- Course overview
- Search within this course
- Introduction to EMBL-EBI resources
- Introduction to programmatic access
- EBI Search, programmatically
- Europe PMC, programmatically
- Ensembl, programmatically
- UniProt, programmatically
- InterPro, programmatically
- PDBe, programmatically
- ChEMBL and UniChem, programmatically
- Sequence analysis tools, programmatically
- EVA, programmatically
- MGnify, programmatically
- Summary
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
Open Targets, programmatically
The Open Targets Platform is a comprehensive tool that supports the systematic identification and prioritisation of potential therapeutic targets.
The Platform integrates publicly available datasets from over 20 different data sources. It uses this evidence to build and score target-disease associations, to assist in drug target identification and prioritisation. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships.
The Platform is a freely available, open source resource that is actively maintained, with four releases a year.
This clip, from a webinar recorded on the 31st January 2024, covers the different ways in which you can access the data in the Platform, depending on the complexity of the query.
For queries about a single entity (disease, target, drug), or a single target-disease association, you can use either:
- The Platform’s web interface, in which individual data tables and visualisations can be downloaded for further analysis
- The GraphQL API, accessible with the programming language of your choice, or API playground with built-in documentation, which is useful for constructing and testing queries
For any more complex queries, we recommend using either:
- The Google BigQuery instance — open-targets-prod — which supports SQL-like queries. Open Targets Platform data is also accessible as a Google Cloud public dataset
The data downloads, to explore specific datasets and integrate them into your own pipelines. Archives are available through FTP