TG-GATEs and DrugMatrix

Processed data (counts and fold changes) based on the transcriptomics data provided by Open TG-GATEs and DrugMatrix
Processed data was generated using a standard workflow. The CEL files have been normalized using the single-channel array normalization function of the SCAN.UPC library available through Bioconductor. Normalized intensities have been used as an input for the differential expression analysis of microarray data using the very well known limma library available through Bioconductor. The data is then made available on EdelweissData for easy access also via APIs. DrugMatrix is one of the world’s largest toxicogenomic reference resources provided by the National Toxicology Program of the US Department of Health and Human Services. It provides access to the toxicogenomic profiles of over 600 different compounds generated with Affymetrix and Codelink microarrays. While both types of microarray cover liver, kidney, thigh muscles, heart and cultured hepatocytes, the Codelink microarrays additionally cover bone marrow, spleen, intestine and brain. At the moment only the processed data for the Affymetrix platform is available. Open TG-GATEs is a Japanese public toxicogenomic database resulting from two joint government-private sector projects (H14-Toxico-001 and H19-Toxico-001) organized by the National Institute of Biomedical Innovation, National Institute of Health Sciences and multiple pharmaceutical companies. The Japanese Toxicogenomics Project generated gene expression and toxicity data in rats and the primary cultured hepatocytes of rats and humans following exposure to 170 compounds (mainly pharmaceutical products). The follow-up Toxicogenomics Informatics Project discovered over 30 different safety biomarkers using the data and generated additional data for verifying the biomarkers and analyzing their mechanisms.

For end-users
For developers
Type:
Database / data source
API Type:
REST under OAS3 specification, OAS3, REST, OpenAPI
Categories:
Omics database
Applicability domain:
Toxicology, Bioinformatics
Topic:
Risk assessment, Information extraction
Biological area:
Omics, Transcriptomics
Targeted industry:
Other consumer products, Food, Cosmetics, Drugs, Chemicals
Targeted users:
Software Developers, Researchers, Risk assessors
Relevant OpenRiskNet case studies:
  • DataCure - Data curation and creation of pre-reasoned datasets and searching
  • TGX - Toxicogenomics-based prediction and mechanism identification

Provided by:
Edelweiss Connect GmbH
Licence:
Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Login required:
No
Implementation status:
Graphical user interface available, OAS v3, Available as web service, Application programming interface available
Technology readiness level:
TRL 8 – system complete and qualified
Integration status:
Integrated application
Service integration operations completed:
Utilises the OpenRiskNet APIs to ensure that each service is accessible to our proposed interoperability layer.
Is annotated according to the semantic interoperability layer concept using defined ontologies.
Is containerised for easy deployment in virtual environments of OpenRiskNet instances.
Has documented scientific and technical background.
Is deployed into the OpenRiskNet reference environment.
Is listed in the OpenRiskNet discovery services.
Is listed in other central repositories like eInfraCentral, bio.tools and TeSS (ELIXIR).
Provides legal and ethical statements on how the service can be used.