The Translational Medicine Ontology: Driving personalized      medicine by bridging the gap from bedside to benchside
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The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to benchside

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The Translational Medicine Ontology provides terminology that bridges diverse areas of translational medicine including hypothesis management, discovery research, drug development and formulation, ...

The Translational Medicine Ontology provides terminology that bridges diverse areas of translational medicine including hypothesis management, discovery research, drug development and formulation, clinical research, and clinical practice. Designed primarily from use cases, the ontology consists of essential terms that are mapped to other ontologies. It serves as a global schema for data integration while simultaneously facilitating the formulation of complex queries across heterogeneous sources. We demonstrate the utility of the ontology through question answering over a prototype knowledge base composed of sample patient data integrated with linked open data. This work forms a basis for the development of a computational platform for managing information relevant to personalized medicine.

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The Translational Medicine Ontology: Driving personalized      medicine by bridging the gap from bedside to benchside The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to benchside Presentation Transcript

  • The Translational Medicine Ontology: driving personalized medicine by bridging the gap from bedside to bench
    1
    Bio-ontologies 2010:July 9, 2010
    Michel Dumontier
    on behalf of the HCLS TMO Subgroup
    Carleton University, Ottawa, Canada
  • 2
    Bio-ontologies 2010:July 9, 2010
  • HCLS TMO subgroup
    BosseAndersson, AstraZeneca, Lund, Sweden
    Colin Batchelor, Royal Society of Chemistry, Cambridge, UK
    Christine Denney, Eli Lilly, Indianapolis, IN, USA
    Christopher Domarew, Warrington Hospital, Warrington, UK
    AnjaJentzsch, FreieUniversitat, Berlin, Germany
    Joanne Luciano, Predictive Medicine Inc., Belmont, MA, USA
    Elgar Pichler, W3C HCLSIG
    Eric Prud'hommeaux, W3C, Cambridge, MA, USA
    Patricia L. Whetzel, Stanford University, Stanford, CA, USA
    Olivier Bodenreider, National Library of Medicine, Bethesda, MD, USA
    Tim Clark, Harvard Medical School, Cambridge, MA, USA ,
    Lee Harland, Pfizer, Sandwich, UK
    VipulKashyap, Cigna, Hartford, CT, USA
    Peter Kos, Harvard Medical School, Cambridge, MA, USA
    Julia Kozlovsky, AstraZeneca, Waltham, MA, USA
    James McGurk, Daiichi Sankyo, NJ, USA
    ChimezieOgbuji Cleveland Clinic, Cleveland,OH, USA
    Matthias Samwald, Digital Enterprise Research Institute, Galway, Ireland
    Lynn Schriml, University of Maryland, Institute for Genome Sciences
    Peter J. Tonellato, Harvard Medical School, Cambridge, MA, USA
    Jun Zhao, University of Oxford, Oxford, UK.
    Susie StephensJohnson & Johnson Pharmaceutical Research & Development L.L.C., Radnor, PA, USA.
    Bio-ontologies 2010:July 9, 2010
    3
  • Goals of the W3C HCLSIG
    Advance the state of the art in knowledge discovery for health care and the life sciences
    Investigate approaches to facilitate the integration of patient care, clinical research and basic life science research
    Provide effective demonstrations of using Semantic Web technologies for knowledge representation, data integration, data visualization and question answering
    Bio-ontologies 2010:July 9, 2010
    4
  • Personalized Medicine
    The ability to offer
    The Right Drug
    To The Right Patient
    For The Right Disease
    At The Right Time
    With The Right Dosage
    Genetic and metabolic data will allow drugs to be tailored to patient subgroups
    5
    Bio-ontologies 2010:July 9, 2010
  • “If it were not for the great variability among individuals, medicine might as well be a science and not an art”
    Sir William Osler, 1892
    6
    Bio-ontologies 2010:July 9, 2010
  • 7
    Bio-ontologies 2010:July 9, 2010
  • 8
    Bio-ontologies 2010:July 9, 2010
  • 9
    Bio-ontologies 2010:July 9, 2010
  • The Semantic Web
    is the new global web of knowledge
    10
    Bio-ontologies 2010:July 9, 2010
    It is about standards for publishing, sharing and querying
    knowledge drawn from diverse sources
    It makes possible the answering
    sophisticated questions using
    background knowledge
  • A growing web of linked data
    11
    Bio-ontologies 2010:July 9, 2010
  • Bio-ontologies 2010:July 9, 2010
    How do we query across these linked data?
    12
  • Formal Ontology as a Strategy
    13
    Bio-ontologies 2010:July 9, 2010
  • Problem Statement
    Growing number of biomedical terminologies
    Over 200 listed at NCBO bioportal
    Ontologies are a formal specification of a conceptualization
    Not all are well formulated, nor properly formalized
    OBO Foundry to create a reference set of ontologies, but the task is enormous, until then, we need working solutions
    Increasing amounts of linked data
    Conceptualization is haphazard
    not formulated using formal ontologies
    Relations and types are not grounded to shared conceptualization.
    ontologies applied to linked data will be useful to integrate and provide support for queries
    Bio-ontologies 2010:July 9, 2010
    14
  • TMO Approach
    Undertake extensive user-focused requirements
    Identify key entities and establish their relations
    Extend the conceptualization as specified by a foundational ontology
    Map linked data types to ontology types
    Develop knowledge base containing ontology + mappings + data
    Demonstrate query answering over TMO KB
    Bio-ontologies 2010:July 9, 2010
    15
  • Survey reveals diverse needs and interests
    Bio-ontologies 2010:July 9, 2010
    16
  • Preparation
    Generate plausible questions of interest
    Generate scenerios
    patient centric
    research centric
    chemoinformatics / drug discovery
    pharmacogenomics
    animal models
    integrative informatics
    drug therapy development
    Bio-ontologies 2010:July 9, 2010
    17
  • Ontology
    • 75 classes out of an initial 90 types spanning material entities, processes, roles, informational entities
    Distinction among different kinds of material entities
    molecular entities vs chemical substances
    active ingredients vs pharmaceutical formulations
    Distinction among different kinds of informational entities
    medical
    medical history (a list of events & bodily features), diagnostic results
    drug
    dosage (specification), toxicity (reports), treatment safety (guidelines)
    Bio-ontologies 2010:July 9, 2010
    18
  • Bio-ontologies 2010:July 9, 2010
    19
    223 class mappings
    from 60 TMO classes to 201 target classes over 40 ontologies
  • Data
    Bio-ontologies 2010:July 9, 2010
    20
  • Linking Open Drug Data (LODD)
    Bio-ontologies 2010:July 9, 2010
    21
  • focus: Alzheimer’s Disease (AD)
    Incurable, degenerative, and terminal disease with few therapeutic options.
    Influenced by a range of genetic, environmental and other factors.
    Identification of prognostic biomarkers would significantly impact and guide the diagnosis, prescription, and development of therapeutic agents would significantly impact future practice.
    Efficient aggregation of relevant information to help understand the pathology would benefit researchers, clinicians, and patients and would also facilitate the development of target compounds to reduce or even prevent the burden of the disease.
    Bio-ontologies 2010:July 9, 2010
    22
  • formalizing the Dubois AD diagnostic criteria
    Bio-ontologies 2010:July 9, 2010
    23
    # the panel is a textual entity
    dubois:panel2 a iao:IAO_0000300 .
    dubois:panel2 rdfs:label "Alzheimer Disease diagnostic criteria as reported in panel 2 of dubois et al - pubmed:17616482 [dubois:panel2]".
    # the panel is about alzheimer disease
    dubois:panel2 iao:is_about diseasome:74.
    # the panel is from the article
    dubois:panel2 ro:part_of <http://bio2rdf.org/pubmed:17616482>.
    # the panel is about diagnostic criterion
    dubois:panel2 iao:is_about tmo:TMO_0068.
    #inclusion criterion
    dubois:10 rdfs:label "Proven AD autosomal dominant mutation within the immediate family [dubois:10]" ;
    a tmo:TMO_0069;
    ro:part_of dubois:panel2;
    iao:is_about diseasome:74.
    # exclusion criterion
    dubois:16 rdfs:label "Major depression [dubois:16]" ;
    a tmo:TMO_0070;
    ro:part_of dubois:panel2;
    iao:is_about diseasome:74.
  • Queries
    Clinic
    Have any AD patients been treated for other neurological conditions
    Patient 2 was found to suffer from AD and depression.
    Clinical Trial
    Since my patient is suffering from drug-induced side effects for AD treatment, identify an AD clinical trial with a different mechanism of action (MOA)
    Of the 438 drugs linked to AD trials, only 58 are in active trials and only 2 (Doxorubicin and IL-2) have a documented MOA. 78 AD-associated drugs have an established MOA.
    Research
    Which existing marketed drugs might potentially be re-purposed for AD because they are known to modulate genes that are implicated in the disease?
    57 compounds or classes of compounds that are used to treat 45 diseases, including AD, hyper/hypotension, diabetes and obesity
    Bio-ontologies 2010:July 9, 2010
    24
    http://esw.w3.org/topic/HCLSIG/PharmaOntology/Queries
  • Future Directions
    Enhancement of ontology to increase coverage
    Increased formalization of patient records so as to facilitate patient recruitment
    Formalization of pathway diagrams and the aggregate set of processes they specify
    Refactoring of linked data
    more explicit representation of quantities/values
    Bio-ontologies 2010:July 9, 2010
    25
  • The Translational Medicine Ontology
    Provides a global schema for the integration of linked data sets
    Establishes accurate mappings to relevant ontologies
    Demonstrative knowledge base focused around AD
    Bio-ontologies 2010:July 9, 2010
    26
  • Bio-ontologies 2010:July 9, 2010
    27
    Acknowledgements