The MGED Ontology: a resource for semantics-based description of microarray experiments

Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene E...

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Veröffentlicht in:	Bioinformatics Jg. 22; H. 7; S. 866 - 873
Hauptverfasser:	Whetzel, Patricia L., Parkinson, Helen, Causton, Helen C., Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, Game, Laurence, Heiskanen, Mervi, Morrison, Norman, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Taylor, Chris, White, Joseph, Stoeckert, Christian J.
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Oxford Oxford University Press 01.04.2006 Oxford Publishing Limited (England)
Schlagworte:	Bioinformatics Biological and medical sciences Computational Biology - methods Computer Simulation Data management Database Management Systems Developmental stages Fundamental and applied biological sciences. Psychology Gene Expression Profiling - methods General aspects Information Storage and Retrieval - methods Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Biological Oligonucleotide Array Sequence Analysis - methods Programming Languages Semantics User-Computer Interface Description Organization Ontology DNA chip Resource Information Microarray Annotation Original document Association Semantics Classification Database Bioinformatics
ISSN:	1367-4803, 1460-2059, 1367-4811
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Abstract	Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at . Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (). Contact:Stoeckrt@pcbi.upenn.edu Supplementary information: Supplementary data are available at Bioinformatics online.
AbstractList	Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at . Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (). Contact:Stoeckrt@pcbi.upenn.edu Supplementary information: Supplementary data are available at Bioinformatics online. MOTIVATION: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. RESULTS: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. AVAILABILITY: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). CONTACT: Stoeckrtcbi.upenn.edu Supplementary information: Supplementary data are available at Bioinformatics online. The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards.MOTIVATIONThe generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards.Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation.RESULTSHere we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation.The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do).AVAILABILITYThe MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do).Stoeckrt@pcbi.upenn.eduCONTACTStoeckrt@pcbi.upenn.eduSupplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at . Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (). Contact: Stoeckrt@pcbi.upenn.edu Supplementary information: Supplementary data are available at Bioinformatics online. The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). Stoeckrt@pcbi.upenn.edu Supplementary data are available at Bioinformatics online. Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). Contact: Stoeckrt@pcbi.upenn.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Author	Parkinson, Helen Taylor, Chris Heiskanen, Mervi Game, Laurence Whetzel, Patricia L. Causton, Helen C. Fostel, Jennifer Rocca-Serra, Philippe Fragoso, Gilberto Sansone, Susanna-Assunta White, Joseph Morrison, Norman Fan, Liju Stoeckert, Christian J.
Author_xml	– sequence: 1 givenname: Patricia L. surname: Whetzel fullname: Whetzel, Patricia L. organization: Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of MedicineUSA – sequence: 2 givenname: Helen surname: Parkinson fullname: Parkinson, Helen organization: European Bioinformatics InstituteWellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK – sequence: 3 givenname: Helen C. surname: Causton fullname: Causton, Helen C. organization: MRC Clinical Sciences Centre, Faculty of Medicine, Imperial CollegeHammersmith Hospital Campus, DuCane Road, London W12 0NN, UK – sequence: 4 givenname: Liju surname: Fan fullname: Fan, Liju organization: Ontology Workshop LLCPO Box 182, Columbia, MD 21045-9998, USA – sequence: 5 givenname: Jennifer surname: Fostel fullname: Fostel, Jennifer organization: NIEHSPO Box 12233 MD F1-05, 111 Alexander Drive Research Triangle Park, NC 27709-2233, USA – sequence: 6 givenname: Gilberto surname: Fragoso fullname: Fragoso, Gilberto organization: NCICB, NCI Center for Bioinformatics6116 Executive Boulevard, Rockville, MD 20852, USA – sequence: 7 givenname: Laurence surname: Game fullname: Game, Laurence organization: MRC Clinical Sciences Centre, Faculty of Medicine, Imperial CollegeHammersmith Hospital Campus, DuCane Road, London W12 0NN, UK – sequence: 8 givenname: Mervi surname: Heiskanen fullname: Heiskanen, Mervi organization: NCICB, NCI Center for Bioinformatics6116 Executive Boulevard, Rockville, MD 20852, USA – sequence: 9 givenname: Norman surname: Morrison fullname: Morrison, Norman organization: Department of Computer Science, Kilburn Building University of ManchesterOxford Road, Manchester M13 9PL, UK – sequence: 10 givenname: Philippe surname: Rocca-Serra fullname: Rocca-Serra, Philippe organization: European Bioinformatics InstituteWellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK – sequence: 11 givenname: Susanna-Assunta surname: Sansone fullname: Sansone, Susanna-Assunta organization: European Bioinformatics InstituteWellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK – sequence: 12 givenname: Chris surname: Taylor fullname: Taylor, Chris organization: European Bioinformatics InstituteWellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK – sequence: 13 givenname: Joseph surname: White fullname: White, Joseph organization: Dana-Farber Cancer Institute44 Binney Street, Boston, MA 02115, USA – sequence: 14 givenname: Christian J. surname: Stoeckert fullname: Stoeckert, Christian J. organization: Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of MedicineUSA
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References	Ball (2023012409104819500_b1) 2005; 33 Bechhofer (2023012409104819500_b3) 2001; 2174 Gardiner-Garden (2023012409104819500_b8) 2001; 2 Navarange (2023012409104819500_b15) 2005; 6 Eilbeck (2023012409104819500_b7) 2005; 5 Kemp (2023012409104819500_b11) 2003; 307 Tomasulo (2023012409104819500_b19) 2002; 21 Covitz (2023012409104819500_b6) 2003; 19 Berman (2023012409104819500_b4) 2000; 28 Ikeo (2023012409104819500_b10) 2003; 326 Rogers (2023012409104819500_b17) 2001; 10 Parkinson (2023012409104819500_b16) 2005; 33 Spellman (2023012409104819500_b18) 2002; 3 Manduchi (2023012409104819500_b13) 2004; 20 Brazma (2023012409104819500_b5) 2001; 29 Mattes (2023012409104819500_b14) 2004; 112 Lindon (2023012409104819500_b12) 2005; 23 Barrett (2023012409104819500_b2) 2005; 33 Wheeler (2023012409104819500_b20) 2005; 33 Gene Ontology Consortium. (2023012409104819500_b9) 2001; 11
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SubjectTerms	Bioinformatics Biological and medical sciences Computational Biology - methods Computer Simulation Data management Database Management Systems Developmental stages Fundamental and applied biological sciences. Psychology Gene Expression Profiling - methods General aspects Information Storage and Retrieval - methods Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Biological Oligonucleotide Array Sequence Analysis - methods Programming Languages Semantics User-Computer Interface
Title	The MGED Ontology: a resource for semantics-based description of microarray experiments
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