InterMine

• data integration
• web application for custom queries, template queries, list analysis
• REST query API with Java and Perl clients
• supports many formats for core organisms:
  • chado, GFF3, FASTA, Ensembl, GO annotation, OBO ontologies
  • UniProt, interactions (BioGrid, IntAct), BioPax, Reactome
  • KEGG, InterPro, PDB, TreeFam, PubMed, Ensembl SNPs, custom data

Sites

• FlyMine -  www.flymine.org
• modENCODE -  intermine.modencode.org
  • $57M project detailed characterisation of fly and worm genomes
• MitoMiner, mitochodria database -  mitominer.mrc-mbu.cam.ac.uk
• FlyTFMine, Drosophila transcription factors -  www.flytf.org
• BOKU, Vienna
• Tufts Neuroscience, Boston
• NIBIO, Tokyo

Mines for MODs

• Joint project with SGD (yeast), RGD (rat), ZFIN (zebrafish). Each will deploy an InterMine at their site.
• RatMine launched in December
• Interoperability is key
  • seamless transfer between Mines based on orthologues, pathways, ontologies, protein domains
  • embedding of results in other Mines
  • interoperability will be simple for the user, simply clicking on links to move lists between Mines:

Progress:

• RatMine released -  ratmine.mcw.edu
• ZFIN prototype - www.intermine.org/zfin
• SGD prototype - www.intermine.org/sgd

New funding

• metabolicMine - a human InterMine for metabolic disease research
• InterMine development and support

Coming year

• interoperation of Mines
• GUI for configuring up InterMine
• new QueryBuilder, experiments with GWT
• InterMine for developers
• GMOD REST API
• new list features, comparison of lists
• better range queries