Proteomics Informatics Standards Working Group Charter

Submitted: 2017-06-13

Template Rev2016b

 

HUPO PSI Proteomics Informatics Standards Working Group Charter

Submitted: 2017-06-13

 

  1. 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 Standards Working Group (PSI-PI W

 

Chair (with affiliation and current email address):

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

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

 

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

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

 

Secretary:

Vacant

 

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

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

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:

psi-pi-dev@lists.sourceforge.net

 

  1. 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, 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 data formats for proteomics workflows.
    • Development of software and adaptation of existing software to support the new mzIdentML version 1.2 (formally released in mid 2017).
    • Extension of mzTab to support the encoding of results coming from Data Independent Acquisition approaches (e.g. SWATH-MS and MSe).
    • Including 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.
    • Completion of formats for proteogenomics (proBed and proBAM). proBed has been formalized already (version 1.0), whereas proBAM is currently undergoing the first round of review of the PSI Document Process. A joint publication including both formats has just been submitted.
    • Work together with the metabolomics standards group to extend mzTab to improve the support for mass spectrometry metabolomics approaches (version 1.1).
    • Work together with the PSI-MS WG to define a set of common metadata and CV for spectral libraries and spectral archives.

 

Goals/Milestones

 

Goal 1: Adapt and further develop existing open source software to support the recently finalised mzIdentML 1.2, promoting its adoption.

Goal 2: Release and publish in a scientific journal the two complementary formats designed for proteogenomics approaches, called proBed (version 1.0 already formalized) and proBAM (still under review in the PSI Document Process).

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: Extend mzTab to support Data Independent Acquisition approaches (e.g. SWATH-MS and MSe).

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: 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 Human Proteome Project guidelines).

Goal 8: 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/proteomics-informatics (and links therein)

             Collaborative software development environment: http://github.com/HUPO-PSI


 

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