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  • Division of Biocomputing
    MSC11 6145
    Research Incubator Bld, Suite 170
    2703 Frontier, NE
    1 University of New Mexico
    Albuquerque, NM 87131 USA
    Fax (505)272-0238

CARLSBAD

(Confederated Annotated Research Libraries of Small-molecule Biological Activity Data)
Chemical pattern detection in biological networks

The Division of Biocomputing (P.I., Tudor Oprea) has been awarded a two‑year NIH grant (R21 award 1R21GM095952-01) for development of a database system integrating multiple bioactivity datasets to provide biomedical scientists with new ways to mine and explore available SAR (structure‑activity relationships) throughout chemical biology space. The new database, CARLSBAD (Confederated Annotated Research Libraries of Small molecule BioActivity Data) will integrate PubChem, ChEMBL, PDSP, IUPHARDb and other datasets in a unified schema. Novel cheminformatics and pattern recognition algorithms will be implemented and deployed for use by domain scientists in convenient, robust, and interoperable ways, including the powerful biological network visualization environment Cytoscape. For further details see specific aims.

News and Progress:

Date Milestone
Dec 2010 NIH R21 grant award notification.
Jan 2011 Work begins: database schema, data acquisition and integration, software method implementation.
Jan 2011  Many "data wrangling" issues to be resolved.  Each source database has its peculiarities and challenges.
Feb 2011 HierS scaffold code rewritten in Java with ChemAxon JChem.
Mar 2011 Initial db version includes IUPHARdb and Wombat. 
Apr 2011 MCES and scaffold data loaded.
Apr 2011 Sub-net extraction code and web app developed ("SNAKE").  XGMML can be imported by Cytoscape.
May 2011 Evaluation of application for biomedical research can begin, along with progress withCytoscape expertise.
Aug 2011 Presentation of CARLSBAD at q-bio computational biology conference in Santa Fe by Tudor Oprea, Jeremy Yang and Gergely Zahoransky-Kohalmi.
Sep 2011 PDSP data integrated and loaded.
Oct 2011 ChEMBL data integrated and loaded.
Nov 2011 PubChem MLP data integrated and loaded.
Jan 2012 CytoscapeWeb v1.0 released and integrated by SNAKE web app for rapid and convenient network analysis.
Feb 2012 Carlsbad database search web app developed for target/compound data exploration and inclusion in suite of tools.  Documentation and community website efforts increased.
March 2012 "Systems Chemical Biology" CINF session at ACS National Meeting in San Diego, co-organized by Tudor Oprea.  CARLSBAD to be presented.  For more info or to submit an abstract, see ACS.org.


Outreach: We invite biomolecular discovery scientists to participate in this project as beta testers and users of the CARLSBAD system. Your expert feedback can advise the development of this system while CARLSBAD helps to advance your research objectives. For more information please contact us ().

References:
  1. Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing; Tudor I. Oprea, Sonny Kim Nielsen, Oleg Ursu, Jeremy J. Yang, Olivier Taboureau, Stephen L. Mathias, Irene Kouskoumvekaki, Larry A. Sklar, Cristian G. Bologa, J. Mol. Info., 30 (2-3), 100-111, 2011.