LION Target Engine 1.0: an Enterprise Platform for Target Identification and ValidationS. 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
firstname.lastname@example.org, LION bioscience AG, Waldhoferstr. 98, 69123 Germany
LION Target Engine: an Enterprise Platform for Target Validation
LION Target EngineTM 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:
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 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.
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 DiscoveryCenterTM, 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.