Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tool...
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| Veröffentlicht in: | Biochimica et biophysica acta Jg. 1844; H. 1; S. 98 - 107 |
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| Sprache: | Englisch |
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Elsevier B.V
01.01.2014
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| ISSN: | 1570-9639, 0006-3002, 1878-1454 |
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| Abstract | This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the “mapping files” used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
► The semantic annotation using ontologies is a prerequisite for the semantic web. ► The HUPO-PSI defined a set of XML-based standard formats for proteomics. ► These standard formats allow the referencing of CV terms defined in obo files. ► The CV terms can be used to enforce MIAPE compliance of the data files. ► The mass spectrometry CV is constantly maintained in a community process. |
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| AbstractList | This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the “mapping files” used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the “mapping files” used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. ► The semantic annotation using ontologies is a prerequisite for the semantic web. ► The HUPO-PSI defined a set of XML-based standard formats for proteomics. ► These standard formats allow the referencing of CV terms defined in obo files. ► The CV terms can be used to enforce MIAPE compliance of the data files. ► The mass spectrometry CV is constantly maintained in a community process. |
| Author | Montecchi-Palazzi, Luisa Vizcaíno, Juan Antonio Meyer, Helmut E. Oveillero, David Eisenacher, Martin Mayer, Gerhard Jones, Andrew R. Deutsch, Eric W. Hermjakob, Henning Binz, Pierre-Alain Orchard, Sandra Julian, Randall Stephan, Christian |
| Author_xml | – sequence: 1 givenname: Gerhard surname: Mayer fullname: Mayer, Gerhard organization: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany – sequence: 2 givenname: Andrew R. surname: Jones fullname: Jones, Andrew R. organization: Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK – sequence: 3 givenname: Pierre-Alain surname: Binz fullname: Binz, Pierre-Alain organization: SIB Swiss Institute of Bioinformatics, Swiss-Prot group, Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland – sequence: 4 givenname: Eric W. surname: Deutsch fullname: Deutsch, Eric W. organization: Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA – sequence: 5 givenname: Sandra surname: Orchard fullname: Orchard, Sandra organization: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK – sequence: 6 givenname: Luisa surname: Montecchi-Palazzi fullname: Montecchi-Palazzi, Luisa organization: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK – sequence: 7 givenname: Juan Antonio surname: Vizcaíno fullname: Vizcaíno, Juan Antonio organization: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK – sequence: 8 givenname: Henning surname: Hermjakob fullname: Hermjakob, Henning organization: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK – sequence: 9 givenname: David surname: Oveillero fullname: Oveillero, David organization: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK – sequence: 10 givenname: Randall surname: Julian fullname: Julian, Randall organization: Indigo BioSystems, Indianapolis, IN 46240, USA – sequence: 11 givenname: Christian surname: Stephan fullname: Stephan, Christian organization: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany – sequence: 12 givenname: Helmut E. surname: Meyer fullname: Meyer, Helmut E. organization: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany – sequence: 13 givenname: Martin surname: Eisenacher fullname: Eisenacher, Martin email: martin.eisenacher@rub.de organization: Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23429179$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | computer analysis computer software Controlled vocabularies data analysis Ontologies in proteomics Ontology editors and software Ontology formats Ontology maintenance Programming Languages proteins Proteomics Proteomics data standards Software Vocabulary, Controlled |
| Title | Controlled vocabularies and ontologies in proteomics: Overview, principles and practice |
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