Yes We Can Yes We Can Yes We Can Yes We Can From biomedical - PowerPoint PPT Presentation

Inauguration de Inauguration de l’Unité l’Unité Inserm Inserm U936 U936 Modélisation Modélisation des des connaissances connaissances biomédicales biomédicales February 6, 2009 February 6, 2009 Yes We Can Yes We Can Yes We Can Yes We Can From biomedical informatics to translational research From biomedical informatics to translational research De De l’informatique l’informatique biomédicale biomédicale à la à la médecine médecine translationelle translationelle Olivier Bodenreider Olivier Bodenreider Lister Hill National Center Lister Hill National Center for Biomedical Communications for Biomedical Communications Bethesda, Maryland Bethesda, Maryland - - USA USA

Outline Outline � National Institutes of Health National Institutes of Health � Translational research Translational research � Enabling translational research Enabling translational research � Anatomy of a translational research experiment � Anatomy of a translational research experiment Anatomy of a translational research experiment Anatomy of a translational research experiment � Promising results Promising results � Challenging issues Challenging issues 2 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

National Institutes of Health National Institutes of Health

National Institutes of Health National Institutes of Health � Research is the heart of the NIH mission Research is the heart of the NIH mission � 27 Institutes and Centers 27 Institutes and Centers � Institutes (Cancer, Heart, Lung & Blood) Institutes (Cancer, Heart, Lung & Blood) � Centers (NCCAM, NCRR) Centers (NCCAM, NCRR) � Intramural Intramural – – 6,000 researchers at NIH Institutes 6,000 researchers at NIH Institutes � Extramural Extramural – – grants for research, research grants for research, research resources, training resources, training http://www.nih.gov/ 8 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Facts about NIH Facts about NIH � $29.5 billion appropriation from Congress $29.5 billion appropriation from Congress � 80% awarded via competitive grants to more than 80% awarded via competitive grants to more than 325,000 researchers at 3,000 organizations 325,000 researchers at 3,000 organizations � 80,000 new applications received every year 80,000 new applications received every year � Average research grant = $355K, 4 years Average research grant = $355K, 4 years � 10% to support the intramural research program 10% to support the intramural research program � 6,000 scientists, mainly on the NIH campus in 6,000 scientists, mainly on the NIH campus in Bethesda, Maryland Bethesda, Maryland 9 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

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National Library of Medicine National Library of Medicine http://www.nlm.nih.gov/ http://www.nlm.nih.gov/ 12 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Collaboration NLM Collaboration NLM- -Inserm Inserm http://ist.inserm.fr/basismesh/mesh.html 13 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Research at NLM Research at NLM � Two research centers Two research centers � National Center for Biotechnology Information (NCBI) National Center for Biotechnology Information (NCBI) � PubMed PubMed � Other knowledge base in the � Other knowledge base in the Other knowledge base in the Entrez Other knowledge base in the Entrez Entrez system ( Entrez system ( system (GenBank system (GenBank GenBank Gene GenBank, Gene, , Gene, Gene PubMedCentral PubMedCentral, , PubChem PubChem, GEO, , GEO, dbGaP dbGaP,…) ,…) � Lister Hill National Center for Biomedical Lister Hill National Center for Biomedical Communications Communications � Unified Medical Language System (UMLS) Unified Medical Language System (UMLS) � ClinicalTrials.gov ClinicalTrials.gov � Genetics Home Reference Genetics Home Reference � … 14 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Medical Ontology Research Medical Ontology Research � Terminology, ontology and knowledge Terminology, ontology and knowledge representation in the biomedical domain representation in the biomedical domain � Basic research Basic research � Applied research Applied research � Applications Applications � Natural language understanding Natural language understanding � Automatic reasoning Automatic reasoning � Information visualization Information visualization � Information integration Information integration 15 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Translational research Translational research (Translational medicine) (Translational medicine)

Translational medicine/research Translational medicine/research � Definition Definition [Butte, JAMIA 2008] � Effective transformation of information gained from Effective transformation of information gained from biomedical research into knowledge that can improve biomedical research into knowledge that can improve the state of human health and disease the state of human health and disease � Goals Goals � Turn basic discoveries into clinical applications more Turn basic discoveries into clinical applications more rapidly (“bench to bedside”) rapidly (“bench to bedside”) � Provide clinical feedback to basic researchers Provide clinical feedback to basic researchers 17 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Combining clinical informatics Combining clinical informatics and bioinformatics and bioinformatics � Associates Associates � Clinical informatics Clinical informatics � Electronic medical records Electronic medical records � Clinical knowledge bases Clinical knowledge bases � Common computational resources C C Common computational resources t ti t ti l l � Biomedical natural language processing Biomedical natural language processing � Biomedical knowledge engineering Biomedical knowledge engineering � Bioinformatics Bioinformatics � Sequence databases Sequence databases � Gene expression Gene expression � Model organism databases Model organism databases 18 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Translational bioinformatics Translational bioinformatics � “… “… the development of storage, analytic, and interpretive the development of storage, analytic, and interpretive methods to optimize the methods to optimize the transformation of increasingly transformation of increasingly voluminous biomedical data voluminous biomedical data into proactive, predictive, into proactive, predictive, preventative, and participatory health. preventative, and participatory health. Translational bioinformatics includes research on the Translational bioinformatics includes research on the development of novel techniques for the integration of biological development of novel techniques for the integration of biological and clinical data and clinical data and the evolution of clinical informatics and the evolution of clinical informatics methodology to encompass biological observations. methodology to encompass biological observations. The end product of translational bioinformatics is The end product of translational bioinformatics is newly found newly found knowledge knowledge from these integrative efforts that can be from these integrative efforts that can be disseminated to a variety of stakeholders, including biomedical disseminated to a variety of stakeholders, including biomedical scientists, clinicians, and patients. ” scientists, clinicians, and patients. AMIA strategic plan http://www.amia.org/inside/stratplan 19 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications

Aspects of translational research Aspects of translational research � Huge volumes of data Huge volumes of data � Publicly available repositories Publicly available repositories � Publicly available tools Publicly available tools � Data Data- -driven research driven research 20 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications