title: The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
abstract: Controlled vocabularies provide a roadmap through complex biological data. Proteomic data is increasing in volume and is currently poorly served by public repositories due to the large number of different formats in which the data is generated and stored. The Human Proteome Organization Proteome Standards Initiative is establishing standards for data transfer and deposition. These standards utilize ontologies and controlled vocabularies to describe experimental procedures and common processes such as sample preparation This paper will discuss the development of such ontologies by the user community and their current utilization in the fields of protein:proein interactions and mass spectrometry.
authors.affiliation: Sequence Database Group, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Sandra
authors.initials: S
authors.lastname: Orchard
authors.forename: Luisa
authors.initials: L
authors.lastname: Montecchi-Palazzi
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Rolf
authors.initials: R
authors.lastname: Apweiler
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D013058:Mass Spectrometry; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D020543:Proteome; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins; D020543:Proteome