Incorporating Commercial and Private Data into an - Open PHACTS PDF
Preview Incorporating Commercial and Private Data into an - Open PHACTS
Incorporating Commercial and Private Data into an Open Linked Data Platform for Drug Discovery Carole Goble, Alasdair J G Gray, Lee Harland, Karen Karapetyan, Antonis Loizou, Ivan Mikhailov, Yrjänä Rankka, Stefan Senger, Valery Tkachenko, Antony J Williams, and Egon L Willighagen www.openphacts.org [email protected] @open_phacts @gray_alasdair Pre-competitive Informatics Pharmaceutical companies are all accessing, processing, storing & re-processing external research data Repeat @ Downloads x Literature Genbank Databases each Patents PubChem company Firewalled Databases Data Integration Data Analysis Lowering industry firewalls: pre-competitive informatics in drug discovery Nature Reviews Drug Discovery (2009) 8, 701-708 doi:10.1038/nrd2944 25/10/2013 ISWC 2013 1 Open PHACTS objective Apps Interactive responses Open Standards Domain API Provenance of data Drug Discovery Platform Production quality 25/10/2013 ISWC 2013 2 Drug Discovery Data Pathways Proteins Interactions Pharmacological Genes Activities Transcripts Clinical Drug Applications Biological Drugs Processes Indications Pathological Diseases Processes Compounds 25/10/2013 ISWC 2013 3 Public Data Pathways Proteins Interactions Pharmacological Genes Activities Transcripts Clinical Drug Applications Biological Drugs Processes Indications Pathological Diseases Processes Compounds 25/10/2013 ISWC 2013 4 Real Business Questions Pathways “Let me compare Proteins MW, logP and PSA for known Interactions “What is thPeh armacological oxidoreductase selectivity profile of Genes Activities inhibitors” known p38 inhibitors?” Transcripts Clinical Drug Applications “Find me compounds Biological Drugs that inhibit targets in Processes Indications NFkB pathway assayed in only functional assays Pathological with a potency <1 μM” Diseases Processes Compounds 25/10/2013 ISWC 2013 5 OPS Discovery Platform Apps Identity “Adenosine Domain Linked Data API Resolution receptor 2a” (RDF/XML, TTL, JSON) Specific Service m Services r o f Identifier t P12374 Semantic Workflow Engine a Management l EC2.43.4 P Service CS4532 e r Chemistry o Data Cache Registration C Normalisatio (Virtuoso Triple Store) n & Q/C Indexing VoID VoID VoID VoID VoID Nanopub Nanopub Nanopub Public Ontologies Db Db Db Db 25/10/2013 ISWC 2013 User 6 Public Content Commercial Annotations Present Content: Public Data Source Initial Records Triples Properties ChEMBL 1,247,403 305,419,649 77 DrugBank 19,628 517,584 74 UniProt ? 533,394,147 82 ENZYME 6,187 73,838 2 ChEBI 40,575 40,575 2 GeneOntology 38,137 1,265,273 26 GOA ? 23,489,501 15 ChemSpider 1,194,437 161,336,857 26 ConceptWiki 2,828,966 3,739,884 1 WikiPathways 946 1,449,981 34 25/10/2013 ISWC 2013 7 Semantic Integration Methodology 1. Define use cases 2. Identify Data – Create RDF – VoID dataset descriptions 3. Create mappings – between data set and known data sets (instance level) – index for text to URL conversion 25/10/2013 ISWC 2013 8 Semantic Integration Methodology 4. Ingest RDF into data cache (i.e. triple store) 5. Define access paths to core concepts in data 6. Extend or create SPARQL queries for API calls 7. Publish API calls 25/10/2013 ISWC 2013 9
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