Department of Bioinformatics - BiGCaT, Maastricht University
The department of Bioinformatics-BiGCaT is part of NUTRIM the school of Nutrition and Translational Research in Metabolism at Maastricht University, the Netherlands. It was founded in 2001 by Prof. dr. Chris Evelo aiming at employing bioinformatics approaches in systems biology to integrate experimental data and data with current knowledge. Integrative Systems Biology is being developed and applied in various research fields. The department has four core research areas; 1) Metabolic diseases, 2) Micronutrients, 3) Toxicity and risk Assessment and 4) Rare diseases. Within these areas different types of data, like transcriptomics, proteomics, metabolomics and (epi)genomics data, are collected , integrated and combined with existing knowledge
BridgeDb is a combination of an application programming interface (API), library, and set of data files for mapping identifiers for identical objects [1]. Identifier mapping databases are available for gene products and metabolites. This Bioconductor Vignette explains how to use BridgeDb in the R...
Keywords: ELIXIR RIR, BridgeDb
Resource type: Tutorial, Vignette
Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. It explains how to download the IMS Docker and identifier mapping databases (link sets), load the link sets, and test the web interface.
Scientific topics: Genomics, Genetic variation
Keywords: ELIXIR RIR, BridgeDb
Resource type: Tutorial
The described network biology workflow uses state-of-the-art pathway and network analysis methods to study the rewiring of the diabetic liver. The integration of experimental data and knowledge on disease-affected biological pathways, including regulatory elements like transcription factors or...
Keywords: Biological networks, Network Visualization
This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API.
Scientific topics: Pharmacology, Drug discovery
Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.
Scientific topics: Metabolomics
Keywords: Metabolomics, Identifiers, ELIXIR RIR, BridgeDb
Resource type: Tutorial
Course given at BioSB 2019 for biologists about SPARQL.
Scientific topics: Biology
Keywords: Sparql queries, Sparql syntax
Resource type: Tutorial
Scholia is a useful tool for finding scientific literature. Based on the main topic of a publication, you can find literature similar to a publication you are looking into or literature you didn’t know about or consider. Additionally, you can take advantage of all of the annotation work of others...
Keywords: Literature
Resource type: Tutorial
Instructions on how to install and use the BridgeDb functionality in Matlab.
Keywords: ELIXIR RIR, BridgeDb
