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

What is InterMine?

InterMine integrates data from different biological sources, providing 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?

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 of 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 data, ranging from mice and fruit flies to a broad range of plants. Visit the InterMine Registry to see them all. (The registry was written by a GSoC student last year!) 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! How can we handle this ambiguity? How can we help the end user make sense of data that is so diverse and complex? One way to help scientists analyse data 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, you can often write code to work with one InterMine and with little or no effort, port it to another InterMine with different data.

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Technologies

  • postgresql
  • java
  • javascript
  • python
  • clojure

Topics

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mail_outline Contact email

InterMine 2018 Projects

  • Aman Dwivedi
    Cross-Intermine Search Tool
    Currently, we have around 30+ mines (and still growing) all around the globe. All mines have their own separate APIs and their own separate portals....
  • Adrián Rodríguez Bazaga
    InterMine Data Browser Tool
    The existing query builder in InterMine requires some experience to obtain statistical data about the different mine categories, which can become...
  • Arunan Sugunakumar
    Intermine Solr deep bio data search
    Currently Intermine uses an old approach to handle bio data search. This project aims to improve the search feature using modern search engines like...
  • Jacob Macneal
    Natural Language Queries for InterMine Databases
    I hope to spend this summer providing much-needed additional functionality to InterMine, a software project which helps researchers create and manage...
  • Nupur Gunwant
    Python Client Expansion
    Python Client is a software intended to make use of the data warehouses of InterMine in a more efficient manner. It is composed of a number of client...
  • innovationchef
    “Buzzbang Google-like bio data search”
    The project is about building a search engine for life sciences data based on Bioschemas.org . The data is scraped from all the relevant websites and...
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2018