University of Pisa, Italy June 14, 2007 NETTAB 2007 - A Semantic Web for Bioinformatics Bio-ontologies The cream in the Semantic Web layer cake Olivier Bodenreider Olivier Bodenreider Lister Hill National Center Lister Hill National Center for Biomedical Communications for Biomedical Communications Bethesda, Maryland - - USA USA Bethesda, Maryland
Semantic Web pastry
Semantic Web layer cake Semantic Web layer cake http://www.axis-of-aevil.net/img/2005_09/tyrnicake1.jpg 3 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
Semantic Web layer cake Semantic Web layer cake http://www.cookingwithkristina.com/uploaded_images/fudgy-702607.jpg 4 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
Semantic Web layer cake Semantic Web layer cake 5 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
Semantic Web layer cake Semantic Web layer cake 6 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
Outline Outline � Historical perspective � Historical perspective � Modern bio Modern bio- -ontologies ontologies � � Tools and formalisms � Tools and formalisms � Institutionalization of bio Institutionalization of bio- -ontologies ontologies � � Bio � Bio- -ontologies and Semantic Web ontologies and Semantic Web 7 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
Briefings in Bioinformatics Briefings in Bioinformatics http://bib.oxfordjournals.org/cgi/reprint/7/3/256?ijkey=1ejwW7ipyG1ASiI&keytype=ref 8 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
A brief history of biomedical terminologies Before we called them bio-ontologies
Why biomedical terminologies? Why biomedical terminologies? � To support a theory of diseases � To support a theory of diseases � To classify diseases To classify diseases � � To support epidemiology � To support epidemiology � To index and retrieve information To index and retrieve information � � To serve as a reference � To serve as a reference 10 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
To support a theory of diseases To support a theory of diseases � Hippocrates � Hippocrates � Dismisses superstition Dismisses superstition � � Four humors Four humors � � Blood Blood � � Phlegm Phlegm � � Yellow bile Yellow bile � � Black bile Black bile � � Thomas Thomas Sydenham Sydenham (1624 (1624- -1689) 1689) � � Medical observations on the history Medical observations on the history � and cure of acute diseases (1676) (1676) and cure of acute diseases 11 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
To classify diseases (and plants) To classify diseases (and plants) � Carolus � Carolus Linnaeus (1707 Linnaeus (1707- -1778) 1778) � Genera Genera Plantarum Plantarum (1737) (1737) � � Genera Genera Morborum Morborum (1763) (1763) � � Fran Franç çois ois Boissier Boissier de La Croix de La Croix � a.k.a. F. B. de Sauvages Sauvages (1706 (1706- -1767) 1767) a.k.a. F. B. de � Methodus Methodus Foliorum Foliorum (1751) (1751) � � Nosologia Nosologia Methodica Methodica (1763/68) (1763/68) � � William Cullen (1710 William Cullen (1710- -1790) 1790) � Methodicae (1785) (1785) � Synopsis Synopsis Nosologiae Nosologiae Methodicae � 12 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
From plants… … From plants 13 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
… to diseases to diseases … � Four categories (W. Cullen) � Four categories (W. Cullen) � Fevers Fevers � � Nervous disorders Nervous disorders � � Cachexias Cachexias � � Local diseases Local diseases � “The distinction of the genera of diseases, “The distinction of the genera of diseases, the distinction of the species of each, and the distinction of the species of each, and often even that of the varieties, I hold to be often even that of the varieties, I hold to be a necessary foundation of every plan of a necessary foundation of every plan of physic, whether dogmatical or empirical.” physic, whether dogmatical or empirical.” – William Cullen, Edinburgh, 1785 – William Cullen, Edinburgh, 1785 Synopsis Nosologia Methodicae Synopsis Nosologia Methodicae (Cited by Chris Chute) 14 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
To support epidemiology To support epidemiology � John � John Graunt Graunt (1620 (1620- -1674) 1674) � Analyzes the vital statistics Analyzes the vital statistics � of the citizens of London of the citizens of London � William Farr (1807 � William Farr (1807- -1883) 1883) � Medical statistician Medical statistician � � Improves Cullen Improves Cullen’ ’s classification s classification � � Contributes to creating ICD Contributes to creating ICD � � Jacques Jacques Berthillon Berthillon (1851 (1851- � -1922) 1922) � Chief of the statistical services (Paris) Chief of the statistical services (Paris) � � Classification of causes of death (161 rubrics) Classification of causes of death (161 rubrics) � 15 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
London Bills of Mortality London Bills of Mortality 16 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
Limitations of existing classifications Limitations of existing classifications “The advantages of a uniform statistical nomenclature, however imperfect, are so “The advantages of a uniform statistical nomenclature, however imperfect, are so obvious, that it is surprising no attention has been paid to its enforcement in Bills obvious, that it is surprising no attention has been paid to its enforcement in Bills of Mortality. Each disease has, in many instances, been denoted by three or four of Mortality. Each disease has, in many instances, been denoted by three or four terms, and each term has been applied to as many different diseases: vague, terms, and each term has been applied to as many different diseases: vague, inconvenient names have been employed, or complications have been registered inconvenient names have been employed, or complications have been registered instead of primary diseases. The nomenclature is of as much importance in this instead of primary diseases. The nomenclature is of as much importance in this department of inquiry as weights and measures in the physical sciences, and department of inquiry as weights and measures in the physical sciences, and should be settled without delay.” should be settled without delay.” – William Farr – William Farr First annual report . First annual report . London, Registrar General of England and Wales, 1839, p. 99. London, Registrar General of England and Wales, 1839, p. 99. 17 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
To index and retrieve information To index and retrieve information � Biomedical literature � Biomedical literature � MEDLINE (15M citations from 4600 journals) MEDLINE (15M citations from 4600 journals) � � Manually indexed Manually indexed � � Medical Subject Headings (MeSH) Medical Subject Headings (MeSH) � � Genome � Genome � Model organisms (Fly, Mouse, Yeast, Model organisms (Fly, Mouse, Yeast, … …) ) � � Manually / semi Manually / semi- -automatically annotated automatically annotated � � Gene Ontology Gene Ontology � 18 Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications Lister Hill National Center for Biomedical Communications
MEDLINE and MeSH MEDLINE and MeSH 19 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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