TY - JOUR
T1 - Design and implementation of microarray gene expression markup language (MAGE-ML)
AU - Spellman, Paul T.
AU - Miller, Michael
AU - Stewart, Jason
AU - Troup, Charles
AU - Sarkans, Ugis
AU - Chervitz, Steve
AU - Bernhart, Derek
AU - Sherlock, Gavin
AU - Ball, Catherine
AU - Lepage, Marc
AU - Swiatek, Marcin
AU - Marks, Wl
AU - Goncalves, Jason
AU - Markel, Scott
AU - Iordan, Daniel
AU - Shojatalab, Mohammadreza
AU - Pizarro, Angel
AU - White, Joe
AU - Hubley, Robert
AU - Deutsch, Eric
AU - Senger, Martin
AU - Aronow, Bruce J.
AU - Robinson, Alan
AU - Bassett, Doug
AU - Stoeckert, Christian J.
AU - Brazma, Alvis
N1 - Publisher Copyright:
© 2002, Spellman et al., licensee BioMed Central Ltd.
PY - 2002/8/1
Y1 - 2002/8/1
N2 - 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.
AB - 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.
KW - Application Programmer Interface
KW - Database Schema
KW - Microarray Experiment
KW - Microarray Gene Expression
KW - Unify Modeling Language
UR - http://www.scopus.com/inward/record.url?scp=0037163144&partnerID=8YFLogxK
U2 - 10.1186/gb-2002-3-9-research0046
DO - 10.1186/gb-2002-3-9-research0046
M3 - Article
C2 - 12225585
AN - SCOPUS:0037163144
SN - 1474-7596
VL - 3
JO - Genome biology
JF - Genome biology
IS - 9
M1 - research0046.1
ER -