Standards > model/format > bsg-s000573


deprecated MicroArray Gene Expression Markup Language

Abbreviation:MAGE-ML


General Information
This record was deprecated on Feb. 16, 2016 for the following reason(s): This resource is a deprecated format and major microarray databases such as ArrayExpress no longer encourage its use. Please see the BioSharing record for MAGE-TAB (https://biosharing.org/bsg-000080) or ISA-TAB (https://biosharing.org/bsg-000078) instead.

This document is a standard that addresses the representation of gene expression data and relevant annotations, as well as mechanisms for exchanging these data. The field of gene expression experiments has several distinct technologies that a standard must include (e.g., single vs. dual channel experiments, cDNA vs. oligonucleotides). Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. With the acceptance of XML Metadata Interchange as an OMG standard it is possible to specify a normative UML model using a tool such as Rational Rose that describes the data structures for Gene Expression

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Record updated: Dec. 28, 2016, 11:41 p.m. by Madekale.




Tools

    No tools defined


Conditions of Use

License

No License Specified.


Schemas

No XSD schemas defined


Access / Retrieve Data

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Connectivity
Related Standards

Reporting Guidelines

No guidelines defined

Models and Formats

No syntax standards defined


Implementing Databases (2)
ArrayExpress
ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.

Stanford Microarray Database
The Stanford Microarray Database is a repository a microarray based gene expression and comparative genomics data. This resource is no longer being maintained please us public repositories NCBI Gene Expression Omnibus or EBI Array Express

Implementing Policies

This record is not implemented by any policy.


Credit

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Funding agency

Maintainer

Grant Number(s)

  • DE-FG02-00ER62893 ( U.S. Department of Energy, Office of Science)


Publications

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

Spellman PT, 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 Jr, Brazma A.
Genome Biology 2002

View Paper (PubMed) View Paper (DOI)