paul groth pgroth/ @pgroth vu university amsterdam convergence meeting: semantic interoperability...

Paul Grothhttp://www.few.vu.nl/~pgroth/

@pgrothVU University Amsterdam

Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe1

We are all doing this many times……Pfizer

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The Problem

Open PHACTS objective

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe3

Platform

Standards

Apps

API

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Partners

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe

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Associate Partners

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe

Sequenomics

6Convergence Meeting: Semantic

Interoperability for Clinical Research & Patient Safety in Europe

ChEMBLChEMBL DrugBankDrugBank Gene Ontology

Gene Ontology WikipathwaysWikipathways

UniProtUniProt

ChemSpiderChemSpider

UMLSUMLS

ConceptWikiConceptWiki

ChEBIChEBI

TrialTroveTrialTrove

GVKBioGVKBio

GeneGoGeneGo

TR IntegrityTR Integrity

“Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM”

“Let me compare MW, logP and PSA for known oxidoreductase inhibitors”

“What is the selectivity profile of known p38 inhibitors?”

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe7

Open PHACTS Explorer

PharmaTrek

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe9

ChemBioNavigtor

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe10

Utopia Documents

Semantic interoperability approach

Principles •Respect data providers•Make it easy for application developers

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe11

Semantic interoperability approach

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe12

Semantic Resources – Data sets

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe13

814,535,923 triples

Semantic Resources - Mappings

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe14

18 Million Mappings

Semantic resources - Summary

• Types of semantic resources– RDF Datasets– Mappings– Terminologies

• Mesh, UMLS, NCIM

– Hierarchies are essential • E.G. Target Ontology, Gene Ontology, Enzyme

classification • Class reasoning is essential

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe15

Methodology for semantic integration

1. Define use cases 2. Data Providers – create RDF with VoID headers3. Create mappings

– between dataset and known datasets (instance level)– index for text to url conversion

4. Ingest RDF into data cache (i.e. triple store)5. Define access paths to core concepts in data6. Extend or create sparql queries for API calls7. Publish api calls

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe16

Its easy to integrate, but difficult to integrate well

Adoption of standards

• Basic Semweb standards– SPARQL 1.1, RDF(S), SKOS

• Dataset descriptions– Vocabulary of Interlinked Datasets (VoID)– VoID linkset descriptions

• QUDT Quantities, Units, Dimensions and Types• Provenance

– W3C PROV, PAV, Nanopublications• BioPortal

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe18

Tooling• Infrastructure

– Linked Data API – Bridge DB - identifier to identifier mapping– Concept Wiki - text to identifier mapping and curation– Chemspider: chemistry registration and services– Triple Store: Virtuoso Professional addition

• Data– VoID descriptions and http and ftp sites– Github for data conversion scripts– Recommend turtle as RDF syntax

• friendly for scripting

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe19

Quality assurance of the semantic resources

• Provenance Everywhere• Validation

• ChemSpider Validation and Standardization Platform (CVSP) for flagging chemical representation issues

• Curation• High quality chemical names and synonyms. • Curation interfaces for terminologies (concept wiki)

• Report data quality issues to data providers

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe20

Semantic interoperability issues

1. Do not underestimate infrastructure2. APIs are important

1. Allows for tuning of sparql queries2. Makes it easy for developers

3. Ontologies- Requirements vs. Recommendation

4. Modeling is hard

Convergence Meeting: Semantic Interoperability for Clinical Research &

Patient Safety in Europe21

Open PHACTS Information

• http://www.openphacts.org• pmu@openphacts.org• @Open_PHACTS• Publications

– Overview paper: Williams, A.J., Harland, L., Groth, P., Pettifer, S., Chichester, C., Willighagen, E.L., Evelo, C.T., Blomberg, N., Ecker, G., Goble, C., Mons, B.: Open PHACTS: Semantic interoperability for drug discovery. Drug Discovery Today. 17, 1188–1198 (2012).

– Technical approach: Gray, A.J.G., Groth, P., Loizou, A., et al.: Applying linked data approaches to pharmacology: Architectural decisions and implementation. Semantic Web. (2012).

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Patient Safety in Europe22