LION Target Engine 1.0: an Enterprise Platform for Target Identification and Validation

S. Bernauer, Z. Bilkic, N. Bojunga, T. Brostroem, D. Croft, N. Delhomme, A. Denagbe, L. Ehrlich, K. Fries, C. Girardot, M. Goeschl, M. Gumbel, J. Hermanns, C. Kaestner, C. Katz, U. Keck, H.-P. Keck, R. Kern, G. Kurapkat, P. Lederer, D. Leon, S. Marcel, S. Markel, B. Markus, J.E.M. Meyer, E. Minch, J. Mistry, C. Muench, S. I O'Donoghue¹, C. Ohr, S. Richter, H.-J. Roemming, R. Russ, S. Schaefer, A. Schafferhans, T. Schlegl, T. Schlueter, A. Schmidt, O. Schmidt, D. Schulz, A. Sooky, A. Sergienko, F. Spangenberg, J. Suckow, B. Sulzer, C. Suter-Crazzolara, A. Tarasenko, E. Vatcheva, H. Voss, M. Weindel, G. Zhang
¹sean.odonoghue@lionbioscience.com, LION bioscience AG, Waldhoferstr. 98, 69123 Germany

LION Target Engine: an Enterprise Platform for Target Validation LION Target Engine^TM is a user-friendly system designed to streamline the identification and validation of targets in an enterprise environment. The system is comprised of several integrated components:

The Gene Hub Component, which contains gene and protein indicies built from LocusLink/RefSeq, ENSEMBL, UniGene, and IPI. Initially created for human genes, it is extensible to other genomes (also planned for later releases). This component enables users to add or modify gene entries, and handles integrating proprietary sequences and build-to-build mapping.
The Registration Component, which enables users to register and curate genes and sequences that may be potential targets.
The Annotation Component, which supports sequence analysis with an extensive suite of bioinformatics applications.
The Text Mining Component, which uses Medline to infer interactions between proteins, genes, compounds, etc. based on co-occurrence or on recognized verb phrases.
A Pathway and Interaction Component, which includes a pathway editor allowing users to easily create, modify and save pathways and interaction networks. This component also includes the KEGG and BIND databases, and users can easily mine interactions from these databases or from Medline (via the Text Mining Component) to quickly assemble novel signalling pathways.
The Protein Structure Component, which enables users to easily find all structures related to a given sequence, and to visualize 3D structures together with sequences, sequence alignments, and sequence features.
The Assay Viewer Component, which enables users to create and share customized views of data from TaqMan, microarray or other experiments.
The Target Tracking Component, for tracking the status and prioritisation of targets in the discovery pipeline.

LION Target Engine provides an intuitive and flexible user interface for browsing, searching, and organizing information about targets. For each gene or sequence, the user can open a ‘Summary Sheet’, a graphical component from which the user can easily navigate to all data in the system related to a given target. Summary Sheets greatly facilitate data sharing, as data created by one user (target annotations, signalling pathways, etc.) can be immediately visible to other users.

The user interface allows easy access to the most needed data simply by browsing, hence largely avoiding the need to manually launch database queries. However, LION Target Engine also provides sophisticated query methods for expert users.

LION Target Engine is implemented within LION DiscoveryCenter^TM, a system for integrating data and application. Client components and client-server interfaces are based on enterprise Java, while data access is based on SRS (for about 60 public domain databases) and Oracle (for user-defined data). Further information about LION Target Engine, LION DiscoveryCenter, and SRS is at www.lionbioscience.com.