InterMine is a powerful open source data warehouse system. Using InterMine, you can create databases of biological data accessed by sophisticated web query tools. InterMine can be used to create databases from a single data set or can integrate multiple sources of data. Support is provided for several common biological formats and there is a framework for adding your own data. InterMine includes an attractive, user-friendly web interface that works 'out of the box' and can be easily customised for your specific needs.

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.

Supported data formats

• Chado
• GFF3
• FASTA
  FASTA
  FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.- History :...
  
  
• GO
  Gene Ontology
  The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
  
   & gene association files
• UniProt
  UniProt
  UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...
  
   XML
• PSI XML (protein interactions, Protein Structure Initiative
  Protein Structure Initiative
  The Protein Structure Initiative is an ongoing effort begun in 2000 to accelerate discovery in structural genomics and contribute to understanding biological function. Funded by the U.S...
  
  )
• InParanoid
  Inparanoid
  INPARANOID is an algorithm which finds orthologous genes and those paralogous genes which arose—most likely by duplication--after some speciation event...
  
   orthologs
• Ensembl
  Ensembl
  Ensembl is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute, which was launched in 1999 in response to the imminent completion of the Human Genome Project...
  
  

Web application

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.

Current projects (not exhaustive list)

• Generic Model Organism Database
  Generic Model Organism Database
  The Generic Model Organism Database Project began as an effort to create reusable software tools for developing Model Organism Databases . MODs describe genome and other information about important experimental organisms in the life sciences...
  
  
• modENCODE
• FlyMine
• metabolicMine
• RatMine
• YeastMine
• TargetMine
• MitoMiner
• ZfinMine

External links

• InterMine
• Department of Genetics, University of Cambridge
• Wellcome Trust