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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Bibliographic Details
Published in:Bioinformatics Vol. 22; no. 7; pp. 866 - 873
Main Authors: 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
Language:English
Published: Oxford Oxford University Press 01.04.2006
Oxford Publishing Limited (England)
Subjects:
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
Online Access:Get full text
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Summary: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.
Bibliography:To whom correspondence should be addressed.
istex:C07FBE356BF06B7A85708267950C4D2EE4A5DEA3
Associate Editor: Alvis Brazma
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ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btl005