InterMine
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.[1]
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
- GO & gene association files
- UniProt XML
- PSI XML (protein interactions, Protein Structure Initiative)
- InParanoid orthologs
- Ensembl
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
- modENCODE
- FlyMine
- metabolicMine
- InitMine (under early development)
- RatMine
- YeastMine
- TargetMine
- MitoMiner
- ZebrafishMine