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ChemBioNavigator: Interactive Exploration of Compounds and Targets

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braima
10 diapositives · 211 Views · Aug 01, 2014

ChemBioNavigator facilitates interactive exploration of compounds and targets using semantic web technologies. Users can search, sort, and drill down on compound data, conduct similarity searches, and store sessions for later analysis. The system integrates data from multiple sources and allows for easy navigation and analysis.

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ChemBioNavigator: Interactive Exploration of Compounds and Targets
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  1. Accessing OpenPHACTS: Interactive exploration of compounds and targets from the semantic web Katrin Stierand ZBH Center forBioinformatics Hamburg

  2. HTML5 JavaScript OPS Data Cache Core API HTTP AJAX API/SPARQL CBN Server „Background Engine“ System calls Apache Webserver with Ruby on Rails Application Server SQL Result DB

  3. www.chembionavigator.org Stierand K., Harder T., Marek T., et al. Molecular Informatics, Volume 31, Issue 8, p. 543–546, August 2012 The ChemBioNavigator (CBN)Google style: Interactive – Simplicity rules

  4. Target panel Compound panel Drawing area ChemBioNavigator GUI

  5. Features Provenance: all data is interlinked with the original source Drill-down: interactive sorting based on public and private properties Housekeeping: put compounds in „buckets“ to retain an overview Searching: based on similarity, substructure or related target Persistence: store a session and resume work later

  6. a b c Workflow I • Start with a single compound name or a SMILES string and extend the molecule set by related compounds: • Find target via assay data and load all compounds from OPS, which are active against this target • Start a similarity search • Define a substructure and start a substructure search

  7. Workflow II Start with target name The CBN loads the target information from OPS. On mouse click, all active compounds are loaded in the CBN.

  8. O=C(O)C(c1ccc(cc1)CC(C)C)CO=C(O)C(c1ccc(cc1)CC2CCC2)CO=C(O)[C@@H](c1ccc(cc1)CC(C)C)CO=C(O)C(c1ccc(cc1)CC2CC2)CO=C(O)[C@@H](c1ccccc1)CO=C(O)C(c1cc(ccc1)CC(c2ccccc2)C)CO=C(O)C(c1ccc(cc1)CC2CCCCC2)CO=C(O)C(c1ccccc1)C(c2ccccc2)c3ccccc3O=C(O)C(c1cc(ccc1)CC)CO=C(O)C(c1cc(ccc1)CCCC)CO=C(O)C(c1ccc(cc1)C(CC)C)C[O-]C(=O)C(c1ccccc1)CC([O-])=OO=C(O)C(c1cc(ccc1)C(CC)CC)CO=C(O)C(c1ccc(cc1)CC2CCCC2)CO=C(O)C(c1ccc(cc1)C(C)C)CO=C(O)C(c1ccc(cc1)CC(C)C)CO=C(O)C(c1ccc(cc1)CC2CCC2)CO=C(O)[C@@H](c1ccc(cc1)CC(C)C)CO=C(O)C(c1ccc(cc1)CC2CC2)CO=C(O)[C@@H](c1ccccc1)CO=C(O)C(c1cc(ccc1)CC(c2ccccc2)C)CO=C(O)C(c1ccc(cc1)CC2CCCCC2)CO=C(O)C(c1ccccc1)C(c2ccccc2)c3ccccc3O=C(O)C(c1cc(ccc1)CC)CO=C(O)C(c1cc(ccc1)CCCC)CO=C(O)C(c1ccc(cc1)C(CC)C)C[O-]C(=O)C(c1ccccc1)CC([O-])=OO=C(O)C(c1cc(ccc1)C(CC)CC)CO=C(O)C(c1ccc(cc1)CC2CCCC2)CO=C(O)C(c1ccc(cc1)C(C)C)C Workflow III Start with a set of SMILES or a SD file: The given compounds are initialized by NAOMI and annotated with data from the OPS.

  9. Example: Find newleadstructuresfor CSF-1 receptorinhibition Start the CBN: www.chembionavigator.org Search for CW-2580 (a highlyselectivekinaseinhibitor) Select thecompoundandexploretheavailabledata on thecompoundpanel on thelefthandside Perform a substructuresearch on theentirecompound Switch totableview (buttons in theupperrightcorner) andexplorethenewcompounds -> forwhichproteinaretheyidentifiedasinhibitors? Select thisprotein(Pharmacologytab on theCompound Panel) Go the Target Panel anddownload all activecompoundsoftheprotein Download thiscompoundset

  10. Acknowledgement Tim Harder – Philips Medical Systems DMC GmbH Lothar Wissler – BioSolveIT GmbH Christian Lemmen– BioSolveIT GmbH Matthias Rarey – ZBH Center forBioinformatics The development of the ChemBioNavigator in the context of the OpenPHACTS project is funded by the Innovative Medicines Initiative Joint Undertaking under grant agreement n° [115191], resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in kind contribution.