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Infectious Disease Ontology

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Infectious Disease Informatics

Abstract

In the last decade, technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. More recently, ontologies have been shown to have significant benefits both for the analysis of data resulting from high-throughput technologies and for automated reasoning applications, and this has led to organized attempts to improve the structure and formal rigor of ontologies in ways that will better support computational analysis and reasoning. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain.

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References

  • Baader F (2007) The description logic handbook: theory, implementation, and applications. Cambridge University Press, Cambridge

    Google Scholar 

  • Baranzini SE, Wang J, Gibson RA, Galwey N, et al (2009) Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. Hum Mol Genet 18:767–778

    Article  CAS  PubMed  Google Scholar 

  • Bard J, Rhee SY, Ashburner M (2005) An ontology for cell types. Genome Biol 6:R21

    Article  PubMed  Google Scholar 

  • Bechhofer S, van Harmelen F, Hendler J, Horrocks I, McGuinness DL et al (2004) OWL Web Ontology Language Reference

    Google Scholar 

  • Blake JA, Eppig JT, Bult CJ, Kadin JA, Richardson JE (2006) The Mouse Genome Database (MGD): updates and enhancements. Nucleic Acids Res 34:D562–D567

    Article  CAS  PubMed  Google Scholar 

  • Blake JA, Hill DP, Smith B (2007) Gene Ontology annotations: what they mean and where they come from, Vienna, pp 79–82

    Google Scholar 

  • Bodenreider O (2006) Lexical, terminological and ontological resources for biological text mining. In: Ananiadou S, McNaught J (eds) Text mining for biology and biomedicine. Artech House, Norwood, MA, pp 43–66

    Google Scholar 

  • Bodenreider O (2008) Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform 67–79

    Google Scholar 

  • Bodenreider O, Stevens R (2006) Bio-ontologies: current trends and future directions. Brief Bioinform 7:256–274

    Article  CAS  PubMed  Google Scholar 

  • Bodenreider O, Smith B, Kumar A, Burgun A (2004) Investigating subsumption in DL-based terminologies: a case study in Snomed-CT, KR-MED Proceedings 2004, pp 12–20

    Google Scholar 

  • Brameier M, Wiuf C (2007) Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. J Biomed Inform 40:160–173

    Article  CAS  PubMed  Google Scholar 

  • Bresell A, Servenius B, Persson B (2006) Ontology annotation treebrowser: an interactive tool where the complementarity of medical subject headings and gene ontology improves the interpretation of gene lists. Appl Bioinform 5:225–236

    Article  CAS  Google Scholar 

  • Buckeridge DL (2007) Outbreak detection through automated surveillance: a review of the determinants of detection. J Biomed Inform 40:370–379

    Article  PubMed  Google Scholar 

  • Buckeridge DL, Burkom H, Campbell M, Hogan WR, Moore AW (2005) Algorithms for rapid outbreak detection: a research synthesis. J Biomed Inform 38:99–113

    Article  PubMed  Google Scholar 

  • Butte AJ, Chen R (2006) Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annu Symp Proc 106–110

    Google Scholar 

  • Camon E, Magrane M, Barrell D, Lee V, Dimmer E et al (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 32:D262–D266

    Article  CAS  PubMed  Google Scholar 

  • Ceusters W, Smith B, Kumar A, Dhaen C (2004a) Mistakes in medical ontologies: where do they come from and how can they be detected? In: Pisanelli D (ed) Ontologies in medicine. IOS, Amsterdam, pp 145–164

    Google Scholar 

  • Ceusters W, Smith B, Kumar A, Dhaen C (2004b) Ontology-based error detection in SNOMED-CT. MedInfo 11:482–486

    Google Scholar 

  • Ceusters W, Smith B, Goldberg L (2005) A terminological and ontological analysis of the NCI thesaurus. Methods Inform Med 44:498–507

    CAS  Google Scholar 

  • Chabalier J, Mosser J, Burgun A (2007) Integrating biological pathways in disease ontologies. Stud Health Technol Inform 129:791–795

    PubMed  Google Scholar 

  • Cherry JM, Ball C, Weng S, Juvik G, Schmidt R et al (1997) Genetic and physical maps of Saccharomyces cerevisiae. Nature 387:67–73

    Article  CAS  PubMed  Google Scholar 

  • Cimino JJ, Zhu X (2006) The practical impact of ontologies on biomedical informatics. Yearb Med Inform 124–135

    Google Scholar 

  • Coleman M, Sharp B, Seocharan I, Hemingway J (2006) Developing an evidence-based decision support system for rational insecticide choice in the control of African malaria vectors. J Med Entomol 43:663–668

    Article  CAS  PubMed  Google Scholar 

  • Coonan KM (2004) Medical informatics standards applicable to emergency department information systems: making sense of the jumble. Acad Emerg Med 11:1198–1205

    Article  PubMed  Google Scholar 

  • Cornet R, de Keizer N (2008) Forty years of SNOMED: a literature review. BMC Med Inform Decis Mak 8 Suppl 1:S2

    Article  Google Scholar 

  • Detwiler LT, Chung E, Li A, Mejino JL Jr, Agoncillo A, et al (2004) A relation-centric query engine for the Foundational Model of Anatomy. Stud Health Technol Inform 107:341–345

    PubMed  Google Scholar 

  • Djebbari A, Karamycheva S, Howe E, Quackenbush J (2005) MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinformatics 21:3324–3326

    Article  CAS  PubMed  Google Scholar 

  • Doms A, Schroeder M (2005) GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 33:W783–W786

    Article  CAS  PubMed  Google Scholar 

  • Grinde B, Gayorfar M, Rinaldo CH (2007) Impact of a polyomavirus (BKV) infection on mRNA expression in human endothelial cells. Virus Res 123:86–94

    Article  CAS  PubMed  Google Scholar 

  • Grumbling G, Strelets V (2006) FlyBase: anatomical data, images and queries. Nucleic Acids Res 34:D484–D488

    Article  CAS  PubMed  Google Scholar 

  • Guarino N (1998) Some ontological principles for designing upper level lexical resources. In: Rubio AGN, Castro R, Tejada A (eds) Proc of First Int Conf Lang Res Eval, Granada, Spain, pp 527–534

    Google Scholar 

  • Hill DP, Blake JA, Richardson JE, Ringwald M (2002) Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res 12:1982–1991

    Article  CAS  PubMed  Google Scholar 

  • Huang D, Wei P, Pan W (2006) Combining gene annotations and gene expression data in model-based clustering: weighted method. OMICS 10:28–39

    Article  CAS  PubMed  Google Scholar 

  • Ide NC, Loane RF, Demner-Fushman D (2007) Essie: a concept-based search engine for structured biomedical text. J Am Med Inform Assoc 14:253–263

    Article  PubMed  Google Scholar 

  • Kim CH, Lillehoj HS, Hong YH, Keeler CL Jr (2008) Comparison of transcriptional changes associated with E. acervulina and E. maxima infections using cDNA microarray technology. Dev Biol 132:121–130

    Article  CAS  Google Scholar 

  • Kohler J, Munn K, Ruegg A, Skusa A, Smith B (2006) Quality control for terms and definitions in ontologies and taxonomies. BMC Bioinform 7:212

    Google Scholar 

  • Lee JA, Sinkovits RS, Mock D, Rab EL, et al (2006) Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinform 7:237

    Article  Google Scholar 

  • Liu J, Wang W, Yang J (2004) Gene Ontology friendly biclustering of expression profiles. Proc IEEE Comput Syst Bioinform Conf 436–447

    Google Scholar 

  • Medigue C, Moszer I (2007) Annotation, comparison and databases for hundreds of bacterial genomes. Res Microbiol 158:724–736

    Article  CAS  PubMed  Google Scholar 

  • Michael J, Mejino JL Jr, Rosse C (2001) The role of definitions in biomedical concept representation. Proc AMIA Symp 463–467

    Google Scholar 

  • Muller HM, Kenny EE, Sternberg PW (2004) Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2:e309

    Article  PubMed  Google Scholar 

  • Natale DA, Arighi CN, Barker WC, Blake J, Chang TC et al (2007) Framework for a protein ontology. BMC Bioinform 8 Suppl 9:S1

    Article  Google Scholar 

  • Nelson SJ, Johnston D, Humphreys BL (2001) Relationships in medical subject headings. In: Bean CA, Green R (eds) Relationships in the organization of knowledge. Kluwer Academic, Dordrecht; sold and distributed in North, Central, and S. America by Kluwer Academic, pp ix, 232 p

    Google Scholar 

  • Ochs MF, Peterson AJ, Kossenkov A, Bidaut G (2007) Incorporation of gene ontology annotations to enhance microarray data analysis. Methods Mol Biol 377:243–254

    Article  CAS  PubMed  Google Scholar 

  • Osborne JD, Zhu LJ, Lin SM, Kibbe WA (2007) Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol 377:223–242

    Article  CAS  PubMed  Google Scholar 

  • Pestotnik SL (2005) Expert clinical decision support systems to enhance antimicrobial stewardship programs: insights from the society of infectious diseases pharmacists. Pharmacotherapy 25:1116–1125

    Article  PubMed  Google Scholar 

  • Pisanelli D (2004) If ontology is the solution, what is the problem? In: Pisanelli D (ed) Ontologies in medicine. IOS, Amsterdam, pp 1–19

    Google Scholar 

  • Racunas SA, Shah NH, Albert I, Fedoroff NV (2004) HyBrow: a prototype system for computer-aided hypothesis evaluation. Bioinformatics 20 Suppl 1:i257–i264

    Article  CAS  PubMed  Google Scholar 

  • Rajapakse M, Kanagasabai R, Ang WT, Veeramani A, Schreiber MJ, et al. (2008) Ontology-centric integration and navigation of the dengue literature. J Biomed Inform 41:806–815

    Article  PubMed  Google Scholar 

  • Rickard KL, Mejino JL Jr, Martin RF, Agoncillo AV, Rosse C (2004) Problems and solutions with integrating terminologies into evolving knowledge bases. MedInfo 11:420–424

    Google Scholar 

  • Rosse C, Mejino JLV (2003) A reference ontology for bioinformatics: the foundational model of anatomy. J Biomed Inform 36:478–500

    Article  PubMed  Google Scholar 

  • Rubin DL, Dameron O, Bashir Y, Grossman D, Dev P, et al (2006) Using ontologies linked with geometric models to reason about penetrating injuries. Artif Intell Med 37:167–176

    Article  PubMed  Google Scholar 

  • Rubin DL, Shah NH, Noy NF (2008) Biomedical ontologies: a functional perspective. Brief Bioinform 9:75–90

    Article  PubMed  Google Scholar 

  • Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O et al (2007) Advancing translational research with the Semantic Web. BMC Bioinform 8 Suppl 3:S2

    Article  Google Scholar 

  • Schonbach C, Nagashima T, Konagaya A (2004) Textmining in support of knowledge discovery for vaccine development. Methods 34:488–495

    Article  PubMed  Google Scholar 

  • Schurink CA, Lucas PJ, Hoepelman IM, Bonten MJ (2005) Computer-assisted decision support for the diagnosis and treatment of infectious diseases in intensive care units. Lancet Infect Dis 5:305–312

    Article  CAS  PubMed  Google Scholar 

  • Sintchenko V, Coiera E, Gilbert GL (2008) Decision support systems for antibiotic prescribing. Curr Opin Infect Dis 21:573–579

    Article  PubMed  Google Scholar 

  • Smith B, Kumar A (2004) On controlled vocabularies in bioinformatics: a case study in the Gene Ontology. BIOSILICO: Drug Discov Today 2:246–252

    Article  CAS  Google Scholar 

  • Smith B, Köhler J, Kumar A (2004) On the application of formal principles to life science data: a case study in the Gene Ontology. Data Integration in the Life Sciences (DILS). Springer, New York, pp 79–94

    Chapter  Google Scholar 

  • Smith B, Ceusters W, Klagges B, Kohler J, Kumar A et al (2005) Relations in biomedical ontologies. Genome Biol 6:R46

    Article  PubMed  Google Scholar 

  • Smith B, Ashburner M, Rosse C, Bard J, Bug W et al (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25:1251–1255

    Article  CAS  PubMed  Google Scholar 

  • Spasic I, Ananiadou S, McNaught J, Kumar A (2005) Text mining and ontologies in biomedicine: making sense of raw text. Brief Bioinform 6:239–251

    Article  CAS  PubMed  Google Scholar 

  • Thursky K (2006) Use of computerized decision support systems to improve antibiotic prescribing. Expert Rev Anti Infect Ther 4:491–507

    Article  PubMed  Google Scholar 

  • Tiffin N, Kelso JF, Powell AR, Pan H, Bajic VB, et al (2005) Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res 33: 1544–1552

    Article  CAS  PubMed  Google Scholar 

  • Tveit H, Mollestad T, Laegreid A (2004) The alignment of the medical subject headings to the Gene Ontology and its application in Gene annotation. Lecture Notes Comput Sci 3066:798–804

    Article  Google Scholar 

  • Valouev A, Johnson DS, Sundquist A, Medina C, et al (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5:829–834

    Article  CAS  PubMed  Google Scholar 

  • Veenema TG, Toke J (2006) Early detection and surveillance for biopreparedness and emerging infectious diseases. Online J Issues Nurs 11:3

    PubMed  Google Scholar 

  • Whetzel PL, Parkinson H, Stoeckert CJ Jr (2006) Using ontologies to annotate microarray experiments. Methods Enzymol 411:325–339

    Article  CAS  PubMed  Google Scholar 

  • Wolting C, McGlade CJ, Tritchler D (2006) Cluster analysis of protein array results via similarity of Gene Ontology annotation. BMC Bioinform 7:338

    Article  Google Scholar 

  • Yu AC (2006) Methods in biomedical ontology. J Biomed Inform 39:252–266

    Article  PubMed  Google Scholar 

  • Zeeberg BR, Feng W, Wang G, Wang MD, et al (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4:R28

    Article  PubMed  Google Scholar 

  • Zhang B, Schmoyer D, Kirov S, Snoddy J (2004) GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinform 5:16

    Article  Google Scholar 

  • Zhang S, Bodenreider O (2005) Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc 864–868

    Google Scholar 

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Acknowledgments

LGC’s contributions were supported by a Career Award from the Burroughs-Wellcome Fund and NIAID grants R01 AI077706 and R01 AI068804. BS’s contributions were funded in part through the NIH Roadmap for Medical Research grant to the National Center for Biomedical Ontology (1 U 54 HG004028). Initial development of the Infectious Disease Ontology as well as the Infectious Disease Ontology meetings were generously supported by the Burroughs-Wellcome Fund.

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  1. Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA

    Lindsay Grey Cowell & Barry Smith

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  1. Lindsay Grey Cowell
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  2. Barry Smith
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Editors and Affiliations

  1. Sydney Medical School, University of Sydney, Sydney, 2006, Australia

    Vitali Sintchenko

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Cowell, L.G., Smith, B. (2010). Infectious Disease Ontology. In: Sintchenko, V. (eds) Infectious Disease Informatics. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-1327-2_19

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