The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary

Research output: Contribution to journalArticle

Standard

The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary. / Mayer, Gerhard; Montecchi-Palazzi, Luisa; Ovelleiro, David; Jones, Andrew R.; Binz, Pierre-Alain; Deutsch, Eric W.; Chambers, Matthew; Kallhardt, Marius; Levander, Fredrik; Shofstahl, James; Orchard, Sandra; Vizcaino, Juan Antonio; Hermjakob, Henning; Stephan, Christian; Meyer, Helmut E.; Eisenacher, Martin.

In: Database: the Journal of Biological Databases and Curation, 2013, p. bat009.

Research output: Contribution to journalArticle

Harvard

Mayer, G, Montecchi-Palazzi, L, Ovelleiro, D, Jones, AR, Binz, P-A, Deutsch, EW, Chambers, M, Kallhardt, M, Levander, F, Shofstahl, J, Orchard, S, Vizcaino, JA, Hermjakob, H, Stephan, C, Meyer, HE & Eisenacher, M 2013, 'The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary', Database: the Journal of Biological Databases and Curation, pp. bat009. https://doi.org/10.1093/database/bat009

APA

Mayer, G., Montecchi-Palazzi, L., Ovelleiro, D., Jones, A. R., Binz, P-A., Deutsch, E. W., ... Eisenacher, M. (2013). The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary. Database: the Journal of Biological Databases and Curation, bat009. https://doi.org/10.1093/database/bat009

CBE

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz P-A, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaino JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M. 2013. The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary. Database: the Journal of Biological Databases and Curation. bat009. https://doi.org/10.1093/database/bat009

MLA

Vancouver

Author

Mayer, Gerhard ; Montecchi-Palazzi, Luisa ; Ovelleiro, David ; Jones, Andrew R. ; Binz, Pierre-Alain ; Deutsch, Eric W. ; Chambers, Matthew ; Kallhardt, Marius ; Levander, Fredrik ; Shofstahl, James ; Orchard, Sandra ; Vizcaino, Juan Antonio ; Hermjakob, Henning ; Stephan, Christian ; Meyer, Helmut E. ; Eisenacher, Martin. / The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary. In: Database: the Journal of Biological Databases and Curation. 2013 ; pp. bat009.

RIS

TY - JOUR

T1 - The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary

AU - Mayer, Gerhard

AU - Montecchi-Palazzi, Luisa

AU - Ovelleiro, David

AU - Jones, Andrew R.

AU - Binz, Pierre-Alain

AU - Deutsch, Eric W.

AU - Chambers, Matthew

AU - Kallhardt, Marius

AU - Levander, Fredrik

AU - Shofstahl, James

AU - Orchard, Sandra

AU - Vizcaino, Juan Antonio

AU - Hermjakob, Henning

AU - Stephan, Christian

AU - Meyer, Helmut E.

AU - Eisenacher, Martin

PY - 2013

Y1 - 2013

N2 - Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)-Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. 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. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies.

AB - Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)-Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. 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. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies.

U2 - 10.1093/database/bat009

DO - 10.1093/database/bat009

M3 - Article

SP - bat009

JO - Database : the journal of biological databases and curation

T2 - Database : the journal of biological databases and curation

JF - Database : the journal of biological databases and curation

SN - 1758-0463

ER -