LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system

Abstract

We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on the encoded proteins produced in functional genomics and proteomics approaches. The database also serves as a sample-tracking system to manage the process from cDNA to experimental read-out and data interpretation. A web interface enables the scientific community to explore and visualize features of the annotated cDNAs and ORFs combined with experimental results, and thus helps to unravel new features of proteins with as yet unknown functions.

Figure 1

Overview of the data flow in LIFEdb. Annotated data from novel full-length cDNAs are entered into both a MS Access database and into the central database, which is based on MS SQL Server 2000. The Access database serves as a laboratory information management system, which is accessible via an internal interface based on Access-derived forms. The data within this database is regularly copied into the central database. LIFEdb also provides a web interface, which is accessible to both the scientific community and via a password-protected area to remote users who retrieve data regarding expression clones, and who in turn can upload experimental results, including pictures of the subcellular localizations. For each cDNA in the central database, a comprehensive bioinformatic analysis of the deduced protein sequences is performed using programs and tasks of the HUSAR system. The results are then stored in the analysis database. The web interface allows for retrieval of these data and presents them, together with annotation data and data from the subcellular localization experiments, to the scientific community.

Figure 2

Example of a database search using the web interface of LIFEdb. Selected information about the cDNAs, the encoded proteins and experimental results stored in LIFEdb are presented as a table, which in addition contains links to external databases (Ensembl, GoldenPath and GeneCards) (A). Table entries are linked to pages with additional data such as general information on a selected cDNA clone (B), representative pictures of the subcellular localization of the encoded protein (C) and a summary of the bioinformatic analysis of the protein (D).