Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

O. Bodenreider

doi:10.1055/s-0038-1638585

Yearbook of Medical Informatics, Inhaltsverzeichnis

Yearb Med Inform 2008; 17(01): 67-79
DOI: 10.1055/s-0038-1638585

Original Article

Georg Thieme Verlag KG Stuttgart

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

O. Bodenreider

¹Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA

› Institutsangaben

Abstract

Summary

Objectives To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support.

MethodsBiomedical ontologies selected for their practical impact are examined from a functional perspective. Examples of applications are taken from operational systems and the biomedical literature, with a bias towards recent journal articles.

Results The ontologies under investigation in this survey include SNOMED CT, the Logical Observation Identifiers, Names, and Codes (LOINC), the Foundational Model of Anatomy, the Gene Ontology, RxNorm, the National Cancer Institute Thesaurus, the International Classification of Diseases, the Medical Subject Headings (MeSH) and the Unified Medical Language System (UMLS). The roles played by biomedical ontologies are classified into three major categories: knowledge management (indexing and retrieval of data and information, access to information, mapping among ontologies); data integration, exchange and semantic interoperability; and decision support and reasoning (data selection and aggregation, decision support, natural language processing applications, knowledge discovery).

Conclusions Ontologies play an important role in biomedical research through a variety of applications. While ontologies are used primarily as a source of vocabulary for standardization and integration purposes, many applications also use them as a source of computable knowledge. Barriers to the use of ontologies in biomedical applications are discussed.

Geissbuhler A, Kulikowski C, editors. IMIA Year book of Medical Informatics 2008.

Keywords

Biomedical ontologies - knowledge management - data integration - decision support

Volltext

Referenzen

References
1 Gersenovic M. The ICD family of classifications. Methods Inf Med 1995; 34 (1-2): 172-5.
2 McCray AT. Conceptualizing the world: lessons from history. J Biomed Inform 2006; 39 (03) 267-73.
3 Chute CG. Clinical classification and terminology: some history and current observations. J Am Med Inform Assoc 2000; 07 (03) 298-303.
4 Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a reference terminology for ontology research and development in the biomedical domain. In: Bodenreider O. editor. Proceedings of the Second International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2006). 2006: 57-65.
5 Ontology, Taxonomy, Folksonomy: Understanding the Distinctions. http://ontolog.cim3.net/cgi-bin/ wiki.pl?OntologySummit2007_Communique
6 Bodenreider O, Stevens R. Bio-ontologies: current trends and future directions. Brief Bioinform 2006; 07 (03) 256-74.
7 Cimino JJ, Zhu X. The practical impact of ontologies on biomedical informatics. Methods Inf Med 2006; 45 Suppl (01) 124-35.
8 Coonan KM. Medical informatics standards applicable to emergency department information systems: making sense of the jumble. Acad Emerg Med 2004; 11 (11) 1198-205.
9 Giannangelo K. editor. Healthcare code sets, clinical terminologies, and classification systems. Chicago, Ill: American Health Information Management Association; 2006
10 Yu AC. Methods in biomedical ontology. J Biomed Inform 2006; 39 (03) 252-66.
11 Bodenreider O, Burgun A. Biomedical ontologies. In: Chen H, Fuller S, Hersh WR, Friedman C. editors. Medical informatics: Advances in knowledge management and data mining in biomedicine. New York: Springer-Verlag; 2005: 211-36.
12 Huff SM. Ontologies, vocabularies, and data models. In: Greenes RA. editor. Clinical desision support: The road ahead. Amsterdam: Academic Press; 2007: 307-24.
13 Lussier YA, Bodenreider O. ontologies for discovery applications. In: Baker CJO, Cheung KH. editors. Semantic Web: Revolutionizing knowledge discovery in the life sciences. New York: Springer; 2007: 101-19.
14 Stevens R, Wroe C, Lord P, Goble C. Ontologies in bioinformatics. In: Staab s, Studer R. editors Handbook on ontologies. Berlin; New York: Springer; 2004: 635-57.
15 Rubin DL, Shah NH, Noy NF. Biomedical ontologies: a functional perspective. Brief Bioinform 2008; 09 (01) 75-90.
16 Hsu C, Goldberg HS. Knowledge-mediated retrieval of laboratory observations. Proc AMIA Symp 1999; 809-13.
17 Baorto DM, Cimino JJ, Parvin CA, Kahn MG. Using Logical Observation Identifier Names and Codes (LOINC) to exchange laboratory data among three academic hospitals. Proc AMIA Annu Fall Symp 1997; 96-100.
18 Baorto DM, Cimino JJ, Parvin CA, Kahn MG. Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC). Int J Med Inform 1998; 51 (01) 29-37.
19 Burgun A. Desiderata for domain reference ontologies in biomedicine. J Biomed Inform 2006; 39 (03) 307-13.
20 Rosse C, Mejino Jr JL. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 2003; 36 (06) 478-500.
21 Donnelly K. SNOMED-CT: The advanced terminology and coding system for eHealth. Stud Health Technol Inform 2006; 121: 279-90.
22 Wang AY, Sable JH, Spackman KA. The SNOMED clinical terms development process: refinement and analysis of content. Proc AMIA Symp 2002; 845-9.
23 SNOMED CT (Systematized Nomenclature of Medicine-Clinical Terms). http://www.ihtsdo.org/ our-standards/
24 Huff SM, Rocha RA, McDonald CJ, De Moor GJ, Fiers T, Bidgood Jr. WD. et al. Development of the Logical Observation Identifiers Names and Codes (LOINC) vocabulary. J Am Med Inform Assoc 1998; 05 (03) 276-92.
25 McDonald CJ, Huff SM, Suico JG, Hill G, Leavelle D, Aller R. et al. LOINC, a universal standard for identifying laboratory observations: a 5-year up-date. Clin Chem 2003; 49 (04) 624-33.
26 Logical Observation Identifiers Names and Codes (LOINC). www.regenstrief.org/loinc/
27 Foundational Model of Anatomy (FMA). http://sig.biostr.washington.edu/projects/fm/
28 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25 (01) 25-9.
29 Lomax J. Get ready to GO! A biologist’s guide to the Gene Ontology. Brief Bioinform 2005; 06 (03) 298-304.
30 Gene Ontology. http://www.geneontology.org/
31 Liu S, Wei M, Moore R. Ganesan VAGV, Nelson SANS. RxNorm: prescription for electronic drug information exchange. ITProfessional 2005; 07 (05) 17-23.
32 Nelson SJ, Brown SH, Erlbaum MS, Olson N, Powell T, Carlsen B. et al. A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF. Proc AMIA Symp 2002; 557-61.
33 RxNorm. http://www.nlm.nih.gov/research/umls/rxnorm/
34 de Coronado S, Haber MW, Sioutos N, Tuttle MS, Wright LW. NCI Thesaurus: using science-based terminology to integrate cancer research results. Medinfo 2004; 11 (Pt 1): 33-7.
35 Sioutos N, de Coronado S, Haber MW, Hartel FW, Shaiu WL, Wright LW. NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform 2007; 40 (01) 30-43.
36 NCIThesaurus. http://www.nci.nih.gov/cancerinfo/ terminologyresources
37 Jakob R, Ustun B, Madden R, Sykes C. The WHO Family of International Classifications. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2007; 50 (07) 924-31.
38 International Classification of Diseases (ICD). http://www.who.int/classifications/icd/en/
39 Nelson SJ, Johnston D, Humphreys BL. Relationships in Medical Subject Headings. In: Bean CA, Green R. editors. Relationships in the organization of knowledge. New York: Kluwer Academic Publishers; 2001: 171-84.
40 Medical Subject Headings (MeSH). http://www.nlm.nih.gov/mesh/
41 Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 2004; 32 (Database issue): D267-70.
42 Lindberg DA, Humphreys BL, McCray AT. The Unified Medical Language System. Methods Inf Med 1993; 32 (04) 281-91.
43 Unified Medical Language System (UMLS). http://www.nlm.nih.gov/research/umls/
44 OWL Web Ontology Language Reference. http://www.w3.org/TR/owl-ref/
45 Bodenreider O. Lexical, terminological and ontological resources for biological text mining. In: Ananiadou S, McNaught J. editors. Text mining for biology and biomedicine. Boston: Artech House; 2006: 43-66.
46 Aronson AR. The effect of textual variation on concept based information retrieval. Proc AMIA Annu Fall Symp 1996; 373-7.
47 Kolarik C, Hofmann-Apitius M, Zimmermann M, Fluck J. Identification of new drug classification terms in textual resources. Bioinformatics 2007; 23 (13) i264-72.
48 Blake JA, Bult CJ. Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform 2006; 39 (03) 314-20.
49 Aronson AR, Mork JG, Gay CW, Humphrey SM, Rogers WJ. The NLM Indexing Initiative’s Medical Text Indexer. Medinfo 2004; 11 (Pt 1): 268-72.
50 Zhang D, Roderer NK, Huang G, Zhao X. Developing a UMLS-based indexing tool for health science repository system. AMIA Annu Symp Proc 2006; 1157.
51 Doms A, Schroeder M. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 2005; 33 (Web Server issue): W783-6.
52 Alexander S, Conner T, Slaughter T. Overview of inpatient coding. Am J Health Syst Pharm. 2003; 60 (21) (Suppl. 06) S11-4.
53 Daniel-Le Bozec C, Steichen O, Dart T, Jaulent MC. The role of local terminologies in electronic health records. The HEGP experience. Medinfo 2007; 12 (Pt 1): 780-4.
54 Richesson RL, Andrews JE, Krischer JP. Use of SNOMED CT to represent clinical research data: a semantic characterization of data items on case report forms in vasculitis research. J Am Med Inform Assoc 2006; 13 (05) 536-46.
55 Liu K, Mitchell KJ, Chapman WW, Crowley RS. Automating tissue bank annotation from pathology reports comparison to a gold standard expert annotation set. AMIA Annu Symp Proc 2005; 460-4.
56 Friedman C, Shagina L, Lussier Y, Hripcsak G. Automated encoding of clinical documents based on natural language processing. J Am Med Inform Assoc 2004; 11 (05) 392-402.
57 Pakhomov SV, Buntrock JD, Chute CG. Automating the assignment of diagnosis codes to patient encounters using example-based and machine learning techniques. J Am Med Inform Assoc 2006; 13 (05) 516-25.
58 Pestian JP, Brew C, Matykiewicz P, Hovermale D, Johnson N, Cohen KB. et al. A shared task involving multi-label classification of clinical free text. In: Biological, translational, and clinical language processing; 2007 2007-06; Prague. Czech Republic: Association for Computational Linguistics; 2007: 97-104.
59 Blaschke C, Leon EA, Krallinger M, Valencia A. Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics 2005; (06) Suppl (Suppl. 01) S16.
60 Couto FM, Silva MJ, Lee V, Dimmer E, Camon E, Apweiler R. et al. GOAnnotator: linking protein GO annotations to evidence text. J Biomed Discov Collab 2006; 01: 19.
61 Crangle CE, Zbyslaw A. Identifying gene ontology concepts in natural-language text. Conf Proc IEEE Eng Med Biol Soc 2004; 04: 2821-3.
62 Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinformatics 2007; 08: 243.
63 Srinivasan P, Qiu XY. GO for gene documents. BMC Bioinformatics 2007; 08 Suppl (Suppl. 09) S3.
64 Shah NH, Rubin DL, Supekar KS, Musen MA. Ontology-based annotation and query of tissue microarray data. AMIA Annu Symp Proc 2006; 709-13.
65 Butte AJ, Chen R. Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annu Symp Proc 2006; 106-10.
66 Aronson AR. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp 2001; 17-21.
67 Tuttle MS, Olson NE, Keck KD, Cole WG, Erlbaum MS, Sherertz DD. et al. Metaphrase: an aid to the clinical conceptualization and formalization of patient problems in healthcare enterprises. Methods Inf Med 1998; 37 (4-5): 373-83.
68 Termine. http://www.nactem.ac.uk/software/termine/
69 Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A. Text processing through web services: calling Whatizit. Bioinformatics 2008; 24: 296-8.
70 Srinivasan P. Retrieval feedback in MEDLINE. J Am Med Inform Assoc 1996; 03 (02) 157-67.
71 Aronson AR, Rindflesch TC. Query expansion using the UMLS Metathesaurus. Proc AMIA Annu Fall Symp 1997; 485-9.
72 Hersh W, Price S, Donohoe L. Assessing thesaurus-based query expansion using the UMLS Metathesaurus. Proc AMIA Symp 2000; 344-8.
73 Hersh W, Hickam DH, Haynes RB, McKibbon KA. Evaluation of SAPHIRE: an automated approach to indexing and retrieving medical literature. Proc Annu Symp Comput Appl Med Care 1991; 808-12.
74 Brandt C, Nadkarni P. Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods. Comput Methods Programs Biomed 2001; 64 (01) 37-43.
75 Bratsas C, Koutkias V, Kaimakamis E, Bamidis P, Maglaveras N. Ontology-basedVector Space Model and Fuzzy Query Expansion to Retrieve Knowledge on Medical Computational Problem Solutions. Conf Proc IEEE Eng Med Biol Soc 2007; 01: 3794-7.
76 Lowe HJ, Antipov I, Hersh W, Smith CA, Mailhot M. Automated semantic indexing of imaging reports to support retrieval of medical images in the multimedia electronic medical record. Methods Inf Med 1999; 38 (4-5): 303-7.
77 Ruiz ME. Combining image features, case descriptions and UMLS concepts to improve retrieval of medical images. AMIA Annu Symp Proc 2006; 674-8.
78 Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics 2006; 22 (14) e547-56.
79 Hersh WR, Donohoe LC. SAPHIRE International: a tool for cross-language information retrieval. Proc AMIA Symp 1998; 673-7.
80 Liu F, Ackerman M, Fontelo P. BabelMeSH: development of a cross-language tool for MEDLINE/ PubMed. AMIA Annu Symp Proc 2006; 1012.
81 Hersh W, Leone TJ. The SAPHIRE server: a new algorithm and implementation. Proc Annu Symp Comput Appl Med Care 1995; 858-62.
82 Ide NC, Loane RF, Demner-Fushman D. Essie: a concept-based search engine for structured biomedical text. JAm Med InformAssoc 2007; 14 (03) 253-63.
83 Muller HM, Kenny EE, Sternberg PW. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2004; 02 (11) e309.
84 Gaudinat A, Ruch P, Joubert M, Uziel P, Strauss A, Thonnet M. et al. Health search engine with edocument analysis for reliable search results. Int J Med Inform 2006; 75 (01) 73-85.
85 Can AB, Baykal N. MedicoPort: a medical search engine for all. Comput Methods Programs Biomed 2007; 86 (01) 73-86.
86 Fontelo P, Liu F, Leon S, Anne A, Ackerman M. PICO Linguist and BabelMeSH: development and partial evaluation of evidence-based multilanguage search tools for MEDLINE/PubMed. Medinfo 2007; 12 (Pt 1): 817-21.
87 Sneiderman CA, Demner-Fushman D, Fiszman M, Ide NC, Rindflesch TC. Knowledge-based methods to help clinicians find answers in MEDLINE. J Am Med Inform Assoc 2007; 14 (06) 772-80.
88 Haynes RB, McKibbon KA, Wilczynski NL, Walter SD, Werre SR. Optimal search strategies for retrieving scientifically strong studies of treatment from Medline: analytical survey. BMJ 2005; 330 (7501): 1179.
89 Huang X, Lin J, Demner-Fushman D. Evaluation of PICO as a knowledge representation for clinical questions. AMIA Annu Symp Proc 2006; 359-63.
90 Whetzel PL, Parkinson H, Stoeckert Jr CJ. Using ontologies to annotate microarray experiments. Methods Enzymol 2006; 411: 325-39.
91 Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A. et al. ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 2007; 35 (Database issue): D747-50.
92 Kato K, Yamashita R, Matoba R, Monden M, Noguchi S, Takagi T. et al. Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res 2005; 33 (Database issue): D533-6.
93 Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M. et al. The Stanford Tissue Microarray Database. Nucleic Acids Res 2008; 36 (Database issue): D871-7.
94 Cole CL, Kanter AS, Cummens M, Vostinar S, Naeymi-Rad F. Using a terminology server and consumer search phrases to help patients find physicians with particular expertise. Medinfo 2004; 11 (Pt 1): 492-6.
95 Boulos MN. A first look at HealthCyberMap medical semantic subject search engine. Technol Health Care 2004; 12 (01) 33-41.
96 Detwiler LT, Chung E, Li A, Mejino Jr. JL, Agoncillo A, Brinkley J. et al. A relation-centric query engine for the Foundational Model of anatomy. Medinfo 2004; 11 (Pt 1): 341-5.
97 Lee M, Wang W, Yu H. Exploring supervised and unsupervised methods to detect topics in biomedical text. BMC Bioinformatics 2006; 07: 140.
98 Yamamoto Y, Takagi T. Biomedical knowledge navigation by literature clustering. J Biomed Inform 2007; 40 (02) 114-30.
99 Darmoni SJ, Neveol A, Renard JM, Gehanno JF, Soualmia LF, Dahamna B. et al. A MEDLINE categorization algorithm. BMC Med Inform Decis Mak 2006; 06: 7.
100 Ruch P. Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics 2006; 22 (06) 658-64.
101 Robinson J, de Lusignan S, Kostkova P, Madge B. Using UMLS to map from a library to a clinical classification: Improving the functionality of a digital library. Stud Health Technol Inform 2006; 121: 86-95.
102 Fung KW, Bodenreider O, Aronson AR, Hole WT, Srinivasan S. Combining lexical and semantic methods of inter-terminology mapping using the UMLS. Medinfo 2007; 12 (Pt 1): 605-9.
103 Sun Y. Methods for automated concept mapping between medical databases. J Biomed Inform 2004; 37 (03) 162-78.
104 Bodenreider O, Nelson SJ, Hole WT, Chang HF. Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies. Proc AMIA Symp 1998; 815-9.
105 Cimino JJ, Johnson SB, Peng P, Aguirre A. From ICD9-CM to MeSH using the UMLS: a how-to guide. Proc Annu Symp Comput Appl Med Care 1993; 730-4.
106 Brown SH, Husser CS, Wahner-Roedler D, Bailey S, Nugent L, Porter K. et al. Using SNOMED CT as a reference terminology to cross map two highly pre-coordinated classification systems. Medinfo 2007; 12 (Pt 1): 636-9.
107 Zhang S, Bodenreider O. Alignment of multiple ontologies of anatomy: deriving indirect mappings from direct mappings to a reference. AMIA Annu Symp Proc 2005; 864-8.
108 Cimino JJ, Bright TJ, Li J. Medication reconciliation using natural language processing and controlled terminologies. Medinfo 2007; 12 (Pt 1): 679-83.
109 Parrish F, Do N, Bouhaddou O, Warnekar P. Implementation of RxNorm as a terminology mediation standard for exchanging pharmacy medication between federal agencies. AMIAAnnu Symp Proc 2006; 1057.
110 Mead CN. Data interchange standards in healthcare IT--computable semantic interoperability: now possible but still difficult, do we really need a better mousetrap?. J Healthc Inf Manag 2006; 20 (01) 71-8.
111 McDonald CJ. The barriers to electronic medical record systems and how to overcome them. J Am Med Inform Assoc 1997; 04 (03) 213-21.
112 Tu SW, Campbell JR, Glasgow J, Nyman MA, McClure R, McClay J. et al. The SAGE Guideline Model: achievements and overview. J Am Med Inform Assoc 2007; 14 (05) 589-98.
113 Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H. et al. Advancing translational research with the Semantic Web. BMC Bioinformatics 2007; 08 (Suppl. 03) S2.
114 Bouhaddou O, Warnekar P, Parrish F, Do N, Mandel J, Kilbourne J. et al. Exchange of Computable Patient Data Between the Department of Veterans Affairs (VA) and the Department of Defense (DoD): Terminology Standards Strategy. J Am Med Inform Assoc. 2007
115 Khan AN, Griffith SP, Moore C, Russell D, Rosario Jr. AC, Bertolli J. Standardizing laboratory data by mapping to LOINC. J Am Med Inform Assoc 2006; 13 (03) 353-5.
116 Dolin RH. Advances in data exchange for the clinical laboratory. Clin Lab Med. 1999; 19 (02) 385419 vii.
117 Fridsma DB, Evans J, Hastak S, Mead CN. The BRIDG Project: A Technical Report. J Am Med Inform Assoc 2008; 15 (02) 130-7.
118 Rector A, Qamar R, Marley T. Binding ontologies & coding Systems to electronic mealth records and messages. In: Bodenreider O. editor. Proceedings of the Second International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2006). 2006: 11-9.
119 Choi J, Jenkins ML, Cimino JJ, White TM, Bakken S. Toward semantic interoperability in home health care: formally representing OASIS items for integration into a concept-oriented terminology. J Am Med InformAssoc 2005; 12 (04) 410-7.
120 Dolin RH, Alschuler L, Boyer S, Beebe C, Behlen FM, Biron PV. et al. HL7 Clinical Document Architecture, Release 2. J Am Med Inform Assoc 2006; 13 (01) 30-9.
121 Komatsoulis GA, Warzel DB, Hartel FW, Shanbhag K, Chilukuri R, Fragoso G. et al. caCORE version 3: Implementation of a model driven, service-oriented architecture for semantic interoperability. J Biomed Inform 2008; 41 (01) 106-23.
122 Hernandez T, Kambhampati S. Integration of biological sources: Current systems and challenges ahead. Sigmod Record 2004; 33 (03) 51-60.
123 Brooksbank C, Quackenbush J. Data standards: a call to action. OMICS 2006; 10 (02) 94-9.
124 Stevens R, Baker P, Bechhofer S, Ng G, Jacoby A, Paton NW. et al. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics 2000; 16 (02) 184-5.
125 Louie B, Mork P, Shaker R, Kolker N, Kolker E, Tarczy-Hornoch P. Integration of data for gene annotation using the BioMediator system. AMIA Annu Symp Proc 2005; 1036.
126 Perez-Rey D, Maojo V, Garcia-Remesal M, Alonso-Calvo R, Billhardt H, Martin-Sanchez F. et al. ONTOFUSION: ontology-based integration of genomic and clinical databases. Comput Biol Med 2006; 36 (7-8): 712-30.
127 Joubert M, Dufour JC, Aymard S, Falco L, Fieschi M. Designing and implementing health data and information providers. Int J Med Inform 2005; 74 (2-4): 133-40.
128 Brandt CA, Lu CC, Nadkarni PM. Automating identification of adverse events related to abnormal lab results using standard vocabularies. AMIA Annu Symp Proc 2005; 903.
129 Gennari JH, Silberfein A, Wiley JC. Integrating genomic knowledge sources through an anatomy ontology. Pac Symp Biocomput 2005; 115-26.
130 Chabalier J, Mosser J, Burgun A. Integrating biological pathways in disease ontologies. Medinfo 2007; 12 (Pt 1): 791-5.
131 Musen MA. Dimensions of knowledge sharing and reuse. Comput Biomed Res 1992; 25 (05) 435-67.
132 Bergeron E, Simons R, Linton C, Yang F, Tallon JM, Stewart TC. et al. Canadian benchmarks in trauma. J Trauma 2007; 62 (02) 491-7.
133 Fang J, Alderman MH, Keenan NL, Croft JB. Declining US stroke hospitalization since 1997: National Hospital Discharge Survey, 1988-2004. Neuroepidemiology 2007; 29 (3-4): 243-9.
134 Lieberman MI, Ricciardi TN, Masarie FE, Spackman KA. The use of SNOMED CT simplifies querying of a clinical data warehouse. AMIA Annu Symp Proc 2003; 910.
135 Steindel S, Loonsk JW, Sim A, Doyle TJ, Chapman RS, Groseclose SL. Introduction of a hierarchy to LOINC to facilitate public health reporting. Proc AMIA Symp 2002; 737-41.
136 Gunnarsdottir OS, Rafnsson V. Seven-year evolution of discharge diagnoses of emergency department users. Eur J Emerg Med 2007; 14 (04) 193-8.
137 Noyes K, Liu H, Holloway R, Dick AW. Accuracy of Medicare claims data in identifying Parkinsonism cases: comparison with the Medicare current benef iciary survey. Mov Disord 2007; 22 (04) 509-14.
138 Schneeweiss S, Robicsek A, Scranton R, Zuckerman D, Solomon DH. Veteran’s affairs hospital discharge databases coded serious bacterial infections accurately. J Clin Epidemiol 2007; 60 (04) 397-409.
139 Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998; 95 (25) 14863-8.
140 Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA. Global functional profiling of gene expression. Genomics 2003; 81 (02) 98-104.
141 Gene Ontology Tools. http://geneontology.org/ GO.tools.shtml
142 Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S. Recent additions and improvements to the Onto-Tools. Nucleic Acids Res 2005; 33 (Web Server issue): W762-5.
143 Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M. et al. Go Miner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003; 04 (04) R28.
144 Zhang B, Schmoyer D, Kirov S, Snoddy J. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 2004; 05: 16.
145 Djebbari A, Karamycheva S, Howe E, Quackenbush J. MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinformatics 2005; 21 (15) 3324-6.
146 Bresell A, Servenius B, Persson B. Ontology annotation treebrowser : an interactive tool where the complementarity of medical subject headings and gene ontology improves the interpretation of gene lists. Appl Bioinformatics 2006; 05 (04) 225-36.
147 Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol 2007; 377: 223-42.
148 Brameier M, Wiuf C. Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. J Biomed Inform 2007; 40 (02) 160-73.
149 Huang D, Wei P, Pan W. Combining gene annotations and gene expression data in model-based clustering: weighted method. OMICS 2006; 10 (01) 28-39.
150 Liu J, Wang W, Yang J. Gene Ontology friendly biclustering of expression profiles. Proc IEEE Comput Syst Bioinform Conf 2004; 436-47.
151 Lord PW, Stevens RD, Brass A, Goble CA. Semantic similarity measures as tools for exploring the gene ontology. Pac Symp Biocomput 2003; 601-12.
152 Wolting C, McGlade CJ, Tritchler D. Cluster analysis of protein array results via similarity of Gene Ontology annotation. BMC Bioinformatics 2006; 07: 338.
153 Achour SL, Dojat M, Rieux C, Bierling P, Lepage E. A UMLS-based knowledge acquisition tool for rule-based clinical decision support system development. J Am Med Inform Assoc 2001; 08 (04) 351-60.
154 KashyapV V, Morales A, Hongsermeier T. On implementing clinical decision support: achieving scalability and maintainability by combining business rules and ontologies. AMIA Annu Symp Proc 2006; 414-8.
155 Greenes RA. Clinical decision support : the road ahead. Amsterdam; Boston: Elsevier Academic Press; 2007
156 Rubin DL, Dameron O, Bashir Y, Grossman D, Dev P, Musen MA. Using ontologies linked with geometric models to reason about penetrating injuries. Artif Intell Med 2006; 37 (03) 167-76.
157 Marquet G, Dameron O, Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWLDL and NCI Thesaurus. AMIA Annu Symp Proc 2007; 508-12.
158 Wolstencroft KJ, Stevens R, Tabernero L, Brass A. PhosphaBase: an ontology-driven database resource for protein phosphatases. Proteins 2005; 58 (02) 290-4.
159 Uzuner O, Goldstein I, Luo Y, Kohane I. Identifying patient smoking status from medical discharge records. J Am Med Inform Assoc 2008; 15 (01) 14-24.
160 Meystre S, Haug PJ. Natural language processing to extract medical problems from electronic clinical documents: performance evaluation. J Biomed Inform 2006; 39 (06) 589-99.
161 Chapman WW, Fiszman M, Dowling JN, Chapman BE, Rindflesch TC. Identifying respiratory findings in emergency department reports for biosurveillance using Meta Map. Medinfo 2004; 11 (Pt 1): 487-91.
162 BioCaster. http://biocaster.nii.ac.jp/
163 EpiSpider. http://www.epispider.org/
164 Rindflesch TC, Fiszman M, Libbus B. Semantic interpretation for the biomedical literature. In: Chen H, Fuller S, Hersh WR, Friedman C. editors. Medical informatics: Advances in knowledge management and data mining in biomedicine. Springer-Verlag; 2005: 399-422.
165 Friedman C, Alderson PO, Austin JH, Cimino JJ, Johnson SB. A general natural-language text processor for clinical radiology. J Am Med Inform Assoc 1994; 01 (02) 161-74.
166 Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C. PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing. Pac Symp Biocomput 2006; 64-75.
167 Tessi. http://www.landcglobal.com/pages/tessi_indexing.php
168 Jacquemart P, Zweigenbaum P. Towards a medical question-answering system: a feasibility study. Stud Health Technol Inform 2003; 95: 463-8.
169 Terol RM, Martinez-Barco P, Palomar M. A knowledge based method for the medical question answering problem. Comput Biol Med 2007; 37 (10) 1511-21.
170 Wedgwood J. MQAF: a medical question-answering framework. AMIA Annu Symp Proc 2005; 1150.
171 EAGLi. http://eagl.unige.ch/EAGLi/
172 Fiszman M, Rindflesch TC, Kilicoglu H. Summarization of an online medical encyclopedia. Medinfo 2004; 11 (Pt 1): 506-10.
173 Reeve LH, Han H, Brooks AD. Biomedical text summarisation using concept chains. International Journal of Data Mining and Bioinformatics 2007; 01 (04) 389-407.
174 Whalen G. Medical textbook summarization and guided navigation using statistical sentence extraction. AMIA Annu Symp Proc 2005; 814-8.
175 Lussier YA, Li J. Terminological mapping for high throughput comparative biology of phenotypes. Pac Symp Biocomput 2004; 202-13.
176 Hristovski D, Peterlin B, Mitchell JA, Humphrey SM. Using literature-based discovery to identify disease candidate genes. Int J Med Inform 2005; 74 (2-4): 289-98.
177 Torvik VI, Smalheiser NR. A quantitative model for linking two disparate sets of articles in MEDLINE. Bioinformatics 2007; 23 (13) 1658-65.
178 Yetisgen-Yildiz M, Pratt W. Using statistical and knowledge-based approaches for literature-based discovery. J Biomed Inform 2006; 39 (06) 600-11.
179 Weeber M, Vos R, Klein H, De Jong-Van Den Berg LT, Aronson AR, Molema G. Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomide. J Am Med Inform Assoc 2003; 10 (03) 252-9.
180 Weinstein JN. ‘Omic’ and hypothesis-driven research in the molecular pharmacology of cancer. Curr Opin Pharmacol 2002; 02 (04) 361-5.
181 Gopalacharyulu PV, Lindfors E, Miettinen J, Bounsaythip CK, Oresic M. An integrative approach for biological data mining and visualisation. International Journal of Data Mining and Bioinformatics 2008; 02 (01) 54-77.
182 Uccelli R, Binazzi A, Altavista P, Belli S, Comba P, Mastrantonio M. et al. Geographic distribution of amyotrophic lateral sclerosis through motor neuron disease mortality data. Eur J Epidemiol 2007; 22 (11) 781-90.
183 Linares C, Diaz J. Impact of high temperatures on hospital admissions: comparative analysis with previous studies about mortality (Madrid). Eur J Public Health. 2007
184 Ramaswamy K, Kozma CM, Nasrallah H. Risk of diabetic ketoacidosis after exposure to risperidone or olanzapine. Drug Saf 2007; 30 (07) 589-99.
185 Jinjuvadia K, Kwan W, Fontana RJ. Searching for a needle in a haystack: use of ICD-9-CM codes in drug-induced liver injury. Am J Gastroenterol 2007; 102 (11) 2437-43.
186 Choy KW, Wang CC, Ogura A, Lau TK, Rogers MS, Ikeo K. et al. Molecular characterization of the developmental gene in eyes: through datamining on integrated transcriptome databases. Clin Biochem 2006; 39 (03) 224-30.
187 Jones CE, Baumann U, Brown AL. Automated methods of predicting the function of biological sequences using GO and BLAST. BMC Bioinformatics 2005; 06: 272.
188 Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A. Integrated analysis of gene expression by Association Rules Discovery. BMC Bioinformatics 2006; 07: 54.
189 Zhou Y, Young JA, Santrosyan A, Chen K, Yan SF, Winzeler EA. In silico gene function prediction using ontology-based pattern identification. Bioinformatics 2005; 21 (07) 1237-45.
190 Huang JC, Frey BJ, Morris QD. Comparing sequence and expression for predicting microRNA targets using GenMiR3. Pac Symp Biocomput 2008; 52-63.
191 Barutcuoglu Z, Schapire RE, Troyanskaya OG. Hierarchical multi-label prediction of gene function. Bioinformatics 2006; 22 (07) 830-6.
192 Sahoo SS, Zeng K, Bodenreider O, Sheth A. From “glycosyltransferase” to “congenital muscular dystrophy”: integrating knowledge from NCBI Entrez Gene and the Gene Ontology. Medinfo 2007; 12 (Pt 2): 1260-4.
193 Camargo A, Azuaje F. Linking gene expression and functional network data in human heart failure. PLoS ONE 2007; 02 (12) e1347.
194 Chabalier J, Mosser J, Burgun A. A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinformatics 2007; 08: 235.
195 Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M. Drug-target network. Nat Biotechnol 2007; 25 (10) 1119-26.
196 RxNav. http://mor.nlm.nih.gov/download/rxnav/
197 Open Biomedical Ontology. http://www.obofoundry.org/
198 UMLS Knowledge Source Server. http://umlsks.nlm.nih.gov/
199 BioPortal. http://www.bioontology.org/tools/ portal/bioportal.html
200 Moreira DA, Musen MA. OBO to OWL: a protege OWL tab to read/save OBO ontologies. Bioinformatics 2007; 23 (14) 1868-70.
201 LexGrid. http://informatics.mayo.edu/LexGrid/
202 Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007; 25 (11) 1251-5.
203 Rogers JE. Quality assurance of medical ontologies. Methods Inf Med 2006; 45 (03) 267-74.
204 Smith B. The evaluation of ontologies: editorial review vs. democratic ranking. Proceedings of the First Interdisciplinary Ontology Meeting 2008; 29-36.