Some generic examples of transcriptomics templates that conform to the MAGE-TAB specification. These templates were created and modified from templates produced by ArrayExpress and GEO.
These templates are generic and non-specific for any particular array platform.
FAIRDOMHub ID: https://seek.sysmo-db.org/assays/17
Investigation: Creating data sheet template for 'omics data
Assay type: Transcriptomics
Technology type: Microarray
Organisms: No organisms
Created: 30th Sep 2009 at 15:11
Last updated: 8th Nov 2017 at 15:21
Institutions: University of Leidenorcid.org/0000-0002-1279-5133
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you!
At the meeting you will:
- Learn why data and model management is
Organisms: Homo sapiens
FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
Data integration is an essential part of Systems Biology. Scientists need to combine different sources of information in order to model biological systems, and relate those models to available experimental data for validation. Currently, only a small fraction of the data and models produced during Systems Biology investigations are deposited for reuse by the community, and only a smaller fraction of that data is standards compliant, semantic content.
By embedding semantic technologies into familiar
Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, Metabolomics Master Template, NimbleGen Transcriptomics Templates, Proteomics Template (gel electrophoresis), Proteomics Templates (Mass spectrometry), RT-PCR Excel Template, Standard-based Excel template for metabolomics data
Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.
Person responsible: Katy Wolstencroft
Snapshots: No snapshots
An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment).
This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)
An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK