Meaningful and inspiring data integration for Garuda + OpenTox

Meaningful and inspiring data integration for Garuda + OpenTox, OpenTox Asia 2018

Johan Nyström-Persson


Douglas Connect


Data Scientist


Data integration remains an important concern in toxicology and life sciences. Data must be integrated in such a way that scientific reliability is maintained, and also in a way that provides a meaningful, if not inspiring, context for researchers to understand information. Furthermore, the problem cannot be solved incrementally, but only by focussing on the entire dataset lifecycle in its totality. It is a concern at the time of data generation and capture, as well as when storing, publishing and using data.

SBI has previously demonstrated meaningful discovery and integration of life sciences applications on an open platform (Garuda). Douglas Connect is now working to also bring exceptional data integration capabilities to this platform by Garudifying its next generation technology, currently under development.

Our approach combines the user-friendliness of web interfaces and interactive notebooks with the correctness and scalability of linked data. We demonstrate uploading a dataset and automatically annotating it with ontology terms. Specifically, we integrate the Liver Toxicity Knowledge Base (LTKB) with DrugBank to study the toxicity of diabetic drugs. We demonstrate how such integration makes data instantly searchable and contextual, both through graphical user interfaces (GUIs) and programmatically. This greatly simplifies integration and use of data at every step of the way.

Workflows with Garuda + OpenTox

This is a companion event to the talk "Meaningful and inspiring data integration for Garuda+OpenTox".

Garuda+OpenTox is a solution being developed jointly by SBX and Douglas Connect for availability and integration of toxicology data on the Garuda platform.

In this talk, we give a demonstration of current OpenTox gadgets on Garuda and their use in a scientific workflow. We demonstrate how to discover samples from Open TG-GATEs, load gene expression data, and visualise pathways in Garuda. These gadgets are freely available for anyone to use.