP guidelines)

 

Website: http://www.psidev.info/proteomics-informatics (and links therein)




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