The Centralized Life Sciences Data (CLSD) service

The CLSD at Indiana University was a compendium of publicly available databases related to biology, genomics, medicine, etc. These resources were federated via IBM's DB2 Information Integrator to allow queries across all included sources.

There were multiple interfaces to the service that included a WSRF web service, a JAX-RPC web service, JDBC-based servlets, AJAX, and the DB2 client library.

The following data re sources were included. I added the GO, TRANSFAC 2005, UNIPROT mapping, and Disease Gene Network resources:

• Resources stored in relational form within CLSD:
• BIND -- Pathways, Gene interactions
• ENZYME -- Enzyme nomenclature
• ePCR -- ePCR results of UniSTS vs Homo sapiens
• SGD -- Saccharomyces Genome Database
• KEGG data sources:
  • LIGAND -- Pathways, Reactions, & Compounds
  • PATHWAY -- Pathway map coordinates
• NCBI data sources:
  • LocusLink -- Genetic Loci. (LocusLink has been inactive since July 1, 2005 when it was retired in favor of UniGene; it is retained for achival use.)
  • UniGene -- Gene clusters
• GO -- Selected Gene Ontology data
• UNIPROT mapping -- The UNIPROT ID cross-reference table, aka "mappings"
• TRANSFAC 2005 -- The publicly available TRANSFAC data (extracts)
• DGN -- The Disease Gene Network data from Goh, et al., 2007
• Federated data sources, where the data is stored:
  • at the originating site:
    • NCBI Nucleotide -- Nucleotide sequences
    • NCBI PubMed -- Journal abstracts
  • on local (mirror) servers external to CLSD but housed at Indiana University:
  • BLAST -- Basic Local Alignment Search Tool (mirrored at IU by UITS)
  • Nucleotide data: NT
  • Protein data: NR and Swiss-Prot
  • dbSNP -- Single Nucleotide Polymorphisms (mirrored at IU by IUSM)