Integrating biological data sources, making it easy to query and analyse data

What is InterMine?

InterMine integrates data from diverse biological sources, and provides a web-based user interface for querying and analysing the data. Users can automatically generate code to run queries using our client libraries in R, Python, Perl, Ruby, Java, and Javascript.

What technologies do we use?

The InterMine core is built in Java, and all data are stored in PostgreSQL. We have a legacy JSP-based user interface, with a Clojurescript user interface in early beta. We're also keen on browser-based datavis tools that use our API, so you'll see a lot of Javascript (or languages that compile to Javascript, like Clojurescript and Coffeescript). Our client libraries provide opportunities to write code in several other languages.

What sort of data does InterMine have?

Since InterMine is open source, many research organisations around the world run InterMines with their own organisms, ranging from mice and fruit flies to a broad range of plants. Visit the InterMine Registry to see them all. (The registry was a GSoC project!) Most InterMines also have a "data sources" tab which tells you more about where the data in that specific instance originates.

What kind of problems does InterMine solve?

Genomic data is often messy, and there is a lot of it. Scientists use different terms to mean the same thing, and even assign the same gene different names! We aim to help scientists make sense of such ambiguity, diversity and complexity.

One way to help is to provide visualisations, so we’re always excited to add and adapt different ways to display our data. How do you visualise the features inside a protein, or the interactions between two sets of genes?

Code you write for InterMine can have a large impact - since there are dozens of different InterMines, we aim to write code that can be easily deployed on any of them.

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  • java
  • python
  • javascript
  • clojure
  • r


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InterMine 2019 Projects

  • Ankur Kumar
    Intermine Cloud: Making Intermine cloud native and easing deployments
    Intermine is a powerful data warehousing, integration and analysis tool used to store and share genomics data. However, setting up an instance of...
  • deepak
    InterMine Schema Validator
    As Intermine is providing integrations with different biological data sources, Intermine has to work with different file formats to read data for the...
  • Rahul-07
    InterMine single sign-in
    In the current scenario, A user logs in the desired intermine and saves the results and the required data. The problem arises when the same user...
  • Akshat Bhargava
    Javascript Data Visualisations
    The current Intermine’s viewer interface works on JavaServer Pages Technology and is planned to be discontinued in a few years. And, a new interface...
  • Prabodh Kotasthane
    Migrate RESTful web services from Struts to Spring
    Presently InterMine uses Struts framework which is outdated. InterMine provides RESTful web-services which facilitates to execute custom or templated...
  • Laksh Singla
    Upgrade dependencies of imjs and im-tables, update Docs, add helper methods and improve build chain of these libraries
    imjs and im-tables, written in CoffeeScript are client-side libraries for querying mine instances and displaying data in tabular format respectively,...