title: The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
abstract: 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. Database URL: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo.
authors.affiliation: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Mayer
authors.forename: Luisa
authors.initials: L
authors.lastname: Montecchi-Palazzi
authors.forename: David
authors.initials: D
authors.lastname: Ovelleiro
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
authors.forename: Pierre-Alain
authors.initials: PA
authors.lastname: Binz
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Matthew
authors.initials: M
authors.lastname: Chambers
authors.forename: Marius
authors.initials: M
authors.lastname: Kallhardt
authors.forename: Fredrik
authors.initials: F
authors.lastname: Levander
authors.forename: James
authors.initials: J
authors.lastname: Shofstahl
authors.forename: Sandra
authors.initials: S
authors.lastname: Orchard
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Christian
authors.initials: C
authors.lastname: Stephan
authors.forename: Helmut E
authors.initials: HE
authors.lastname: Meyer
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
mesh_terms: D006801:Humans; D013058:Mass Spectrometry / Q000592:standards*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000592:standards*; D012015:Reference Standards; D013223:Statistics as Topic; D018875:Vocabulary, Controlled; D057188:Workflow
chemical_list: D020543:Proteome