An Ontology for Microarray Experiments and Analysis

Introduction

Although MAGE has proven to be a valuable standard for the reporting of DNA microarray data, its use at present has been largely limited to communicating raw data from individual functional genomics experiments. While the MIAME standards specify that data transformations including normalisation and criteria for the selection of “significant genes” should be part of any microarray report, we still lack a consistent and unambiguous way of describing these analyses. A controlled vocabulary is required to allow researchers to effectively communicate the quantitation types used in any analysis and to allow for an unbiased assessment of the quality of each individual hybridisation, and of the value of assessing the overall confidence in any measurement arising from a complete microarray study.

A Normalisation and Transformation Ontology (NTO)

As part of the MGED ontology, a normalisation and transformation ontology is being developed to describe data transformations. The ontology will cover aspects of microarray data such as normalisation techniques, quality metrics and quality control and data transformation. The development of this ontology will employ several strategies including from workshop group discussion, analysis of current vocabulary and from text mining of relevant literature.

Term Submission

If you would like to suggest or submit candidate terms to the NTO, please see the template term spreadsheet which can be found below. This is the preferred format for term submission, that is, each term having a name, definition and, if appropriate, an indication of parent or child relationship (shown as indentation in the excel spreadsheet only - this is lost on google doc version). Note that a description of input, transformation and output is also included where appropriate in the description. Also note CamelCase format.