Why would I use InterMine?

This page gives three example use cases for InterMine. For all examples you will need to run a PostgreSQL database and a Tomcat web server (see prerequisites). We have some basic recommedations of hardware needed here?. If you would like any more information about using InterMine please contact us: info@intermine.org.

In each case, once data is loaded the web application will work automatically whatever the data model. You will be able to configure the web interface and create your own branding. It is easy to create new template queries and public lists, you will be able to use existing widgets for list analysis or create your own.

1. I have some data and I would like to let people query it on the web.

The simplest way to do this is to transform your data into InterMine data XML? that conforms to the core data model (based on the sequence ontology. This can be done in any language, we support Java and Perl APIs to help. If you need to load data not already represented represented you can easily add to the model just by creating another XML file, you could even create your own data model entirely.

2. I would like to build an integrated biological database so I can query multiple types of data at once.

This is what InterMine was designed to do, see FlyMine as an example. You could integrate publicly available data for the organisms you are interested in to query across. Perhaps you would like to include your own data to use it in the context of other resources.

InterMine can import many biological data types into a core data model?. In most cases using these sources is as simple as specifying the organisms required and location of data files in a project XML file. You can write new parsers to include your own data or data types we don't yet handle. It is simple to add additional classes to the data model.

3. I have a database and I would like a companion data warehouse for flexible querying.

If you have an existing biological database and would like a web interface to enable complex queries, templates and list operations you could periodically load it into an InterMine data warehouse. You would write a parser to convert data from your schema into the core model?, with the option to add classes not already represented (or create an entirely new model). It would be simple to integrate data from the common sources that you may not already deal with.

We have an example parser to import from a chado database and we aim to make this a simple matter of adding configuration in future.

We will soon be working on functionality to allow InterMine to integrate seamlessly with an existing web interface.