Design and implementation of microarray gene expression markup language (MAGE-ML).

Paul Spellman, Michael Miller, Jason Stewart, Charles Troup, Ugis Sarkans, Steve Chervitz, Derek Bernhart, Gavin Sherlock, Catherine Ball, Marc Lepage, Marcin Swiatek, W. L. Marks, Jason Goncalves, Scott Markel, Daniel Iordan, Mohammadreza Shojatalab, Angel Pizarro, Joe White, Robert Hubley, Eric DeutschMartin Senger, Bruce J. Aronow, Alan Robinson, Doug Bassett, Christian J. Stoeckert, Alvis Brazma

Research output: Contribution to journalArticle

340 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
JournalGenome Biology
Volume3
Issue number9
StatePublished - Aug 23 2002
Externally publishedYes

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gene expression
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Gene Expression
Biota
information exchange
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ingredients
Software
experiment
software
modeling

ASJC Scopus subject areas

  • Genetics

Cite this

Spellman, P., Miller, M., Stewart, J., Troup, C., Sarkans, U., Chervitz, S., ... Brazma, A. (2002). Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology, 3(9).

Design and implementation of microarray gene expression markup language (MAGE-ML). / Spellman, Paul; Miller, Michael; Stewart, Jason; Troup, Charles; Sarkans, Ugis; Chervitz, Steve; Bernhart, Derek; Sherlock, Gavin; Ball, Catherine; Lepage, Marc; Swiatek, Marcin; Marks, W. L.; Goncalves, Jason; Markel, Scott; Iordan, Daniel; Shojatalab, Mohammadreza; Pizarro, Angel; White, Joe; Hubley, Robert; Deutsch, Eric; Senger, Martin; Aronow, Bruce J.; Robinson, Alan; Bassett, Doug; Stoeckert, Christian J.; Brazma, Alvis.

In: Genome Biology, Vol. 3, No. 9, 23.08.2002.

Research output: Contribution to journalArticle

Spellman, P, Miller, M, Stewart, J, Troup, C, Sarkans, U, Chervitz, S, Bernhart, D, Sherlock, G, Ball, C, Lepage, M, Swiatek, M, Marks, WL, Goncalves, J, Markel, S, Iordan, D, Shojatalab, M, Pizarro, A, White, J, Hubley, R, Deutsch, E, Senger, M, Aronow, BJ, Robinson, A, Bassett, D, Stoeckert, CJ & Brazma, A 2002, 'Design and implementation of microarray gene expression markup language (MAGE-ML).', Genome Biology, vol. 3, no. 9.
Spellman P, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology. 2002 Aug 23;3(9).
Spellman, Paul ; Miller, Michael ; Stewart, Jason ; Troup, Charles ; Sarkans, Ugis ; Chervitz, Steve ; Bernhart, Derek ; Sherlock, Gavin ; Ball, Catherine ; Lepage, Marc ; Swiatek, Marcin ; Marks, W. L. ; Goncalves, Jason ; Markel, Scott ; Iordan, Daniel ; Shojatalab, Mohammadreza ; Pizarro, Angel ; White, Joe ; Hubley, Robert ; Deutsch, Eric ; Senger, Martin ; Aronow, Bruce J. ; Robinson, Alan ; Bassett, Doug ; Stoeckert, Christian J. ; Brazma, Alvis. / Design and implementation of microarray gene expression markup language (MAGE-ML). In: Genome Biology. 2002 ; Vol. 3, No. 9.
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