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Design and implementation of microarray gene expression markup language (MAGE-ML)
- Source :
- Genome Biology, Europe PubMed Central
- Publication Year :
- 2002
- Publisher :
- BioMed Central, 2002.
-
Abstract
- Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.<br />Background Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies. Results To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems. Conclusions MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
- Subjects :
- Markup language
Microarray
business.industry
Minimum information about a microarray experiment
Microarray analysis techniques
Research
Gene Expression Profiling
Database schema
Computational biology
Sequence Analysis, DNA
Biology
computer.software_genre
Models, Biological
Gene expression profiling
Microarray gene expression
Microarray databases
Computer Simulation
Programming Languages
Artificial intelligence
business
computer
Natural language processing
Oligonucleotide Array Sequence Analysis
Subjects
Details
- Language :
- English
- ISSN :
- 14656914 and 14656906
- Volume :
- 3
- Issue :
- 9
- Database :
- OpenAIRE
- Journal :
- Genome Biology
- Accession number :
- edsair.doi.dedup.....530ada04a2e267bab229d266f075783a