Ontologies and Processing Patterns for Microarrays
Mónica Miguélez Rico (University of A Coruña, Spain), José Antonio Seoane Fernández (University of A Coruña, Spain) and Julián Dorado de la Calle (University of A Coruña, Spain)
Copyright: © 2009
The researchers currently have a new tool for dealing with the solution of biomedical problems: the Microarrays. These devices support the study and the acquisition of information related to many genes at the same time by means of a unique experiment, providing multiple potential applications such as mutation detection of microorganism identification. Some of the problems that exist when working with this type of technologies are the high number of data and the complex technical nomenclature to be dealt with. These facts imply the need of using several standards and ontologies when performing this type of experiments.
Main Focus Of The Chapter
This paper presents a description of the most important standards and ontologies for working with microarrays experiments; it also tackles the integration options of some of these ontologies and standards into an information system for managing microarrays.
The first standardisation initiatives appeared in 1998. They were more or less isolated initiatives where three standardisation areas could be distinguished: hardware, fixed material and procedures for analysis and storage of studies information. Several organisations as the MGED Normalization Working Group (MGED Data, 2006) were created for the standardisation of the information. The MGED (Microarray Gene Expression Data) Society is an international organisation devoted to the standardisation and to the exchange of information related to microarrays experiments. Other organisations to be mentioned are the OMG (Object Management Group) (OMG, 2006) or the UCL/HGNC (Human Gene Nomenclature) (HGNC, 2006).
Key Terms in this Chapter
MIAME: Minimum Information About a Microarray Experiment. Standard that indicates the minimal information needed for microarrays experiments.
MicroArrays: A technology using a high-density array of nucleic acids, protein, or tissue for simultaneously examining complex biological interactions which are identified by specific location on a slide array. A scanning microscope detects the bound, labelled sample and measures the visualized probe to ascertain the activity of the genes of interest in genotyping, cellular studies, and expression analysis.
R: Language and programming environment for graphic and statistical analysis.
Ontology: In computer science this term refers to the attempt of formulate an exhaustive and rigorous conceptual schema into a given domain, with the aim of making communication and information sharing among systems easier.
MAGE-stk: MAGE Software Toolkit. Open Source Package collection that implements the MAGE (MAGE-OM) model of objects in several programming languages.
MAGE-OM: MicroArray and Gene Experiment Object Model. Standard that defines the model of objects for the gene expression-based experiments.
MAGE-ML: Microarray Gene Expression Markup Language. Formal language designed for describing and communicating the experiment-based microarrays information.