Cover Pages: Microarray Markup Language (MAML)

As of 2002-02-08, "MAML (Microarray Markup Language) is no longer supported by MGED and has been replaced by MAGE-ML."

Background to MAML proposal in the EMBL-EBI submission to the OMG's Gene Expression RFP: "The proposal is supported by the Microarray Gene Expression Database (MGED) group and has been prepared by the Microarray Markup Language (MAML) working group of MGED. The MGED group is an open discussion group established at the Microarray Gene Expression Database meeting MGED I on November 16-17, 1999, in Cambridge, UK. The goal of the group is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalization methods. The underlying goal is to facilitate the establishing of gene expression data repositories, comparability of gene expression data from different sources and interoperability of different gene expression databases and data analysis software. Since 1999 the group has had two general meetings and the third one is scheduled for March 28-30, 2001, in Stanford US. MGED group includes representatives from the EMBL-EBI, National Center for Biotechnology Information (NCBI), National Center for Genome Research (NCGR), DNA Databank of Japan (DDBJ), National Human Genome Research Institute, German Cancer Research Centre, Stanford University, University of California at Berkeley, University of Colorado, Rockefeller University, Whitehead Institute, Affymetrix, Incyte and Gene Logic Ltd. MGED has established five working groups, including MAML working group, which is coordinated by Paul Spellman from the University of California at Berkeley (UCLB)."

"We propose a framework for describing information about a DNA-array experiment and a data format -- Microarray Markup Language (MAML) -- for communicating this information. The information includes details about: (1) Experimental design: the set of the hybridization experiments as a whole; (2) Array design: each array used and each element (spot) on the array; (3) Samples: samples used, the extract preparation and labeling; (4) Hybridizations: procedures and parameters; (5) Measurements: images, quantitation, specifications; (6) Controls: types, values, specifications. MAML is based on the Extensible Markup Language XML. MAML is independent of the particular experimental platform and provides a framework for describing experiments done on all types of DNA-arrays, including spotted and synthesized arrays, as well as oligo-nucleotide and cDNA arrays, and is independent of the particular image analysis and data normalization methods. MAML does not impose any particular image analysis or data normalization method, but instead provides format to represent microarray data in a flexible way, which allows to represent data obtained from not only any existing microarray platforms, but also many of the possible future variants, including protein arrays. The format allows representation of raw and processed microarray data. The format is compatible with the definition of the 'minimum information about a microarray experiment' (MIAME) proposed by the MGED group, see http://www.mged.org/. The MGED group is an open discussion group initially established at the Microarray Gene Expression Database meeting MGED 1 (November, 1999, Cambridge, UK). The goal of the group is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalization methods. The underlying goal is to facilitate the establishing of gene expression data repositories, comparability of gene expression data from different sources and interoperability of different gene expression databases and data analysis software. In the next two sections, we describe the MIAME standard, which describes the content of the information that has to be represented by a data format for microarray gene expression data representation (according to MGED recommendations), followed by the MAML DTD, which defines the actual XML based data format..."

References:

Microarray Gene Expression Database (MGED) Group - "The MGED group is an open discussion group initially established at the Microarray Gene Expression Database meeting MGED 1 (November, 1999, Cambridge, UK). The goal of the group is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalisation methods. The underlying goal is to facilitate the establishing of gene expression data repositories, comparability of gene expression data from different sources and interoperability of different gene expression databases and data analysis software. Since 1999 the group has had two general meetings and the third one is planned for 2001. In between the meetings most of the work is done within the five workinggroups established at the first meeting."
Gene Expression RFP Response. Initial Submission from EMBL-EBI (European Bioinformatics Institute). Version 1.0. 20 November 2000. OMG document # lifesci/2000-11-16. Response to: OMG Document lifesci/00-03-09 (Gene Expression RFP). [cache PDF, text]
MAML XML DTD - From the EMBL-EBI response to the OMG RFP
MAML XML DTD. From: bioxml-dev
See also: axml.dtd An XML DTD for marking up array based data. [cache]
Array XML Working Group - Microarray data XML exchange format. "unofficial website of the microarray-format working group for the MGED project, which is charged with developing a consensus based standard for exchanging and storing data from microarray experiments."Chair is Paul Spellman.
MicroArray Informatics at the EBI
"One-stop shop for microarray data." By Alvis Brazma, Alan Robinson, Graham Cameron, and Michael Ashburner (European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK). In Nature 403 (February 2000), 699-700. "Fortuitously, many problems in the storage and description of gene-expression data and experiments parallel current problems with the Internet -- too much information, which is hard to search without being deluged by irrelevant information. One reason is that HTML, the language used for documents on the Internet, cannot describe any semantics of the information it carries -- hence the development of XML (Extensible Markup Language) for defining data formats for storing semi-structured and structured information. XML has been designed specifically to allow people to create their own customized mark-up languages for storing any type of data and their semantic content. XML seems well suited as a format for the formal description and annotation of microarray information, and ways to describe microarray experiments using this language are being developed. This will mark an important milestone in the formalization of standards for microarray data and facilitate exchange of information among researchers. XML specifications have already been proposed for genome annotation, biomolecular sequences and computational analyses. Several of the largest microarray laboratories in academic institutions -- Stanford University and the Whitehead Institute, among others -- are developing their own internal databases, as are the larger commercial microarray companies such as Affymetrix and Incyte. GeneLogic is creating a commercial gene-expression database using data obtained on the Affymetrix platform. Harvard University has created a database that compiles and represents data from several public sources in a consistent format. The Computational Biology and Informatics Laboratory of the University of Pennsylvania is incorprating ontologies to describe samples. There are at least three projects for large, public gene-expression data repositories: GeneX at the US National Center for Genome Resources; the Gene Expression Omnibus at the US National Center for Biotechnology Information; and ArrayExpress at the European Bioinformatics Institute (EBI). Compatibility between these projects requires common standards for data representation, annotation and exchange, and discussions between these bodies are thus being focused on XML... Progress towards such standards was made last November, when many of the main academic and commercial users and developers of microarray technology accepted a list of recommendations for data representation and annotation (see http://www.ebi.ac.uk/microarray/). Five working groups, coordinated by US and European specialists, have been set up to develop standards in experiment description and data representation; microarray data XML exchange format; ontologies for sample description; normalization, quality control and cross-platform comparison; and data-query language and data-mining approaches. The users will meet again in May to discuss detailed recommendations from the working groups. Meanwhile, the EBI, in collaboration with the German Cancer Research Centre, is developing ArrayExpress, a gene-expression database compliant with the current recommendations. The first draft of the data model used in ArrayExpress was posted on the Internet in October (see http://www.ebi.ac.uk/arrayexpress/). This model will be refined in the light of discussions by working groups, and the next draft will be released in a few months' time, together with a database schema. The schema will be implemented with data from collaborating institutions, creating a prototype database by the spring. But it is a giant leap from a prototype to a working database, with associated tools for submitting and retrieving microarray data."
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