standards > model/format > DOI:10.25504/FAIRsharing.x964fb


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 is a deprecated format and major microarray databases such as ArrayExpress no longer encourage its use. Please see the FAIRsharing record for MAGE-TAB (https://FAIRsharing.org/bsg-000080) or ISA-TAB (https://FAIRsharing.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/

Homepage http://www.mged.org/Workgroups/MAGE/mage-ml.html

Countries that developed this resource European Union , United States

Taxonomic range




How to cite this record FAIRsharing.org: MAGE-ML; MicroArray Gene Expression Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.x964fb; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Nov 20 2019 10:19 p.m.


Record updated: May 21, 2018, 2:31 p.m. by The FAIRsharing Team.

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contact form http://www.mged.org/contact.html
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online documentation http://www.omg.org/technology/documents/ ...
online documentation http://sourceforge.net/projects/mged/fil ...
online documentation http://www.mged.org/Workgroups/MAGE/mage ...

Additional Information

Contact Ugis Sarkans   ORCID

Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use





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

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Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics 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

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This record is not implemented by any policy.


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Grant Number(s)

  • DE-FG02-00ER62893 (United States Department of Energy, Office of Science, USA)