2011-11-28 Open PHACTS at RSC CICAG
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Presented by Richard Kidd at "The Future Information Needs of Pharmaceutical & Medicinal Chemistry", Monday 28 November 2011 at The Linnean Society, Burlington Square, London run by the RSC CICAG group.
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2011-11-28 Open PHACTS at RSC CICAG
- 1. Pharmacological information discovery with Open PHACTS www.openphacts.org
- 5. Pharma are accessing, processing, storing & re-processing Public Domain Drug Discovery Data
- 10. Developers (Builders) End users (Drivers) A use case driven approach Prioritised research questions Prioritised data sources Target dossiers about targets, incorporating related information on sequences, structures, pathways, diseases and small molecules Chem/bio space navigator of sets of pharmacologically annotated small molecules, by chemical substructures, pharmacophores, biological activities Polypharmacology browser map coverage of the chemo-biological space for polypharmacological profiling of small molecules Exemplars
- 11. Developers (Builders) End users (Drivers) A use case driven approach Target validation work-bench: in silico target validation studies Fusion/aggregation of data from different domains to improve predictions of drug-transporter interactions Combination of physicochemical data & data from transporter interaction for prediction of blood-brain barrier permeation and tissue distribution Prioritised research questions Prioritised data sources Bench mark Pilots
- 18. rdf mapping id mapping concept mapping interface data Sources triple store chemical resolution Chem2Bio2RDF text mining
- 19. GUI - User suggestions for workflow Select question (“template” from category) Fill in template variables Via “relation browser” and add filters (IC50 value, dates etc) View results, filter and export dataset Select relevant data sources Execute search Modify query (change concepts and attributes) www.openphacts.org
- 22. LSP4All (Lundbeck) Generic Interface search by enzyme family Q15: All oxidoreductase inhibitors active <100nMolars in both human & mouse Credit: Sune Askjær / Claus Stie Kallesøe (Lundbeck) Pharmacological data Exact and structure search Navigate from compounds to targets
- 23. UTOPIA Documents (U Manchester)
- 24. PathVisio (Maastricht U) Biological data Genes suggestion for selected protein
- 27. Nanopublications Capturing scientific information in the Triple Store
- 28. OPS Component Stack www.openphacts.org
- 35. http://www.openphacts.org slideshare.com/open_phacts @Open_Phacts Thanks to Carole Goble, Lee Harland, Antony Williams
Editor's Notes
- -
- Services sit on top of semantic fabric
- Chem-Bio Navigator: querying and visualization of sets of pharmacologically annotated small molecules, on basis of chemical substructures, pharmacophores, biological activities Target Dossier: in silico dossiers about targets, incorporating related information on sequences, structures, pathways, diseases and small molecules Heavy on the text mining Polypharmacology Browser: map coverage of the chemo-biological space, to facilitate the polypharmacological profiling of small molecules Polypharmacology – drug hits many targets Main architecture, technical implementation and primary capabilities driven by a set of prioritised research questions Based on the main research questions define prioritised data sources Three Exemplars will be developed to demonstrate the capabilites of the OPS System and to define interfaces and input/output standards Three Use cases have been defined to benchmark the OPS system towards current standard workflows in data retrieval and mining The Apps must provide answers to relevant research questions Interrogation model GUI/interactivity Presentation of results
- Data retrieval and data/text mining The Apps must provide answers to relevant research questions Interrogation model GUI/interactivity Presentation of results Main architecture, technical implementation and primary capabilities driven by a set of prioritised research questions Based on the main research questions define prioritised data sources Three Exemplars will be developed to demonstrate the capabilites of the OPS System and to define interfaces and input/output standards Three Use cases have been defined to benchmark the OPS system towards current standard workflows in data retrieval and mining The Apps must provide answers to relevant research questions Interrogation model GUI/interactivity Presentation of results
- ( http://bioassayontology.org/)
- Fraunhofer SCAI: SCAIView Sparql interface to LarKC backend PDSP receptor database - The grey box is a set of Web Services API that provide nicer interfaces for GUI developers. Currently, these did not get implemented. Instead, we are issuing sparql queries directly from the various GUIs. - The set of purple boxes circled in red - are a set of facilities for allowing us to track provenance, curate data that has been aggregated in the cache, and do aggregated quality measures. These ended up *not* being in the lashup do to time. All these are allowing us to give feedback about the quality of the integrated data. (b) The red words are correct. I would say we don't do data mapping. We translate or get rdf versions of the data. The mapping is performed at runtime based on mappings. The updated architecture diagram with lessons learned from the lashup (Slide 17 in the bootstrapping development slides). Maybe you can show before and after? RE: Scalability (from a paper on the Larkc platform) LarKC aims to be the platform to address these issues, and is built on the following principles: • Achieve scalability through parallelisation. Different possibilities are offered either through tight integration of parallel processes on cluster-style hardware, or through much looser coupled wide-area distributed computing. • Achieve scalability through giving up completeness. Partial reasoning results are useful in many domains of application. Significant speedups and can be obtained by incompleteness in many stages of the reasoning process, ranging from selection of the axioms to incomplete reasoning over those axioms. • Do not build a single reasoning engine that is supposed to be suited for all kinds of use-cases, but instead build a configurable platform on which different components can be plugged in to obtain different scale/efficiency trade-offs, as required by different use- cases. RE: technologies being used in lashup larkc, lsp4all, ChemSpider but the next step is to incorporate ConceptWik and bridgeDB technologies The GUIs in the lashup demo were Utopia, Pathvisio, and the generic interface from Lundbeck RE: how larkc was populated loading RDF from source, but we have plans for an automated system that uses semantic site map standards
- Search by enzyme family SMILES: The S implified M olecular I nput L ine E ntry S pecification (SMILES) a line notation for molecules.
- A series of are a key vehicle for building the OPS community and encouraging wider engagement. These OPS Workshops will be hosted twice-annually, and focus on different aspects of drug discovery, the technology used, data sharing, sustainability, licensing and practical applications.