Difference between revisions of "InterMine"

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[http://www.intermine.org/ InterMine] makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the [http://sequenceontology.org Sequence Ontology] and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an [[Glossary#XML|XML]] format to help import custom data. Currently supported formats include:
 
[http://www.intermine.org/ InterMine] makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the [http://sequenceontology.org Sequence Ontology] and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an [[Glossary#XML|XML]] format to help import custom data. Currently supported formats include:
  

Revision as of 21:40, 6 December 2010

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{{#icon: InterMineLogo.png|InterMine||http://gmod.org/wiki/InterMine#Logo}}


InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the Sequence Ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data. Currently supported formats include:

  • Chado, GFF3, FASTA, GO & gene association files, UniProt XML, PSI XML (protein interactions), InParanoid orthologs, Ensembl

A web application allows creation of custom queries, includes template queries (web forms to run 'canned' queries) and can upload and operate on lists of data. It is possible to configure/create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded.

Chado Integration

We are developing a parser to load data from the GMOD Chado database schema into a companion InterMine warehouse. This will provide a web environment to perform rapid, complex queries on imported Chado data with minimal development effort. The eventual aim is to allow import of any Chado database with some configuration, the parser is currently used in FlyMine and the modENCODE project to import genome annotation from FlyBase and WormBase Chado databases. More information: http://www.intermine.org/wiki/ChadoDBSource


Demo

FlyMine is an example of InterMine in use.


Requirements

InterMine is written in Java and uses the PostgreSQL database. The web application requires Apache Tomcat. For more details on requirements see: http://www.intermine.org/wiki/Prerequisites


Documentation

Documentation is available at: http://www.intermine.org/

For a quick tour of the web application features go to FlyMine and click 'Take a tour'.

Presentations

Contact

Mailing List Link Description Archive(s)
InterMine dev InterMine support and development list. InterMine, Nabble (2010/05+)

Some Interesting Email Threads

Downloads

All code is released under the LGPL license and is available in subversion.

The InterMine logo was created by Sean O'Connell, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.