Olivier Bodenreider's Publications

2009

An L, Obradovic Z, Smith D, Bodenreider O, Megalooikonomou V.
Mining association rules among gene functions in clusters of similar gene expression maps
Workshop proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM09) -- Workshop on Data Mining in Functional Genomics 2009:254-259.
[download PDF]
Bodenreider O.
Biomedical ontology in action. [editorial]
Applied Ontology 2009;4(1):1-4.
[download PDF]
Bodenreider O.
Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting.
AMIA Annu Symp Proc 2009:45-49.
[download PDF]
Bodenreider O.
Provenance information in biomedical knowledge repositories – A use case.
Proceedings of the First International Workshop on the role of Semantic Web in Provenance Management (SWPM 2009) 2009:(electronic proceedings: http://ceur-ws.org/Vol-526/).
[download PDF]
Bodenreider O, Burgun A.
Desiderata for an ontology of diseases for the annotation of biological datasets.
Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:39-42.
[download PDF]
Bodenreider O, Peters LB.
A graph-based approach to auditing RxNorm.
Journal of Biomedical Informatics 2009;42(3):558-570.
[download PDF] [PubMed: 19394440]
Burgun A, Mougin F, Bodenreider O.
Two approaches to integrating phenotype and clinical information.
AMIA Annu Symp Proc 2009:75-79.
[download PDF]
Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M.
The caBIG terminology review process.
Journal of Biomedical Informatics 2009;42(3):571-580.
[download PDF] [PubMed: 19154797]
Denney C, Batchelor C, Bodenreider O, Cheng S, Hart J, Hill J, Madden J, Musen M, Pichler E, Samwald M, Szalma S, Schriml L, Sedlock D, Soldatova L, Sonoda K, Statham D, Whetzel P, Wu E, Stephens S.
Creating a translational medicine ontology. [poster]
Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:164.
[download PDF]
Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spounge J, Landsman D.
Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.
Methods Mol Biol 2009;541:1-22.
[download PDF] [PubMed: 19381547] [PubMedCentral: 2719765]
Mougin F, Bodenreider O, Burgun A.
Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS.
Journal of Biomedical Informatics 2009;42(3):440-451.
[download PDF] [PubMed: 19303057]
Pathak J, Peters L, Chute CG, Bodenreider O.
Comparing and evaluating terminology services APIs: RxNav, UMLSKS, and LexBIG. [abstract]
AMIA Annu Symp Proc 2009:515.
[download PDF]
Schulz S, Beisswanger E, van den Hoek L, Bodenreider O, van Mulligen EM.
Alignment of the UMLS Semantic Network with BioTop: Methodology and assessment.
Bioinformatics 2009;25(12):i69-i76.
[download PDF] [PubMed: 19478019] [PubMedCentral: 2687948]
Vizenor LT, Bodenreider O, McCray AT.
Auditing associative relations across two knowledge sources.
Journal of Biomedical Informatics 2009;42(3):426-439.
[download PDF] [PubMed: 19475724]

2008

Bodenreider O.
Comparing SNOMED CT and the NCI Thesaurus through Semantic Web technologies.
Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008) 2008:37-43 (electronic proceedings: http://ceur-ws.org/Vol-410/).
[download PDF]
Bodenreider O.
Issues in mapping LOINC laboratory tests to SNOMED CT.
AMIA Annu Symp Proc 2008:51-55.
[download PDF] [PubMed: 18999311] [PubMedCentral: 2655945]
Bodenreider O.
Biomedical ontologies in action: role in knowledge management, data integration and decision support.
Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med 2008;47(Suppl 1):67-79.
[download PDF] [PubMed: 18660879] [PubMedCentral: 2592252]
Bodenreider O.
Ontologies and data integration in biomedicine: Success stories and challenging issues In: Bairoch A, Cohen-Boulakia S, Froidevaux C, editors. Proceedings of the Fifth International Workshop on Data Integration in the Life Sciences (DILS 2008) [abstract]. Berlin Heidelberg New York: Springer; 2008. p. 1-4.
[download PDF]
Bodenreider O.
Towards a metaontology for the biomedical domain [editorial]
Applied Ontology 2008;3(4):201-203.
[download PDF]
Bodenreider O, Coban Z, Doganay M, Erdem E, Kosucu H.
A preliminary report on answering complex queries related to drug discovery using answer set programming.
Proceedings of the 3rd International Workshop on Applications of Logic Programming to the (Semantic) Web and Web Services (ALPSWS2008) 2008:85-90 (electronic proceedings: http://ceur-ws.org/Vol-434/).
[download PDF]
Bodenreider O, Sahoo SS.
Semantic Web for translational biomedicine: Two pilot experiments. [abstract]
Proceedings of the AMIA Summit on Translational Bioinformatics 2008:141.
[download PDF]
Burgun A, Bodenreider O.
Accessing and integrating data and knowledge for biomedical research.
Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med 2008;47(Suppl 1):91-99.
[download PDF] [PubMed: 18660883] [PubMedCentral: 2553094]
Gruninger M, Bodenreider O, Olken F, Obrst L, Yim P.
Ontology Summit 2007 – Ontology, taxonomy, folksonomy: Understanding the distinctions. [Communiqué]
Applied Ontology 2008;3(3):191-200.
[download PDF]
Mougin F, Bodenreider O.
Auditing the NCI thesaurus with Semantic Web technologies.
AMIA Annu Symp Proc 2008:500-504.
[download PDF] [PubMed: 18999265] [PubMedCentral: 2655981]
Mougin F, Burgun A, Bodenreider O, Chabalier J, Loréal O, Le Beux P.
Automatic methods for integrating biomedical data sources in a mediator-based system In: Bairoch A, Cohen-Boulakia S, Froidevaux C, editors. Proceedings of the Fifth International Workshop on Data Integration in the Life Sciences (DILS 2008). Berlin Heidelberg New York: Springer; 2008. p. 61-76.
[download PDF]
Nelson SJ, Zeng K, Bodenreider O.
MyMedicationList: Integrating personal medication records with resources. [demo]
AMIA Annu Symp Proc 2008:1228.
[download PDF] [PubMed: 18998987]
Peters L, Bodenreider O.
Using the RxNorm web services API for quality assurance purposes.
AMIA Annu Symp Proc 2008:591-595.
[download PDF] [PubMed: 18999038] [PubMedCentral: 2656097]
Rogers J, Bodenreider O.
SNOMED CT: Browsing the browsers.
Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008) 2008:30-36 (electronic proceedings: http://ceur-ws.org/Vol-410/).
[download PDF]
Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP.
An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence.
Journal of Biomedical Informatics 2008;41:752-765.
[download PDF] [PubMed: 18395495]
Sharp M, Bodenreider O, Wacholder N.
A framework for characterizing drug information sources.
AMIA Annu Symp Proc 2008:662-666.
[download PDF] [PubMed: 18999182] [PubMedCentral: 2656044]
Tharakaraman K, Bodenreider O, Landsman D, Spouge JL, Mariño-Ramírez L.
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.
Nucleic Acids Res 2008;36(8):2777–2786.
[download PDF] [PubMed: 18367472] [PubMedCentral: 2377430]
Zeng K, Bodenreider O, Kilbourne J, Nelson SJ.
Standards, security and usability: Experience with MyMedicationList. [abstract]
Proceedings of the AMIA Spring Congress 2008.
[download PDF]
Zeng K, Bodenreider O, Nelson SJ.
Design and implementation of a personal medication record--MyMedicationList.
AMIA Annu Symp Proc 2008:844-848.
[download PDF] [PubMed: 18998962] [PubMedCentral: 2656100]

2007

Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, Névéol A, Peters L, Rogers WJ.
From indexing the biomedical literature to coding clinical text: Experience with MTI and machine learning approaches.
Proceedings of the ACL'2007 Workshop "BioNLP" 2007:105-112.
[download PDF]
Bodenreider O, Burgun A.
Oncologic pathology in biomedical terminologies: Challenges for data integration. [abstract]
Proceedings of the APIII conference on "Anatomic Pathology Informatics and Imaging Support for Translational Medicine", Pittsburgh, Pennsylvania, September 9-12, 2007 2007:Abstract 342.
[download PDF]
Bodenreider O, Smith B, Kumar A, Burgun A.
Investigating subsumption in SNOMED CT: An exploration into large Description Logic-based biomedical terminologies.
Artificial Intelligence in Medicine 2007;39(3):183-195.
[download PDF] [PubMed: 17241777] [PubMedCentral: 2442845]
Burgun A, Bodenreider O.
Issues in integrating epidemiology and research information in oncology: Experience with ICD-O3 and the NCI Thesaurus.
AMIA Annu Symp Proc 2007:85-89.
[download PDF] [PubMed: 18693803] [PubMedCentral: 2655924]
Fung KW, Bodenreider O, Aronson AR, Hole WT, Srinivasan S.
Combining lexical and semantic methods of inter-terminology mapping using the UMLS.
Stud Health Technol Inform 2007;129:605-609.
[download PDF] [PubMed: 17911788] [PubMedCentral: 2430093]
Lussier YA, Bodenreider O.
Clinical ontologies for discovery applications In: Baker CJO, Cheung K-H, editors. Semantic Web: Revolutionizing knowledge discovery in the life sciences. New York: Springer; 2007. p. 101-119.
[download PDF]
Mougin F, Chabalier J, Bodenreider O, Burgun A.
Méthodes de mapping situées aux niveaux instance et schéma pour l'intégration de sources de données hétérogènes.
In: Trichet F, editor. Proceedings of the 18th Journées Francophones d'Ingénierie des Connaissances (IC 2007); Toulouse: Cépaduès; 2007. p. 37-48.
[download PDF]
Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung K-H.
Advancing translational research with the Semantic Web.
BMC Bioinformatics 2007;8(Suppl 3):S2.
[download PDF] [PubMed: 17493285] [PubMedCentral: 1892099]
Sahoo SS, Bodenreider O, Zeng K, Sheth AP.
An experiment in integrating large biomedical knowledge resources with RDF: Application to associating genotype and phenotype information.
Proceedings of the workshop on Health Care and Life Sciences Data Integration for the Semantic Web at the 16th International World Wide Web Conference (WWW2007) 2007:(electronic proceedings: http://www2007.org/workshops/paper_2149.pdf).
[download PDF]
Sahoo SS, Zeng K, Bodenreider O, Sheth AP.
From "glycosyltransferase" to "congenital muscular dystrophy": Integrating knowledge from NCBI Entrez Gene and the Gene Ontology.
Stud Health Technol Inform 2007;129:1260-1264.
[download PDF] [PubMed: 17911917] [PubMedCentral: 2562001]
Zeng K, Bodenreider O.
Experience in integrating large RDF-based biomedical knowledge resources with Oracle. [abstract]
Proceedings of the 8th International Oracle Life Sciences User Group Meeting 2007:(electronic proceedings: http://www.olsug.org/wiki/images/d/d1/Kelly_Zheng.pdf).
[download PDF]
Zeng K, Bodenreider O.
Integrating the UMLS into an RDF-based biomedical knowledge repository. [poster]
AMIA Annu Symp Proc 2007:1170.
[download PDF] [PubMed: 18694266]
Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
RxNav: Towards an integrated view on drug information. [poster]
Medinfo 2007:P386.
[download PDF]
Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
RxNav: An integrated view on drug information. [demo]
AMIA Annu Symp Proc 2007:1202.
[download PDF]
Zhang S, Bodenreider O.
Experience in aligning anatomical ontologies.
International Journal on Semantic Web and Information Systems 2007;3(2):1-26.
[download PDF] [PubMed: 18974854] [PubMedCentral: 2575410]
Zhang S, Bodenreider O.
Lessons learned from cross-validating alignments between large anatomical ontologies.
Stud Health Technol Inform 2007;129:822-826.
[download PDF] [PubMed: 17911831] [PubMedCentral: 2408442]
Zhang S, Bodenreider O.
Identifying mismatches in alignments of large anatomical ontologies.
AMIA Annu Symp Proc 2007:851-855.
[download PDF] [PubMed: 18693957] [PubMedCentral: 2655858]
Zhang S, Bodenreider O.
Hybrid alignment strategy for anatomical ontologies: Results of the 2007 ontology alignment contest.
Proceedings of the Ontology Alignment Evaluation Initiative 2007 Campaign (OAEI 2007) 2007:139-149 (electronic proceedings: http://CEUR-WS.org/Vol-304/).
[download PDF]
Zhang S, Bodenreider O, Mork P, Bernstein PA.
Comparing two approaches for aligning representations of anatomy.
Artificial Intelligence in Medicine 2007;39(3):227-236.
[download PDF] [PubMed: 17250997] [PubMedCentral: 1973160]

2006

Azuaje F, Wang H, Zheng H, Bodenreider O, Chesneau A.
Predictive integration of Gene Ontology-driven similarity and functional interactions In: Proceedings of IEEE International Conference on Data Mining (ICDM) 2006, Workshop on Data Mining in Bioinformatics: IEEE Computer Society Press; 2006. p. 114 -119.
[download PDF]
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. p. 43-66.
[download PDF]
Bodenreider O, editor.
Proceedings of the Second International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2006) "Biomedical Ontology in Action", Baltimore, Maryland, November 8, 2006: (electronic proceedings: http://ceur-ws.org/Vol-222/); 2006
[download PDF]
Bodenreider O, Rindflesch TC.
Advanced library services: Developing a biomedical knowledge repository to support advanced information management applications.
Technical report. Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library of Medicine; September 14, 2006.
[download PDF]
Bodenreider O, Stevens R.
Bio-ontologies: Current trends and future directions.
Briefings in Bioinformatics 2006;7(3):256-274.
[download PDF] [PubMed: 16899495] [PubMedCentral: 1847325]
Bodenreider O, Zhang S.
Comparing the representation of anatomy in the FMA and SNOMED CT.
AMIA Annu Symp Proc 2006:46-50.
[download PDF] [PubMed: 17238300] [PubMedCentral: 1839313]
Bretonnel Cohen K, Bodenreider O, Hirschman L.
Linking biomedical information through text mining In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, editors. Pacific Symposium on Biocomputing 2006 [editorial]: World Scientific; 2006. p. 1-3.
[download PDF]
Golbreich C, Zhang S, Bodenreider O.
The Foundational Model of Anatomy in OWL: Experience and perspectives.
Journal of Web Semantics: Science, Services and Agents on the World Wide Web 2006;4(3):181-195.
[download PDF] [PubMed: 18360535] [PubMedCentral: 2270940]
Mariño-Ramírez L, Bodenreider O, Kantz N, Jordan IK.
Co-evolutionary rates of functionally-related yeast genes.
Evolutionary Bioinformatics Online 2006;2:295–300.
[download PDF] [PubMed: 18345352] [PubMedCentral: 2267758]
Mougin F, Bodenreider O.
Eliminer les cycles dans les systèmes terminologiques: Comparaison de deux approches [Comparing two approaches to eliminating cycles from terminological systems].
Proceedings of the 15th conference on Pattern Recognition and Artificial Intelligence (RFIA 2006) 2006:(electronic proceedings).
[download PDF]
Mougin F, Burgun A, Bodenreider O.
Data integration through data elements: Mapping data elements to terminological resources.
Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM-2006) 2006:52-59 (electronic proceedings: http://ceur-ws.org/Vol-177/).
[download PDF]
Mougin F, Burgun A, Bodenreider O.
Using WordNet to improve the mapping of data elements to UMLS for data sources integration.
AMIA Annu Symp Proc 2006:574-578.
[download PDF] [PubMed: 17238406] [PubMedCentral: 1839757]
Mougin F, Burgun A, Bodenreider O.
Mapping data elements to terminological resources for integrating biomedical data sources.
BMC Bioinformatics 2006;7(Suppl 3):S6.
[download PDF] [PubMed: 17134479] [PubMedCentral: 1764450]
Névéol A, Zeng K, Bodenreider O.
Besides precision & recall: Exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE.
AMIA Annu Symp Proc 2006:589-593.
[download PDF] [PubMed: 17238409] [PubMedCentral: 1839480]
Sahoo SS, Bodenreider O, Zeng K, Sheth AP.
Adapting resources to the Semantic Web: Experience with Entrez Gene. [abstract]
Proceedings of the workshop on Semantic Web Health Care & Life Sciences at ISWC 2006 2006:(electronic proceedings).
[download PDF]
Stevens R, Bodenreider O, Lussier YA.
Semantic webs for life sciences In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, editors. Pacific Symposium on Biocomputing 2006 [editorial]: World Scientific; 2006. p. 112-115.
[download PDF] [PubMed: 17094232]
Tsaparas P, Mariño-Ramírez L, Bodenreider O, Koonin EV, Jordan IK.
Global similarity and local divergence in human and mouse gene co-expression networks.
BMC Evol Biol 2006;6(1):70.
[download PDF] [PubMed: 16968540] [PubMedCentral: 1601971]
Vizenor L, Bodenreider O.
Using dependence relations in MeSH as a framework for the analysis of disease information in Medline.
Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM-2006) 2006:76-83 (electronic proceedings: http://ceur-ws.org/Vol-177/).
[download PDF]
Vizenor L, Bodenreider O, Peters L, McCray AT.
Enhancing biomedical ontologies through alignment of semantic relationships: Exploratory approaches.
AMIA Annu Symp Proc 2006:804-808.
[download PDF] [PubMed: 17238452] [PubMedCentral: 1839588]
Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
RxNav: A web service for standard drug information. [poster]
AMIA Annu Symp Proc 2006:1198.
[download PDF] [PubMed: 17238775] [PubMedCentral: 1839335]
Zeng K, Bodenreider O, Kilbourne JT, Nelson SJ.
RxNav: Providing standard drug information. [demo]
AMIA Annu Symp Proc 2006:1156.
[download PDF] [PubMedCentral: 1839369]
Zhang S, Bodenreider O.
Law and order: Assessing and enforcing compliance with ontological modeling principles.
Computers in Biology and Medicine 2006;36(6-7):674-693.
[download PDF] [PubMed: 16144698] [PubMedCentral: 1784072]
Zhang S, Bodenreider O.
Aligning anatomical ontologies: The role of complex structural rules.
IIAS-Transactions on Systems Research and Cybernetics -- Proceedings of the 18th International Conference on Systems Research, Informatics and Cybernetics (InterSymp 2006) 2006;VI(2):27-32.
[download PDF]
Zhang S, Bodenreider O.
Aligning multiple anatomical ontologies through a reference.
Proceedings of the International Workshop on Ontology Matching (OM 2006) 2006:201-205 (electronic proceedings: http://ceur-ws.org/Vol-225/).
[download PDF]
Zhang S, Bodenreider O.
NLM anatomical ontology alignment system: Results of the 2006 ontology alignment contest.
Proceedings of the Ontology Alignment Evaluation Initiative 2006 Campaign (OAEI 2006) 2006:153-164 (electronic proceedings: http://ceur-ws.org/Vol-225/).
[download PDF]
Zhang S, Bodenreider O, Golbreich C.
Experience in reasoning with the Foundational Model of Anatomy in OWL DL In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, editors. Pacific Symposium on Biocomputing 2006: World Scientific; 2006. p. 200-211.
[download PDF] [PubMed: 17094240]

2005

Azuaje F, Wang H, Bodenreider O.
Ontology-driven similarity approaches to supporting gene functional assessment.
Proceedings of the ISMB'2005 SIG meeting on Bio-ontologies 2005:9-10.
[download PDF]
Bodenreider O, Aubry M, Burgun A.
Non-lexical approaches to identifying associative relations in the Gene Ontology In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2005: World Scientific; 2005. p. 91-102.
[download PDF] [PubMed: 15759617] [PubMedCentral: 2224899]
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. p. 211-236.
[download PDF]
Bodenreider O, Burgun A.
Linking the Gene Ontology to other biological ontologies.
Proceedings of the ISMB'2005 SIG meeting on Bio-ontologies 2005:17-18.
[download PDF]
Bodenreider O, Hayamizu TF, Ringwald M, de Coronado S, Zhang S.
Of mice and men: Aligning mouse and human anatomies.
AMIA Annu Symp Proc 2005:61-65.
[download PDF] [PubMed: 16779002] [PubMedCentral: 1560846]
Bodenreider O, Mitchell JA, McCray AT.
Biomedical ontologies In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2005 [editorial]: World Scientific; 2005. p. 76-78.
[download PDF] [PubMed: 15759615]
Burgun A, Bodenreider O.
An ontology of chemical entities helps identify dependence relations among Gene Ontology terms.
Proceedings of the First International Symposium on Semantic Mining in Biomedicine (SMBM-2005) 2005:(electronic proceedings: http://ceur-ws.org/Vol-148/).
[download PDF]
Burgun A, Bodenreider O, Jacquelinet C.
Issues in the classification of disease instances with ontologies.
Stud Health Technol Inform 2005;116:695-700.
[download PDF] [PubMed: 16160339] [PubMedCentral: 1784521]
Burgun A, Bodenreider O, Mougin F.
Classifying diseases with respect to anatomy: a study in SNOMED CT.
AMIA Annu Symp Proc 2005:91-95.
[download PDF] [PubMed: 16779008] [PubMedCentral: 1560776]
Cantor MN, Sarkar IN, Bodenreider O, Lussier YA.
GenesTrace: Phenomic knowledge discovery via structured terminologies In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2005: World Scientific; 2005. p. 103-114.
[download PDF] [PubMed: 15759618]
Fung KW, Bodenreider O.
Utilizing the UMLS for semantic mapping between terminologies.
AMIA Annu Symp Proc 2005:266-270.
[download PDF] [PubMed: 16779043] [PubMedCentral: 1560893]
Golbreich C, Zhang S, Bodenreider O.
Migrating the FMA from Protégé to OWL.
Proceedings of the Eighth International Protégé Conference 2005:108-111.
[download PDF]
Golbreich C, Zhang S, Bodenreider O.
The Foundational Model of Anatomy in OWL: Experience and perspectives.
Proceedings of the Workshop on "OWL: Experiences and Directions" (OWLED 2005) 2005:(electronic proceedings).
[download PDF]
Mougin F, Bodenreider O.
Approaches to eliminating cycles in the UMLS Metathesaurus: Naïve vs. formal.
AMIA Annu Symp Proc 2005:550-554.
[download PDF] [PubMed: 16779100] [PubMedCentral: 1560864]
Verspoor K, Joslyn C, Ambrosiano J, Backer A, Bodenreider O, Hirschman L, Karp P, Kelly H, Loranger S, Musen M, Sriram R, Wroe C.
Knowledge integration for bio-threat response.
Technical report. Los Alamos, New Mexico: Los Alamos National Laboratory, 2005.
[download PDF]
Wang H, Azuaje F, Bodenreider O.
An ontology-driven clustering method for supporting gene expression analysis.
Proceedings of the 18th IEEE International Symposium on Computer-Based Medical Systems (CBMS'2005) 2005:389-394.
[download PDF]
Zeng K, Bodenreider O, Nelson SJ.
Implementing RxNav, a RxNorm browser. [poster]
Proceedings of Medical Informatics Europe 2005 (CD-ROM) 2005:1268.
[download PDF]
Zeng K, Bodenreider O, Nelson SJ.
RxNav: A progress report. [poster]
AMIA Annu Symp Proc 2005:1168.
[download PDF] [PubMed: 16779454] [PubMedCentral: 1560640]
Zhang S, Bodenreider O.
Alignment of multiple ontologies of anatomy: Deriving indirect mappings from direct mappings to a reference.
AMIA Annu Symp Proc 2005:864-868.
[download PDF] [PubMed: 16779163] [PubMedCentral: 1560629]

2004

Azuaje FJ, Bodenreider O.
Incorporating ontology-driven similarity knowledge into functional genomics: An exploratory study.
Proceedings of the IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE-2004) 2004:317-324.
[download PDF]
Azuaje FJ, Bodenreider O, Wang H, Dopazo J.
Gene Ontology-driven similarity for gene expression correlation analysis. [abstract]
Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:47.
[download PDF]
Bodenreider O.
The Unified Medical Language System (UMLS): Integrating biomedical terminology.
Nucleic Acids Res 2004;32 Database issue:D267-270.
[download PDF] [PubMed: 14681409] [PubMedCentral: 308795]
Bodenreider O, Aubry M, Burgun A.
From functional similarity among gene products to dependence relations among Gene Ontology terms. [abstract]
Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:53.
[download PDF]
Bodenreider O, Burgun A.
Aligning knowledge sources in the UMLS: Methods, quantitative results, and applications.
Medinfo 2004:327-331.
[download PDF] [PubMed: 15360828]
Bodenreider O, Mitchell JA, McCray AT.
Biomedical ontologies In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2004 [editorial]: World Scientific; 2004. p. 164-165.
[download PDF]
Bodenreider O, Nelson SJ.
RxNav: A semantic navigation tool for clinical drugs. [poster]
Medinfo 2004:1530.
[download PDF]
Bodenreider O, Smith B, Burgun A.
The ontology-epistemology divide: A case study in medical terminology In: Varzi AC, Vieu L, editors. Proceedings of the Third International Conference on Formal Ontology in Information Systems (FOIS 2004): IOS Press; 2004. p. 185-195.
[download PDF]
Bodenreider O, Smith B, Kumar A, Burgun A.
Investigating subsumption in DL-based terminologies: A case study in SNOMED CT In: Hahn U, Schulz S, Cornet R, editors. Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004); 2004. p. 12-20 (electronic proceedings: http://ceur-ws.org/Vol-102/).
[download PDF]
Burgun A, Bodenreider O, Aubry M, Mosser J.
Dependence relations in Gene Ontology: A preliminary study.
Workshop on The Formal Architecture of the Gene Ontology - Leipzig, Germany, May 28-29, 2004 2004:(electronic proceedings).
[download PDF]
Sarkar IN, Cantor MN, Bodenreider O, Lussier YA.
GenesTrace(TM): Biological knowledge discovery via structured terminology. [poster]
Medinfo 2004:1842.
[download PDF]
Sehgal AK, Srinivasan P, Bodenreider O.
Gene names and English words: An ambiguous mix.
Proceedings of the SIGIR 2004 Workshop on Search and Discovery in Bioinformatics 2004:(electronic proceedings).
[download PDF]
Tringali M, Rindflesch TC, Kilicoglu H, Fiszman M, Bodenreider O.
Strategies for mapping concepts in gastrointestinal endoscopy reports to the UMLS Metathesaurus. [poster]
Medinfo 2004:1885.
[download PDF]
Wang H, Azuaje F, Bodenreider O, Dopazo J.
Gene expression correlation and gene ontology-based similarity: An assessment of quantitative relationships.
Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'2004) 2004:25-31.
[download PDF]
Zhang S, Bodenreider O.
Investigating implicit knowledge in ontologies with application to the anatomical domain In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2004: World Scientific; 2004. p. 250-261.
[download PDF] [PubMed: 14992508]
Zhang S, Bodenreider O.
Comparing associative relationships among equivalent concepts across ontologies.
Medinfo 2004:459-463.
[download PDF] [PubMed: 15360855]
Zhang S, Mork P, Bodenreider O.
Lessons learned from aligning two representations of anatomy In: Hahn U, Schulz S, Cornet R, editors. Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004); 2004. p. 102-108 (electronic proceedings: http://ceur-ws.org/Vol-102/).
[download PDF]

2003

Bodenreider O.
Strength in numbers: Exploring redundancy in hierarchical relations across biomedical terminologies.
AMIA Annu Symp Proc 2003:101-105.
[download PDF] [PubMed: 14728142] [PubMedCentral: 1480297]
Bodenreider O, Burgun A, Mitchell JA.
Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: A feasibility study.
Stud Health Technol Inform 2003;95:379-384.
[download PDF] [PubMed: 14664016] [PubMedCentral: 1893008]
Bodenreider O, McCray AT.
Exploring semantic groups through visual approaches.
Journal of Biomedical Informatics 2003;36(6):414-432.
[download PDF] [PubMed: 14759816] [PubMedCentral: 1997308]
Bodenreider O, Mitchell JA.
Graphical visualization and navigation of genetic disease information. [poster]
AMIA Annu Symp Proc 2003:792.
[download PDF] [PubMed: 14728297] [PubMedCentral: 1479900]
Bodenreider O, Mitchell JA, McCray AT.
Biomedical ontologies In: Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2003 [editorial]: World Scientific; 2003. p. 562-564.
[download PDF]
Bodenreider O, Pakhomov S.
Exploring adjectival modification in biomedical discourse across two genres.
Proceedings of the ACL'2003 Workshop "Natural Language Processing in Biomedicine" 2003:105-112.
[download PDF]
Bodenreider O, Zhang S.
Semantic Integration in Biomedicine.
Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference (ISWC 2003) 2003:156-157.
[download PDF]
Cantor MN, Sarkar IN, Hartel F, Bodenreider O, Lussier YA.
An evaluation of hybrid methods for matching biomedical terminologies: Mapping the Gene Ontology to the UMLS.
Stud Health Technol Inform 2003:62-67.
[download PDF] [PubMed: 14663964] [PubMedCentral: 1796946]
Kayaalp M, Aronson AR, Humphrey SM, Ide NC, Tanabe LK, Smith LH, Demner D, Loane RR, Mork JG, Bodenreider O.
Methods for accurate retrieval of MEDLINE citations in functional genomics.
Proceedings of the Text Retrieval Conference (TREC-2003) 2003:175-184.
[download PDF]
Mitchell JA, McCray AT, Bodenreider O.
From phenotype to genotype: Issues in navigating the available information resources.
Methods of Information in Medicine 2003;42(5):557-563.
[download PDF] [PubMed: 14654891] [PubMedCentral: 1800828]
Zhang S, Bodenreider O.
Knowledge augmentation for aligning ontologies: An evaluation in the biomedical domain.
Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference (ISWC 2003) 2003:109-114.
[download PDF]
Zhang S, Bodenreider O.
Aligning representations of anatomy using lexical and structural methods.
AMIA Annu Symp Proc 2003:753-757.
[download PDF] [PubMed: 14728274] [PubMedCentral: 1480279]

2002

Bodenreider O.
GenNav: Visualizing Gene Ontology as a graph. [poster]
Proceedings of AMIA Annual Symposium 2002:978.
[download PDF] [PubMedCentral: 2244208]
Bodenreider O.
Experiences in visualizing and navigating biomedical ontologies and knowledge bases.
Proceedings of the ISMB'2002 SIG meeting "Bio-ontologies" 2002:29-32.
[download PDF]
Bodenreider O, Burgun A.
Characterizing the definitions of anatomical concepts in WordNet and specialized sources.
Proceedings of the First Global WordNet Conference 2002:223-230.
[download PDF]
Bodenreider O, Burgun A, Rindflesch TC.
Assessing the consistency of a biomedical terminology through lexical knowledge.
International Journal of Medical Informatics 2002;67(1-3):85-95.
[download PDF] [PubMed: 12460634]
Bodenreider O, Mitchell JA, McCray AT.
Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics.
Proceedings of AMIA Annual Symposium 2002:61-65.
[download PDF] [PubMed: 12463787] [PubMedCentral: 2244306]
Bodenreider O, Rindflesch TC, Burgun A.
Unsupervised, corpus-based method for extending a biomedical terminology.
Proceedings of the ACL'2002 Workshop "Natural Language Processing in the Biomedical Domain" 2002:53-60.
[download PDF]
Burgun A, Bodenreider O, Le Duff F, Mounssouni F, Loréal O.
Representation of roles in biomedical ontologies: a case study in functional genomics.
Proceedings of AMIA Annual Symposium 2002:86-90.
[download PDF] [PubMed: 12463792] [PubMedCentral: 2244301]
McCray AT, Bodenreider O.
A conceptual framework for the biomedical domain In: Green R, Bean CA, Myaeng SH, editors. The semantics of relationships: an interdisciplinary perspective. Dordrecht; Boston: Kluwer Academic Publishers; 2002. p. 181-198.
[download PDF]
McCray AT, Browne AC, Bodenreider O.
The lexical properties of the Gene Ontology (GO).
Proceedings of AMIA Annual Symposium 2002:504-508.
[download PDF] [PubMed: 12463875] [PubMedCentral: 2244431]
Mitchell JA, McCray AT, Bodenreider O.
From phenotype to genotype: Navigating the available information resources. [poster]
Proceedings of AMIA Annual Symposium 2002:1109.
[download PDF] [PubMedCentral: 2244561]
Srinivasan P, Mitchell JA, Bodenreider O, Pant G, Menczer F.
Web crawling agents for retrieving biomedical information In: Proceedings of the International Workshop on Bioinformatics and Multi-Agent Systems (BIXMAS 2002), Bologna, Italy, July 15, 2002; 2002. p. (electronic proceedings).
[download PDF]
Travers D, Bodenreider O.
Identifying medical concepts in free text chief complaint data. [abstract]
Academic Emergency Medicine 2002;9(5):511.
[download PDF]

2001

Bodenreider O.
An object-oriented model for representing semantic locality in the UMLS.
Medinfo 2001;10(Pt 1):161-165.
[download PDF] [PubMed: 11604725]
Bodenreider O.
Circular hierarchical relationships in the UMLS: Etiology, diagnosis, treatment, complications and prevention.
Proceedings of AMIA Annual Symposium 2001:57-61.
[download PDF] [PubMed: 11825155] [PubMedCentral: 2243677]
Bodenreider O.
Medical Ontology Research.
Technical report. Bethesda, Maryland: Lister Hill National Center for Biomedical Communications, National Library of Medicine; May 17, 2001.
[download PDF]
Bodenreider O, Bean CA.
Relationships among knowledge structures: Vocabulary integration within a subject domain In: Bean CA, Green R, editors. Relationships in the organization of knowledge. Dordrecht; Boston: Kluwer Academic Publishers; 2001. p. 81-98.
[download PDF]
Bodenreider O, Burgun A, Rindflesch TC.
Lexically-suggested hyponymic relations among medical terms and their representation in the UMLS.
Proceedings of TIA'2001 "Terminology and Artificial Intelligence" 2001:11-21.
[download PDF]
Burgun A, Bodenreider O.
Methods for exploring the semantics of the relationships between co-occurring UMLS concepts.
Medinfo 2001;10(Pt 1):171-175.
[download PDF] [PubMed: 11604727]
Burgun A, Bodenreider O.
Comparing terms, concepts and semantic classes in WordNet and the Unified Medical Language System.
Proceedings of the NAACL'2001 Workshop, "WordNet and Other Lexical Resources: Applications, Extensions and Customizations" 2001:77-82.
[download PDF]
Burgun A, Bodenreider O.
Aspects of the taxonomic relation in the biomedical domain In: Welty C, Smith B, editors. Collected papers from the Second International Conference "Formal Ontology in Information Systems": ACM Press; 2001. p. 222-233.
[download PDF]
Burgun A, Bodenreider O.
Mapping the UMLS Semantic Network into general ontologies.
Proceedings of AMIA Annual Symposium 2001:81-85.
[download PDF] [PubMed: 11833483] [PubMedCentral: 2243467]
McCray AT, Bodenreider O, Malley JD, Browne AC.
Evaluating UMLS strings for natural language processing.
Proceedings of AMIA Annual Symposium 2001:448-452.
[download PDF] [PubMed: 11825228] [PubMedCentral: 2243606]
McCray AT, Burgun A, Bodenreider O.
Aggregating UMLS semantic types for reducing conceptual complexity.
Medinfo 2001;10(Pt 1):216-220.
[download PDF] [PubMed: 11604736]

2000

Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ.
The NLM Indexing Initiative.
Proceedings of AMIA Annual Symposium 2000:17-21.
[download PDF] [PubMed: 11079836] [PubMedCentral: 2243970]
Bodenreider O.
Using UMLS semantics for classification purposes.
Proceedings of AMIA Annual Symposium 2000:86-90.
[download PDF] [PubMed: 11079850] [PubMedCentral: 2243905]
Bodenreider O.
A semantic navigation tool for the UMLS. [poster]
Proceedings of AMIA Annual Symposium 2000:971.
[download PDF] [PubMedCentral: 2244094]
Bodenreider O.
Comment les usagers accèdent à l'information médicale aux USA: l'exemple de MEDLINEplus [How consumers access health information in the USA: MEDLINEplus as an example].
Innovation et Technologie en Biologie et Médecine 2000;21(5):286-290.
[download PDF]
Bodenreider O, Zweigenbaum P.
Stratégies d'identification des noms propres à partir de nomenclatures médicales parallèles [Strategies for identifying proper names in parallel medical terminologies].
Traitement Automatique des Langues 2000;41(3):727-757.
[download PDF]
Bodenreider O, Zweigenbaum P.
Identifying proper names in parallel medical terminologies.
Stud Health Technol Inform 2000;77:443-447.
[download PDF] [PubMed: 11187591] [PubMedCentral: 1790050]
Botti G, Bodenreider O, Burgun A, Le Beux P, Fieschi M.
De la classification à la connaissance des maladies: une réflexion à partir de la Classification Internationale des Maladies [From classification to knowledge about diseases: Thoughts about the International Classification of Diseases].
Innovation et Technologie en Biologie et Médecine 2000;21(5):291-297.
[download PDF]
Jacquelinet C, Bodenreider O, Burgun A.
Modelling syllepse in medical knowledge bases with application in the domain of organ failure and transplantation.
Proceedings of OntoLex 2000 (Workshop on Ontologies and Lexical Knowledge Bases) 2000.
[download PDF]

1999

Nelson SJ, Aronson AR, Doszkocs TE, Wilbur WJ, Bodenreider O, Chang HF, Mork J, McCray AT.
Automated assignment of Medical Subject Headings. [poster]
Proceedings of AMIA Annual Symposium 1999:1127.
[download PDF] [PubMedCentral: 2232883]

1998

Bodenreider O, Burgun A, Botti G, Fieschi M, Le Beux P, Kohler F.
Evaluation of the Unified Medical Language System as a medical knowledge source.
J Am Med Inform Assoc 1998;5(1):76-87.
[download PDF] [PubMed: 9452987] [PubMedCentral: 61277]
Bodenreider O, McCray AT.
From French vocabulary to the Unified Medical Language System: a preliminary study.
Medinfo 1998;9(Pt 1):670-674.
[download PDF] [PubMed: 10384539]
Bodenreider O, Nelson SJ, Hole WT, Chang HF.
Beyond synonymy: exploiting the UMLS semantics in mapping vocabularies.
Proceedings of AMIA Annual Symposium 1998:815-819.
[download PDF] [PubMed: 9929332] [PubMedCentral: 2232139]
Bouchet C, Bodenreider O, Kohler F.
Integration of the analytical and alphabetical ICD10 in a coding help system. Proposal of a theoretical model for the ICD representation.
Medinfo 1998;9(Pt 1):176-179.
[download PDF] [PubMed: 10384443]
Burgun A, Bodenreider O, Denier P, Delamarre D, Botti G, Oberlin P, Leveque JM, Bremond M, Fieschi M, Le Beux P.
A collaborative approach to building a terminology for medical procedures using a Web-based application: from specifications to daily use.
Medinfo 1998;9(Pt 1):596-599.
[download PDF] [PubMed: 10384524]
Guichet JM, Braillon P, Bodenreider O, Lascombes P.
Periosteum and bone marrow in bone lengthening: a DEXA quantitative evaluation in rabbits.
Acta Orthop Scand 1998;69(5):527-531.
[PubMed: 9855238]

1997

Burgun A, Denier P, Bodenreider O, Botti G, Delamarre D, Pouliquen B, Oberlin P, Leveque JM, Lukacs B, Kohler F, Fieschi M, Le Beux P.
A Web terminology server using UMLS for the description of medical procedures.
J Am Med Inform Assoc 1997;4(5):356-363.
[download PDF] [PubMed: 9292841] [PubMedCentral: 61253]
Gillois P, Garin H, Bodenreider O, Kohler F.
Case mix of elderly in-patients in the 29 hospitals in Lorraine in 1994 and 1995.
Stud Health Technol Inform 1997;43 Pt A:455-459.
[PubMed: 10179590]

1996

Burgun A, Botti G, Bodenreider O, Delamarre D, Leveque JM, Lukacs B, Mayeux D, Bremond M, Kohler F, Fieschi M, Le Beux P.
Methodology for using the UMLS as a background knowledge for the description of surgical procedures.
Int J Biomed Comput 1996;43(3):189-202.
[download PDF] [PubMed: 9032008]

1995

Burgun A, Bodenreider O, Denier P, Delamarre D, Botti G, Lukacs B, Mayeux D, Bremond M, Kohler F, Fieschi M.
Knowledge acquisition from the UMLS sources: application to the description of surgical procedures.
Medinfo 1995;8(Pt 1):75-79.
[PubMed: 8591317]

1994

Grasser B, Pinelli G, Carteaux J-P, Bodenreider O, Sadoul N, Aliot E, Villemot J-P.
Chirurgie coronaire après 70 ans : analyse des facteurs de risque de mortalité opératoire [Coronary artery surgery after 70 years: an analysis of the risk factors of operative mortality].
Arch. Mal. Coeur Vaiss. 1994;87(9):1169-1175.
[PubMed: 7646230]

1993

Faller B, Genestier S, Bodenreider O, Brignon P, Boess G.
Experience regarding reduction of peritonitis rates in continuous ambulatory peritoneal dialysis. [abstract]
Peritoneal Dialysis International 1993;13(suppl. 2):319-321.
[PubMed: 8399598]

Last modified by Olivier Bodenreider: Thu Nov 19 17:34:56 2009