This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR and BED files. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.
Description: This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR...
SEEK ID: https://fairdomhub.org/data_files/929
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Created: 22nd Mar 2012 at 12:20

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Version 2 (latest) Created 22nd Mar 2012 at 12:20 by Katy Wolstencroft
Updated experimental design type
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Projects: SysMO DB, HUMET Startup, FAIRDOM, Consensus Hallmark Annotation, NL-Bioimaging FAIR Metadata Templates, FAIR Functional Enrichment, Benefit for All FAIR Data
Institutions: University of Leiden, LIACS

Expertise: Biochemistry, Bioinformatics, Data Management
Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies, semantic web
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.
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
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 ...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Not specified
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 ...
Submitter: Olga Krebs
Studies: Creating Templates for Proteomics, Creating Templates for Transcriptomics, Creating template for metabolomics data
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
Snapshots: Snapshot 1, Snapshot 2
Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.
Submitter: Katy Wolstencroft
Investigation: Creating data sheet template for 'omics data
Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, NimbleGen Transcriptomics Templates, RT-PCR Excel Template
Snapshots: No snapshots
Some examples of transcriptomics templates for Affymetrix data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: 3' or Whole Gene Expression Array Template (Aff..., Chip-chip Array Template (Affymetrix)
Snapshots: No snapshots