InterMine user manual

InterMine integrates biological data sources, making it easy to query and analyse data. It is a downloadable platform that operators can install and integrate with their own systems.

InterMine is a generic model-based platform that is used to provide data to end users in many different life science domains, such as synthetic biology and biomedical research. It is particularly popular with model organism projects.

This documentation is for users of an InterMine installation. Among other things, it describes how they can search for biological entities (gene, protein, pathway, etc.), run sophisticated queries over integrated data, analyze query results and gene lists (gene ontology enrichment analysis, for example) and download or interact with data programmatically (e.g. by scripts written in Python, R and other languages).

This documentation is related to the new user interface BlueGenes.

For documentation for operators of InterMine installations please see

Keywords: Data querying, data visualization, Data download, FAIR

Resource type: Documentation

Target audience: Life Science Researchers, Bioinformaticians

Difficulty level: Beginner

Authors: Rachel Lyne, Julie Sullivan, Gos Micklem, Sergio Contrino, Yo Yehudi, Daniela Butano, Justin Clark-Casey, Kevin Herald Reierskog

External resources:



InterMine user manual Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine using the new user interface. Data querying, data visualization, Data download, FAIR Life Science Researchers Bioinformaticians