Mining gene-disease associations and drug target validation with Open Targets New
Open Targets was founded by three global leading institutions in the fields of pharmaceuticals, bioinformatics and genomics, GSK, EMBL-EBI, the Wellcome Trust Sanger Institute, and recently joined by Biogen, the world’s oldest independent biotechnology company.
We combine large-scale genomic experiments with objective statistical and computational techniques to identify and validate the causal links between targets, pathways and diseases. Cross-cutting several therapeutic areas, we generate cellular models of disease through gene editing technologies or single cell analysis. In addition to clinical samples, iPS cells and cellular organoids are resourced to provide cellular phenotyping with high physiological relevance. Open Targets integrates comprehensive datasets from a myriad of renowned public databases, such as UniProt, ChEMBL, Ensembl, NHGRI-EBI GWAS, EuropePMC, COSMIC, GTEx, among others. The data and analytical processes are developed by a set of interlinking projects.
The purpose of this half-day workshop is to acquaint participants with the Open Targets project and its Target Validation interface and introduce the tools for visualisation and interpretation of gene-disease associations and target validation based on a comprehensive platform with data from various publicly available databases. By the end of this half-day workshop, users will be able to carry out effective searches of data, use the web application to visualise genes, variants, ontology, pathways (and more) in the context of human disease and therapeutics.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.
- This course is suitable for all users who have an interest in biomedical research and therapeutics with a special emphasis on drug discovery and target validation. It is also useful to those who seek to find out how large-scale genomic experiments, cellular models of disease and computational techniques are used to identify and validate the causal links between targets, pathways and diseases.
- Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
- Further details regarding eligibility criteria are available here
Some prior knowledge of basic genetics and molecular biology in addition to familiarity with some existing reference sources (e.g. Ensembl, UniProt) is desirable to make the best use of this course.
Number of sessions: 1
| # | Date | Time | Venue | Trainer | |
|---|---|---|---|---|---|
| 1 | Mon 17 Oct 2016 13:00 - 17:00 | 13:00 - 17:00 | Bioinformatics Training Room, Craik-Marshall Building | map | Denise Carvalho-Silva |
After this course you should be able to:
- Find diseases associated to human genes
- Get information on protein, variation, gene expression, ontology, pathways (and more) and their association with drug targets
- Retrieve a list of publications supporting target and disease information
- Get disease and phenotype evidence based on animal models
- Access this data programmatically with the REST API
During this course you will learn about:
- The Open Targets project and its goals
- The Target Validation Platform and the integration of the different datasets available
- How to visualise and interpret gene - disease associations according to the different datasets
- How to browse gene, protein, genetic variants and expression data in the context of human diseases
- What alternative ways are available to retrieve this dataset, e.g. through the REST API and data dumps
Presentations, demonstrations and practicals
- Free for University of Cambridge students
- £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
- £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
- £ 100/day for all Industry participants. These charges must be paid at registration
- Further details regarding the charging policy are available here
0.5
A number of times per year
Booking / availability