1. A plant-specific annotation and submission tool for the incorporation of Arabidopsis gene expression data into ArrayExpress, the EBI’s public DNA microarray database Gaurab Mukherjee, Susanna Sansone, Helen Parkinson, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Philippe Rocca- Serra, Ugis Sarkans, Mohammad Shojatalab, Jaak Vilo and Alvis Brazma. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK CONCEPTS MIAME (1) (Minimum Information about a Microarray Experiment): A set of guidelines to describe the minimum information required to unambiguously interpret microarray data and to subsequently allow independent verification of this data at a later stage if required. MIAMExpress: This is the data annotation and submission tool for ArrayExpress. MIAMExpress is presented in the form of a questionnaire, where the required fields are taken from MIAME concepts. Therefore, it generates MIAME compliant information. ArrayExpress (2) : The EBI’s public repository of DNA microarray data, is aimed at storing well annotated data in accordance with MIAME recommendations. ArrayExpress is based on the MAGE-OM object model and is implemented in Oracle. MGED (Microarray Gene Expression Data) Society: Has been developing ontologies for microarray experiment description, and biological material (biomaterial) annotation in particular. The existing biomaterial ontology provides gene expression specific concepts and terms, and references external ontologies whenever possible. http://www.ebi.ac.uk/microarray References: 1 Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. A Brazma, et.al. 2001 Nature Genetics, vol.29, pp 365-371 2 Microarray Data Representation, Annotation and Storage. A Brazma et. al. 2002 Advances in Biochemical Engineering/Biotechnology, vol.77(Chip Technology), pp113-139 FUTURE DEVELOPMENT -The MGED ontology is now being extended to encompass further plant-specific terms where these cannot be referenced externally. -With this aim, a controlled vocabulary describing Arabidopsis growth and development is being produced. The group is collaborating with the GO (Gene Ontology) and TAIR (The Arabidopsis Information Resource) consortiums on producing such an ontology. Other plant-specific ontologies such as PO (Plant Ontology) and TO (Trait Ontology) may be used to further extend the capacity of MIAMExpress. -The EBI is collaborating with the CAGE (Compendium of Arabidopsis Gene Expression) project. The aim is to build a compendium of mRNA expression profile of Arabidopsis thaliana and to produce a plant-specific MIAMExpress interface to help submit gene expression data and host it in ArrayExpress. -The MGED ontology with the biomaterial package showing some of its classes (©), and its mapping to experimental factors. A worked-example microarray experiment submitted in MIAMExpress and its correct annotation using the MGED ontology classes (©) and the corresponding external references. “Novel defence response pathways associated with nonhost resistance of Arabidopsis to the potato blight pathogen Phytophthora infestans……” -The MIAMExpress submission pages consists of web- based forms with controlled vocabularies. The user fills in the form to describe the experiment. -The current user interface is generic, a plant-specific interface is being developed. -Wherever possible external references are utilised. -Protocols for RNA extraction, labelling, hybridization and scanning can be submitted by the user as forms or uploaded directly to MIAMExpress. TAIR ontology (DAG-edit view) ©-BioMaterialDescription ©-Biosource Property ©-Organism ©-Genotype ©-Phenotype ©-BiosourceProvider ©-DevelopmentStage ©-BioMaterialManipulation ©-EnvironmentalHistory; ©-Treatment ©-GrowthCondition ©-Temperature ©-Humidity ©-Light ©-Infection MGED Ontology Instances Arabidopsis thaliana ID: 3702 Wild Type Col-3, Columbia Ecotype Stock No. CS908 Complete rosette;ID: 0000418 21 C 30-40% 16h light/8h dark cycle Phytophthora infestans External References NCBI Taxonomy TAIR Arabidopsis Ontology ABRC/NASC stock code