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Paul Groth http:// www.few.vu.nl /~ pgroth / @ pgroth VU University Amsterdam Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe. The Problem. We are all doing this many times……. Pfizer. AZ. GSK. Merck. n. Open PHACTS objective. Platform.

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Paul Groth

http://www.few.vu.nl/~pgroth/

@pgroth

VU University Amsterdam

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

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


The Problem

We are all doing this many times……

Pfizer

AZ

GSK

Merck

n


Open PHACTS objective

Platform

Apps

Standards

API

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


Partners

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


Associate Partners

Sequenomics

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


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

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

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

DrugBank

Wikipathways

GeneGo

ChEMBL

Gene Ontology

ChEBI

UniProt

UMLS

GVKBio

ConceptWiki

ChemSpider

TrialTrove

TR Integrity

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


Open PHACTS Explorer

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


PharmaTrek


ChemBioNavigtor

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


Utopia

Documents

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


Semantic interoperability approach

Principles

  • Respect data providers

  • Make it easy for application developers

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


Semantic interoperability approach

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


Semantic Resources – Data sets

  • 814,535,923 triples

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


Semantic Resources - Mappings

18 Million

Mappings

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


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 Europe


Methodology for semantic integration

  • Define use cases

  • Data Providers – create RDF with VoID headers

  • Create mappings

    • between dataset and known datasets (instance level)

    • index for text to url conversion

  • Ingest RDF into data cache (i.e. triple store)

  • Define access paths to core concepts in data

  • Extend or create sparql queries for API calls

  • Publish api calls

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


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 InterlinkedDatasets (VoID)

    • VoIDlinkset descriptions

  • QUDT Quantities, Units, Dimensions and Types

  • Provenance

    • W3C PROV, PAV, Nanopublications

  • BioPortal

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


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 Europe


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 Europe


    Semantic interoperability issues

    • Do not underestimate infrastructure

    • APIs are important

      • Allows for tuning of sparql queries

      • Makes it easy for developers

    • Ontologies- Requirements vs. Recommendation

    • Modeling is hard

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


    Open PHACTS Information

    • http://www.openphacts.org

    • [email protected]

    • @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).

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


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