Www.zbh.uni-hamburg.deJune 2014Katrin Stierand Accessing OpenPHACTS: Interactive exploration of compounds and targets from the semantic web Katrin Stierand.

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Presentation transcript:

2014Katrin Stierand Accessing OpenPHACTS: Interactive exploration of compounds and targets from the semantic web Katrin Stierand ZBH Center for Bioinformatics Hamburg

2014Katrin Stierand 2 OPS Data Cache Core API API/SPARQL HTTP AJAX HTML5 JavaScript CBN Server Result DB Apache Webserver with Ruby on Rails Application Server SQL „Background Engine“ System calls

2014Katrin Stierand The ChemBioNavigator (CBN) Google style: Interactive – Simplicity rules 3 Stierand K., Harder T., Marek T., et al. Molecular Informatics, Volume 31, Issue 8, p. 543–546, August 2012

2014Katrin Stierand 4 ChemBioNavigator GUI

2014Katrin Stierand 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 5

2014Katrin Stierand Workflow I Start with a single compound name or a SMILES string and extend the molecule set by related compounds: a)Find target via assay data and load all compounds from OPS, which are active against this target b)Start a similarity search c)Define a substructure and start a substructure search 6 a b c

2014Katrin Stierand 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. 7

2014Katrin Stierand 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. 8 O=C(O)C(c1ccc(cc1)CC(C)C)C O=C(O)C(c1ccc(cc1)CC2CCC2)C O=C(O)C(c1ccc(cc1)CC2CC2)C O=C(O)C(c1cc(ccc1)CC(c2ccccc2)C)C O=C(O)C(c1ccc(cc1)CC2CCCCC2)C O=C(O)C(c1ccccc1)C(c2ccccc2)c3ccccc3 O=C(O)C(c1cc(ccc1)CC)C O=C(O)C(c1cc(ccc1)CCCC)C O=C(O)C(c1ccc(cc1)C(CC)C)C [O-]C(=O)C(c1ccccc1)CC([O-])=O O=C(O)C(c1cc(ccc1)C(CC)CC)C O=C(O)C(c1ccc(cc1)CC2CCCC2)C O=C(O)C(c1ccc(cc1)C(C)C)C

2014Katrin Stierand Example: Find new lead structures for CSF-1 receptor inhibition Start the CBN: Search for CW-2580 (a highly selective kinase inhibitor) Select the compound and explore the available data on the compound panel on the left hand side Perform a substructure search on the entire compound Switch to table view (buttons in the upper right corner) and explore the new compounds -> for which protein are they identified as inhibitors? Select this protein (Pharmacology tab on the Compound Panel) Go the Target Panel and download all active compounds of the protein Download this compound set 9

2014Katrin Stierand Acknowledgement Tim Harder – Philips Medical Systems DMC GmbH Lothar Wissler – BioSolveIT GmbH Christian Lemmen – BioSolveIT GmbH Matthias Rarey – ZBH Center for Bioinformatics 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/ ) and EFPIA companies’ in kind contribution. 10

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