MGED

Introduction

The MGED Society is an international organization of biologists, computer scientists, and data analysts that aims to facilitate biological and biomedical discovery through data integration. Our approach is to promote the sharing of large data sets generated by high throughput functional genomics technologies. Historically, MGED began with a focus on microarrays and gene expression data. However, the scope of MGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

Members of MGED work to establish standards for data quality, management, annotation and exchange; facilitate the creation of tools that leverage these standards; and work with other standards organizations and promoting the sharing of high quality, well annotated data within the life sciences and biomedical communities.

Defined MGED Standards:

Collaborative Standards Working Groups:

Read more about:

News

Published Dataset Availability.

25 Nov 2009

The MGED Society mission includes facilitating deposition of functional genomics datasets (e.g. microarray studies) in public archives. In addition to addressing what and how data gets deposited, we are very much concerned with seeing that authors adhere to journal requirements for data deposition. A new service is available for facilitating data deposition. We will document the results to assist others seeking the same dataset and to aid reviewers of related publications and grants.

GEO and ArrayExpress agree to exchange UHTS sequencing data.

05 Nov 2009

ArrayExpress and GEO have entered into a metadata exchange agreement, meaning that ultra high throughput sequencing (UHTS) experiments will appear in both databases regardless of where they were submitted. This complements the exchange of underlying raw data between the short read archives, SRA and ERA. Raw sequencing data submitted to ArrayExpress or GEO will be sent to ERA or SRA respectively. You do not need to submit to the sequence repositories separately.

Annotare - MAGE-TAB annotation tool

05 Nov 2009

Annotare is an annotation tool for high throughput gene expression experiments in MAGE-TAB format. Biologists can describe their investigations with the investigators’ contact details, experimental design, protocols that were employed and references to publications, details of biological samples, arrays, and experimental data produced in the investigation. Annotare is open source and free to download. See the tutorial.

Repeatability of published microarray studies

05 Feb 2009

A Nature Genetics article details the reproducibility of published gene expression studies. It concludes that journals should do more to enforce public data availability and better descriptions for data processing and analysis.

Events

MGED 13 Meeting

05 Nov 2009

MGED 13 meeting, July 13-15, 2010, Boston, Massachusetts in conjunction with ISMB.

MGED Sponsors