Www.zbh.uni-hamburg.deJune 2014Katrin Stierand Accessing OpenPHACTS: Interactive exploration of...

www.zbh.uni-hamburg.deJune 2014Katrin Stierand

Accessing OpenPHACTS:Interactive exploration of compounds and targets from the semantic web

Katrin Stierand

ZBH Center for Bioinformatics Hamburg


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OPS

Data

Cache

Core API

API/SPARQL HTTPAJAX

HTML5JavaScript

CBN Server

Result DB

Apache Webserverwith

Ruby on RailsApplication Server

SQL

„Background Engine“

Systemcalls


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The ChemBioNavigator (CBN)Google style: Interactive – Simplicity rules

www.chembionavigator.org

Stierand K., Harder T., Marek T., et al. Molecular Informatics, Volume 31, Issue 8, p. 543–546, August 2012

www.zbh.uni-hamburg.deJune 2014Katrin Stierand4Compound panel Drawing area Target panel

ChemBioNavigator GUI


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FeaturesProvenance: all data is interlinked with the original sourceDrill-down: interactive sorting based on public and private propertiesHousekeeping: put compounds in „buckets“ to retain an overviewSearching: based on similarity, substructure or related targetPersistence: store a session and resume work later


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Workflow IStart 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 searchc) Define a substructure and start a substructure search

a

b

c


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Workflow IIStart with target nameThe CBN loads the target information from OPS. On mouse click, all active compounds are loaded in the CBN.


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Workflow IIIStart with a set of SMILES or a SD file:The given compounds are initialized by NAOMI and annotated with data from the OPS.

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)C


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Example: Find new lead structures for CSF-1 receptor inhibitionStart the CBN: www.chembionavigator.orgSearch 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 compoundSwitch 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 proteinDownload this compound set


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Acknowledgement

Tim Harder – Philips Medical Systems DMC GmbHLothar Wissler – BioSolveIT GmbHChristian Lemmen – BioSolveIT GmbHMatthias 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 (FP7/2007-2013) and EFPIA companies’ in kind contribution.

Www.zbh.uni-hamburg.deJune 2014Katrin Stierand Accessing OpenPHACTS: Interactive exploration of...

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