standards > terminology artifact > DOI:10.25504/FAIRsharing.sxh2dp


ready HUPO PSI Mass Spectrometry Controlled Vocabulary

Abbreviation: PSI-MS CV


General Information
The PSI-MS Controlled Vocabulary is developed in common with the PSI-Proteomics Informatics group. It consists of a large collection of structured terms covering description and use of Mass Spectrometry instrumentation as well as Protein Identification and Quantitation software. The source of the terms are multiple: they include vocabulary and definitions in chapter 12 of the IUPAC nomenclature book, instrument and software vendors and developers and other user-submitted terms. Although its structure and use is linked to mzML, mzIdentML and mzQuantML, it is dynamically maintained in a OBO format. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS–related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary.

Homepage http://www.psidev.info/groups/mass-spectrometry#controlled

Countries that developed this resource Germany , Sweden , Switzerland , United Kingdom , United States

Created in 2012

Taxonomic range




How to cite this record FAIRsharing.org: PSI-MS CV; HUPO PSI Mass Spectrometry Controlled Vocabulary; DOI: https://doi.org/10.25504/FAIRsharing.sxh2dp; Last edited: March 11, 2019, 12:25 p.m.; Last accessed: Aug 25 2019 10:01 p.m.

Publication for citation  The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Mayer G,Montecchi-Palazzi L,Ovelleiro D,Jones AR,Binz PA,Deutsch EW,Chambers M,Kallhardt M,Levander F,Shofstahl J,Orchard S,Vizcaino JA,Hermjakob H,Stephan C,Meyer HE,Eisenacher M; Database (Oxford) ; 2013; 10.1093/database/bat009;


This record is maintained by HUPO PSI  (HUPOPSI)

Record updated: March 11, 2019, 12:25 p.m. by The FAIRsharing Team.

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In Collections
OBO Foundry
H2020 Phenome and Metabolome aNalysis (PhenoMenal) Project
eTRIKS Standards Starter Pack
FAIRDOM Community Standards
HUPO Proteomics Standards Initiative



Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Release

Download (OBO) https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

Data Access

browse https://www.ebi.ac.uk/ols/ontologies/ms



Publications

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G,Montecchi-Palazzi L,Ovelleiro D,Jones AR,Binz PA,Deutsch EW,Chambers M,Kallhardt M,Levander F,Shofstahl J,Orchard S,Vizcaino JA,Hermjakob H,Stephan C,Meyer HE,Eisenacher M
Database (Oxford) 2013

View Paper (PubMed) View Publication

MS Ontology Display

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View in OBO Foundry.



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Reporting Guidelines

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Terminology Artifacts

Models and Formats

Identifier Schemas

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Implementing Databases (4)
MetaboLights
MetaboLights is a database is a collection of metabolite structures. This resource provides information on the compound origins,the biological roles, locations and concentrations, as well as experimental data from metabolic experiments. The tools and capabilities of this database is firmly routed in collaborative working worldwie with the metabolomics community such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).
Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.
Japan Proteome Standard Repository
jPOSTrepo (Japan ProteOme STandard Repository) is a data repository of sharing MS raw/processed data.
OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

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Credit

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Funds

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Grant Number(s)

  • BB/H024654/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • BB/I000909/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • EU FP7 grant number 260558 (ProteomeXchange)

  • P50 GM076547 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)

  • R01 GM087221 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)

  • WT085949MA (Wellcome Trust, UK)