[Psidev-pi-dev] HUPO PSI recommendation document (Universal Spectrum Identifier), 60-days public review

[Martin E. <mar...@ru...>]

Dear colleague,

dear member of the Mass Spectrometry community,

 

please forward this message to potentially interested colleagues!

 

The HUPO Proteomics Standards Initiative (PSI) develops standards 

for documentation and storage of Proteomics data (see 

 <http://www.psidev.info> http://www.psidev.info for an overview of
activities).

 

A recommendation document specifying
the Universal Spectrum Identifier (USI)

has been submitted to the PSI document process.

 

Because it is not a file format, there is neither a Schema definition
nor XML / tab example files, but some practical examples of USIs from 

ProteomeXchange member DBs and others (included in the document).

 

Specification document:
https://github.com/HUPO-PSI/usi/blob/master/Specification/USI_SpecDoc_1.0.dr
aft07_2020-09-29.docx?raw=true

Use case examples: http://www.psidev.info/usi

(USIs used in repository URLs).

Development background:  <https://github.com/HUPO-PSI/usi>
https://github.com/HUPO-PSI/usi

 

After having passed a 30-day review of the PSI steering group 

with minor changes, the proposed document version 1.0.0 DRAFT 7

now goes through 60-days public comments and external 

review phase (end: 18th December 2020).

 

Purpose of the standard (excerpt from the spec. doc.):
"This document presents a specification for a multi-part identifier 

of the form mzspec:<collection>:<msRun>:<indexType>:<indexNumber>:<optional
interpretation> 

for mass spectra so that they may be easily and universally referenced for 

subsequent access. The Universal Spectrum Identifier (USI) describes a 

virtual path to locate a spectrum plus a possible interpretation of that 

spectrum. The USI is being implemented at most ProteomeXchange partner 

repositories and can be freely used by any other software. While initially

implemented for the field of proteomics, its design is amenable to other 

fields that use mass spectrometers for analyte detection."

 

PLEASE SEND COMMENTS directly to mar...@ru...

for example regarding the following criteria:

 

- That it is well formed - that is, it is presented in accordance with the
templates and is clearly written.

- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.

 

This message is to encourage you to contribute to the standards

development activity by commenting on the material that is attached 

as well as available online. We invite both positive and negative comments.

If negative comments are being made, these could be on the relevance, 

clarity, correctness, appropriateness, etc, of the proposal as 

a whole or of specific parts of the proposal.

 

If you do not feel well placed to comment on this document, but 

know someone who may be, please consider forwarding this request. 

There is no requirement that people commenting should have had any 

prior contact with the PSI.

 

    Many thanks for your valuable time and participation

      Martin Eisenacher (PSI Editor)

 

 

--

PD DR. MARTIN EISENACHER

Department Leader

DEPARTMENT Medical Bioinformatics

Medizinisches Proteom-Center

Medical Faculty

&

Medical Proteome Analysis

Center for Proteindiagnostics (PRODI)

 

Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum

Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496

E-mail  <mailto:mar...@ru...> mar...@ru...

 <http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de