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Years:  2009  2008  2007  2006  2005  2004  2003  2002  2001  2000
Year 2009Back to top
A Graph-based Approach to Auditing RxNorm
Bodenreider O, Peters LB
Journal of Biomedical Informatics 2009;42(3):558-570
(Abstract)
Alignment of the UMLS Semantic Network with BioTop: Methodology and Assessment
Schulz S, Beisswanger, van den Hoek L, Bodenreider O, van Mulligen EM
Bioinformatics 2009;25(12):i69-i76
(Abstract)
Analyzing Polysemous Concepts from a Clinical Perspective: Application to Auditing Concept Categorization in the UMLS
Mougin FL, Bodenreider O, Burgun A
J Biomed Inform. 2009 Jun;42(3):440-51. Epub 2009 Mar 18
(Abstract)
Auditing Associative Relations Across Two Knowledge Sources
Vizenor LT, Bodenreider O, McCray AT
Journal of Biomedical Informatics 2009;42(3):426-439
(Abstract)
Identification of cis-regulatory Elements in Gene Co-expression Networks Using A-GLAM
Marino-Ramirez L, Tharakaraman K, Bodenreider O, Spounge J, Landsman D
Methods Mol Biol. 2009;541:1-22
(Abstract)
The caBIG Terminology Review Process
Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M
J Biomed Inform. 2009 Jun;42(3):571-80. Epub 2008 Dec 25
(Abstract)
 
Year 2008Back to top
A Balanced Approach to Health Information Evaluation: A Vocabulary-based Naive Bayes Classifier and Readability Formulas
Leroy G, Miller T, Rosemblat G, Browne A
In Journal of the American Society for Information Science and Technology (JASIST), 59(9):1409-1419, 2008
(Abstract) (PDF)
Accessing and Integrating Data and Knowledge for Biomedical Research
Burgun A, Bodenreider O
Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med 2008;47(Suppl 1):91-99
(Abstract) (PDF)
A Framework for Characterizing Drug Information Sources
Sharp M, Bodenreider O, Wacholder N
AMIA Annu Symp Proc 2008:662-666
(Abstract)
An Ontology-driven Semantic Mash-up of Gene and Biological pathway information: Application to the domain of nicotine dependence
Sahoo SS, Bodenreider O, Rutter JL, Skinner KJ, Sheth AP
Journal of Biomedical Informatics 2008
(Abstract)
Auditing the NCI Thesaurus with Semantic Web Technologies
Mougin F, Bodenreider O
Auditing the NCI thesaurus with Semantic Web technologies
(Abstract) (PDF)
Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System
Mougin F, Burgun A, Bodenreider O, Chabalier J, Loreal O, Le Beux P
Proceedings of the Fifth International Workshop on Data Integration in the Life Sciences (DILS 2008). Berlin Heidelberg New York: Springer; 2008. p. 61-76
(Abstract) (PDF)
Automatic Summarization of MEDLINE Citations for Evidence-based Medical Treatment: A Topic-oriented Evaluation
Fiszman M, Demner-Fushman D, Kilicoglu H, Rindflesch TC
J Biomed Inform. 2008 Nov 5
(Abstract)
Beyond Surface Characteristics: A New Health Text-specific Readability Measurement
Kim H, Goryachev S, Rosemblat G, Browne A, Keselman A, Zeng-Treitler Q
AMIA Annu Symp Proc. 2007 Oct 11:418-22
(Abstract)
Biological Entity Recognition with Conditional Random Fields
He Y, Kayaalp M
AMIA Annu Symp Proc. 2008 Nov 6:293-7
(Abstract)
Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support
Bodenreider O
Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med 2008;47(Suppl 1):67-79
(Abstract)
Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies
Bodenreider O
Proc. KR-MED 2008
(Abstract)
Design and Implementation of a Personal Medication Record - MyMedicationList
Zeng K, Bodenreider O, Nelson SJ
AMIA Annu Symp Proc 2008:844-848
(Abstract) (PDF)
Essie: a concept-based search engine for structured biomedical text
Ide NC, Loane RF, Demner-Fushman D
J Am Med Inform Assoc. 2007 May-Jun;14(3):253-63. Epub 2007 Feb 28
(Abstract)
Identifying Risk Factors for Metabolic Syndrome in Biomedical Text
Fiszman M, Rosemblat G, AhlersCB, Rindflesch TC
AMIA Annu Symp Proc. 2007 Oct 11:249-53
(Abstract)
Issues in Mapping LOINC Laboratory Tests to SNOMED CT
Bodenreider O
AMIA Annu Symp Proc 2008:51-55
(Abstract)
Leveraging Semantic Knowledge in IRB Databases to Improve Translation Science
Hurdle JF, Botkin J, Rindflesch TC
AMIA Annu Symp Proc. 2007 Oct 11:349-53
(Abstract)
Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing
Aronson AR, Mork JG, Shooshan SE, Demner-Fushman D
AMIA Annu Symp Proc. 2008 Nov 6:21-5
(Abstract)
Moving Towards Transparency of Clinical Trials
Zarin DA, Tse T
Science. 2008 Mar 7;319(5868):1340-2
(Abstract)
MyMedicationList: Integrating Personal Medication Records with Resources
Nelson SJ, Zeng K, Bodenreider O
AMIA Annu Symp Proc 2008:1228
(Abstract) (PDF)
Ontologies and Data Integration in Biomedicine: Success Stories and Challenging Issues
Bodenreider O
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. 1-4
(Abstract) (PDF)
Semantic Processing to Support Clinical Guideline Development
Fiszman M, Ortiz E, Bray BE, Rindflesch TC
AMIA Annu Symp Proc. 2008 Nov 6:187-91
(Abstract)
Semantic Web for Translational Biomedicine: Two Pilot Experiments
Bodenreider O
Proc. MIA Summit on Translational Bioinformatics 2008:141
(Abstract) (PDF)
SNOMED CT: Browsing the Browsers
Rogers J, Bodenreider O
Proc of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008) 2008:30-36
(Abstract)
Standards, Security and Usability: Experience with MyMedicationList
Zeng K, Bodenreider O, Kilbourne J, Nelson SJ
Proc. AMIA Spring Congress 2008
(PDF)
The Biological Function of Some Human Transcription Factor Binding Motifs Varies with Position Relative to the Transcription Start Site
Tharakaraman K, Bodenreider O, Landsman D, Spouge JL, Marino-Ramirez
Nucleic Acids Res 2008;36(8):2777-2786
(Abstract)
Toward Automatic Recognition of High Quality Clinical Evidence.
Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB
AMIA Annu Symp Proc. 2008 Nov 6:368
(Abstract)
Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence
Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB
J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31. Epub 2008 Oct 24
(Abstract)
Using the Literature-based Discovery Paradigm to Investigate Drug Mechanisms
Ahlers CB, Hristovski D, Kilicoglu H, Rindflesch TC
AMIA Annu Symp Proc. 2007 Oct 11:6-10
(Abstract)
Using the RxNorm Web Services API for Quality Assurance Purposes
Peters L, Bodenreider O
AMIA Annu Symp Proc 2008:591-595
(Abstract)
 
Year 2007Back to top
Advancing Translational Research with the Semantic Web
Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, et al
BMC Bioinformatics 2007;8(Suppl 3):S2.
(Abstract) (PDF)
Aligning Anatomical Ontologies: The Role of Complex Structural Rules
Zhang S, Bodenreider O, Kantz N
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.
(Abstract) (PDF)
A Multidiscipline Conceptual Framework for Consumer Health Informatics
Logan RA, Tse T
Medinfo 2007 12 (Pt2):1169-1173.
(Abstract) (PDF)
An Experiment in Integrationg Large Biomedical Knowledge Resources with RDF: Application to Associating Genotype and Phenotype Information
Sahoo S, Bodenreider O, Zeng K, Sheth AP
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) (electronic proceedings: http://www2007.org/workshops/paper_149.pdf)
(Abstract) (PDF)
Assessing Consumer Health Vocabulary Familiarity: An Exploratory Study
Keselman A, Tse T, Crowell J et al
J Med Internet Res. 2007 Mar 14;9(1):e5
(Abstract) (PDF)
Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations
Neveol A, Mork JG, Aronson R
Proc BioNLP 2007 Workshop, 183-92.
(Abstract) (PDF)
Clinical, Classroom or Personal Education: Attitudes About Health Literacy
Logan RA
JMLA 95:2 (April 2007): 127-137.
(Abstract) (PDF)
Clinical Ontologies for Discovery Applications
Lussier YA, Bodenreider O
In: Baker CJO, Cheung K-H, editors. Semantic Web: Revolutionizing knowledge discovery in the life sciences. New York: Springer; 2007. p. 101-119.
(Abstract) (PDF)
Co-evolutionary Rates of Functionally Related Yeast Genes
Marino-Ramirez L, Bodenreider O, Kantz N, Jordan IK
Evolutionary Bioinformatics Online 2006;2:295-300.
(Abstract) (PDF)
Combining Lexical and Semantic Methods of Inter-terminology Mapping Using the UMLS
Fung KW, Bodenreider O, Aronson AR, Hole WT, Srinivasan S
Medinfo 2007:605-609.
(Abstract) (PDF)
Combining Resources to Find Answers to Biomedical Questions
Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, et al
Proc TREC 2007, 205-14
(Abstract) (PDF)
Comparing Two Approaches for Aligning Representations of Anatomy
Zheng S, Mork P, Bodenreider O, Bernstein PA
Artificial Intelligence in Medicine 2007;39(3):227-236.
(Abstract) (PDF)
Essie: A Concept-based Search Engine for Structured BiomedicalText
Ide NC, Loane RF, Demner-Fushman D
J Am Med Inform Assoc 2007;14(3):253-263.
(Abstract) (PDF)
Experience in Aligning Anatomical Ontologies
Zhang S, Bodenreider O
International Journal on Semantic Web and Information Systems 2007;3(2):1-26.
(Abstract) (PDF)
Experience in Integrating Large RDF-based Biomedical Knowledge Resources with Oracle
Zeng K, Bodenreider O
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)
(Abstract) (PDF)
Extracting Semantic Predications from MEDLINE Citations for Pharmacogenomics
Ahlers C, Fiszman M, Demner-Fushman D, Lang F, Rindflesch TC
Pacific Symposium on Biocomputing 2007 12:209-220
(Abstract) (PDF)
Extractive Summarization in Clinical Trials Protocol Summaries: A Case Study
Rosemblat G, Graham L, Tse T
In: Proceedings, 3rd Indian International Conference on Artificial Intelligence (IICAI-2007), pp. 1824-1837
(Abstract) (PDF)
Fine-Grained Indexing of the Biomedical Literature: MeSH Subheading Attachment for a MEDLINE Indexing Tool
Neveol A, Shooshan SE, Mork JG, Aronson AR
AMIA Annu Symp Proc. 2007;:553-7
(Abstract) (PDF)
From 'Glycosyltransferase' to 'Congenital Muscular Dystrophy': Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology
Sahoo SS, Zeng K, Bodenreider O, Sheth A
MEDINFO 2007:1260-1264
(Abstract) (PDF)
From Indexing the Biomedical Literature to Coding Clinical Text: Experience with MTI and Machine Learning Approaches
Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, Neveol A, Peters L, Rogers WJ
Proc. 2007 Workshop on Biomedical Natural Language Processing (BioNL'07), June 2007, pp. 105-112, Prague, Czech Republic.
(Abstract) (PDF)
Hybrid Alignment Strategy for Anatomical Ontologies Results of the 2007 Ontology Alignment Contest
Zhang S, Bodenreider O
Proc. OAEI 2007:139-149.
(Abstract) (PDF)
Identifying Mismatches in Alignments of Large Anatomical Ontologies
Zhang S, Bodenreider O
Proc AMIA Annu Symp; 2007:851-855
(Abstract) (PDF)
Integrating the UMLS into an RDF-Based Biomedical Knowledge Repository
Zeng K, Bodenreider O
Proc AMIA Annu Symp; 2007:1170
(Abstract) (PDF)
Interpreting Comparative Constructons in Biomedical Text
Fiszman M, Demner-Fushman D, Lang FM, Goetz P, Rindflesch TC
Proc. 2007 Workshop on Biomedical Natural Language Processing (BioNL'07), June 2007, pp. 137-144, Prague, Czech Republic.
(Abstract) (PDF)
Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-based Biomedical Terminologies
Bodenreider O, Smith B, Kumar A, Burgun A
Artificial Intelligence in Medicine 2007;39(3):183-195.
(Abstract) (PDF)
Issues in Integrating Epidemiology and Research Information in Oncology: Experience with ICD-O3 and the NCI Thesaurus
Burgun A, Bodenreider O
Proc AMIA Annu Symp; 2007:pp 85-89.
(Abstract) (PDF)
Issues in the Registration of Clinical Trials
Zarin DA, Ide NC, Tse T, Harlan WR, West JC, Lindberg DAB
JAMA 2007:297(19):2112-2120.
(Abstract) (PDF)
Keeping the Promises Associated with Your Digital Assets: Is it Possible?
Gallagher ME
In: Archiving 2007 Final Program and Proceedings, pp.146-149, 2007.
(Abstract) (PDF)
Knowledge-Based Methods to Help Clinicians Find Answers in MEDLINE
Sneiderman CA, Demner-Fushman D, Fiszman M, Ide NC, Rindflesch TC
2007 Nov-Dec;14(6):772-80. Epub 2007 Aug 21
(Abstract) (PDF)
Lessons Learned from Cross-Validating Alignments Between Large Anatomical Ontologies
Zhang S, Bodenreider O
MEDINFO 2007:822-826.
(Abstract) (PDF)
Multiple Approaches to Fine-Grained Indexing of the Biomedical Literature
Neveol A, Shooshan SE, Humphrey SM, Rindflesch TC, Aronson AR
Pacific Symposium on Biocomputing 2007 12:293-303
(Abstract) (PDF)
Oncologic Pathology in Biomedical Terminologies: Challenges for Data Integration
Bodenreider O, Burgun A
Proc. of the APIII conference on "Anatomic Pathology Informatics and Imaging Support for Translational Medicine", Pittsburgh, Pennsylvania, September 9-12, 2007 2007:Abstract 342.
(Abstract) (PDF)
PDF File Migration to PDF/A: Technical Considerations
Walker FL, Gallagher ME, Thoma GR
Proc. IS&T Archiving 2007. Arlington, Virginia, May 2007; 6-11.
(Abstract) (PDF)
Registering a Clinical Trial in ClinicalTrials.gov
Zarin DA, Keselman A
Chest 2007;131;909-912; Prepublished online February 15, 2007; DOI10.1378/chest.06-2450
(Abstract) (PDF)
RxNav: An Integrated View on Drug Information
Zeng K, Bodenreider O, Kilbourne J, Nelson SJ
Proc AMIA Annu Symp; 2007:1202
(Abstract) (PDF)
RxNav: Towards an Integrated View on Drug Information
Zeng K, Bodenreider O, Kilbourne J, Nelson S
MEDINFO 2007:386.
(Abstract) (PDF)
Term Identification Methods for Consumer Health Vocabulary Development
Zeng QT, Tse T, Divita G et al
J Med Internet Res. 2007 Feb 28;9(1):e4
(Abstract) (PDF)
The Consumers' Perspective: Text Features and Readability of Consumer Health Text
Rosemblat G, Logan R
Mednet 2007: Germany. 12 Oct 2007.
(Abstract)
Using Discourse Analysis to Improve Text Categorization in MEDLINE
Ruch P, Geissbuhler A, Gobeill J, Lisacek F, Tbahriti I, Veuthey A, Aronson AR
Medinfo 2007:710-715.
(Abstract) (PDF)
 
Year 2006Back to top
A Pragmatic Approach to Summary Extraction in Clinical Trials
Rosemblat G, Graham L
In Proceedings of the BioNLP Workshop on Linking Natural Language Processing and Biology at HLT-NAACL 06, pages 124-125, New York City, June 2006.
(Abstract) (PDF)
Argumentative Feedback: A Linguistically-motivated Term Expansion for Information Retrieval
Ruch P, Tbahriti I, Bobeill J, Aronson AR
Proc. COLING/ACL 2006, 675-82
(Abstract) (PDF)
Argument-predicate Distance as a Filter for Enhancing Precision in Extracting Predications on the Genetic Etiology of Disease
Masseroli M, Kilicoglu H, Lang F-M, Loane RF, Rindflesch TC
BMC Bioinformatics 2006; 7:291
(Abstract) (PDF)
Assessing Consumer Health Vocabulary Familiarity: An Exploratory Study
Keselman A, Tse T, Crowell J, Browne A, Ngo L, Zeng Q
Mednet 2006
(Abstract) (PDF)
Besides Precision and Recall: Exploring Alternative Approaches to Evaluating an Automatic Indexing Tool for MEDLINE
Neveol A, Zeng K, Bodenreider O
Proc AMIA Symp 2006:589-593
(Abstract) (PDF)
Bio-ontologies: Current Trends and Future Directions
Bodenreider O, Stevens R
Briefings in Bioinformatics 2006;7(3):256-274
(Abstract) (PDF)
Challenges and Strategies of the Genetics Home Reference
Mitchell JA, Fomous C, Fun J
Journal of Web Semantics: Science, Services and Agents on the World Wide Web 2006;4(3):181-195.
(Abstract) (PDF)
Comparing the Representation of Anatomy in the FMA and SNOMED CT
Bodenreider O, Zhang S
Proc AMIA Symp 2006:46-50
(Abstract) (PDF)
Comparing Two Approaches to Eliminating Cycles in Terminological Systems
Mougin F, Bodenreider O
Proceedings of the 15th conference on Pattern Recognition and Artificial Intelligence (RFIA 2006)(electronic proceedings)
(Abstract) (PDF)
Cross-Language Search in a Monolingual Health Information System: Flexible Designs and Lexical Processes
Rosemblat G, Graham L
In Proceedings of the 9th ISKO Conference, pages 173-182, Vienna, Austria, July 2006.
(Abstract) (PDF)
Data Integration Through Data Elements: Mapping Data Elements to Terminological Resources
Mougin F, Burgun A, Bodenreider O
Proceedings of the Second Interntional Symposium on Semantic Mining in Biomedicine (SMBM-2006) 2006:52-59
(Abstract) (PDF)
dTagger: A POS Tagger
Divita G, Browne AC, Loanne R
AMIA 2006 Symposium Proceedings pp 201-203
(Abstract) (PDF)
Enhancing Biomedical Ontologies through Alignment of Semantic Relationships: Exploratory Approaches
Bodenreider O, Peters L, McCray A
Proc AMIA Symp 2006:804-808
(Abstract) (PDF)
Experience in Reasoning with the Foundational Model of Anatomy in OWL DL
Zhang S, Bodenreider O, Golbreich C
In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, editors. Pacific Symposium on Biocomputing 2006: World Scientific; 2006. p. 200-211.
(Abstract) (PDF)
Exploiting Semantic Relations for Literature-Based Discovery
Hristovski D, Friedman C, Rindflesch TC
AMIA Annu Symp Proc. 2006; 349-53
(Abstract) (PDF)
Exploring and Developing Consumer Health Vocabularies
Zeng QT, Tse T
Journal of the American Medical Informatics Association. 2006 Jan/Feb;(1)24-9.
(Abstract) (PDF)
Exploring User Navigation during Online Health Information Seeking
Graham L, Tse T, Keselman A
Proc. AMIA 2006
(Abstract) (PDF)
Finding Relevant Passages in Scientific Articles: Fusion of Automatic Approaches vs. an Interactive Team Effort
Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ, Aronson AR
Proc TREC 2006, 569-76
(Abstract) (PDF)
Genetics Home Reference: Helping Patients Understand the Role of Genetics in Health and Disease
Fomous C, Mitchell JA, McCray A
Community Genet 2006;9:274-278
(Abstract) (PDF)
Global Similarity and Local Divergence in Human and Mouse Gene Co-expression Networks
Tsaparas P, Marino-Ramirez L, Bodenreider O
BMC Evol Biol 2006;6(1):70
(Abstract) (PDF)
Information Rx: Evaluation of a New Informatics Tool for Physicians, Patients, and Libraries
Siegel ER, Logan RA, Harnsberger RL, Cravedi K, Krause JA, Lyon B, Hajarian K, Uhl J, Ruffin A, Lindberg DA
Information Services and Use. 2006: 16(1): 1-10
(Abstract) (PDF)
Interpretation of Data and Identification of Information are Sine Qua Non for Modern Digital Information Services
He Y, Kayaalp M
Proceedings of AMIA Symposium, 2006
(Abstract) (PDF)
Law and Order: Assessing and Enforcing Compliance with Ontological Modeling Principles in the Foundational Model of Anatomy
Zhang S, Bodenreider O
Computers in Biology and Medicine 2006; 36(6-7):674-693
(Abstract) (PDF)
Lexical, Terminological and Ontological Resources for Biological Text Mining
Bodenreider O
Ananiadou S, McNaught J, editors. Text mining for biology and biomedicine: Artech House; 2006. p. 43-66.
(Abstract) (PDF)
Mapping Data Elements to Terminological Resources for Integrating Biomedical Data Sourcse
Mougin F, Burgun A, Bodenreider O
BMC Bioinformatics 2006;7(Suppl 3):S6
(Abstract) (PDF)
NLM Anatomical Ontology Alignment system: Results of the 2006 ontology alignment contest
Zhang S, Bodenreider O
Proceedings of the Ontology Alignment Evaluation Initiative 2006 Campaign (OAEI 2006) 2006:145-156
(Abstract) (PDF)
Predictive Integration of Gene Ontology-Driven Similarity and Functional Interactions
Azuaje F, Wang H, Zheng H, Bodenreider O, Chesneau A
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
(Abstract) (PDF)
RxNav: A Web Service for Standard Drug Information
Zeng K, Bodenreider O, Kilbourne J, Nelson SJ
Proc AMIA Symp 2006:1198
(Abstract) (PDF)
Semantic Representation of Consumer Questions and Physician Answers
Slaughter LA, Soergel D, Rindflesch TC
Int J Med Inform. 2006;75(7):513-29
(Abstract) (PDF)
Summarizing Drug Information in Medline Citations
Fiszman M, Rindflesch TC, Kilicoglu H
AMIA Annu Symp Proc. 2006; 254-8
(Abstract) (PDF)
Surviving Change: The First Step Toward Sustaining Your Digital Library
Gallagher ME, Moffatt C
J. Trant and D. Bearman (eds.). Museums and the Web 2006: Proceedings, Toronto: Archives and Museum Informatics, published 2006 Mar.
(Abstract) (PDF)
Text Features and Readability: Expert Evaluation of Consumer Health Text
Rosemblat G, Logan R, Tse T, Graham L
Mednet 2006: 11th World Congress on Internet in Medicine the Society for Internet in Medicine. October 14-16, 2006. Toronto, Canada.
(Abstract) (PDF)
The Effect of User Factors on Consumer Familiarity with Health Terms: Using Gender as a Proxy for Background Knowledge about Gender-Specific Illnesses
Keselman A, Massengale L, Ngo L, Browne A, Zeng Q
ISBMDA 2006: 472-481
(Abstract) (PDF)
The Foundational Model of Anatomy in OWL: Experience and Perspectives
Golbreich C, Zhang S, Bodenreider O
Journal of Web Semantics: Science, Services and Agents on the World Wide Web 2006;4(3):181-195.
(Abstract) (PDF)
The Role of the National Library of Medicine Web Sites in Newborn Screening Education
Fomous C, Miller N
Ment Retard Dev Disabil Res Rev. 2006;12(4):305-12
(Abstract) (PDF)
User Study of a Spanish-language ClinicalTrials.gov Prototype System
Rosemblat G, Tse T
To appear in Proceedings of the American Medical Informatics Association Annual Conference (AMIA 2006), Washington, DC, November 2006 pp 659-664.
(Abstract) (PDF)
Using Dependence Relations in MeSH as a Framework for the Analysis of Disease Information in Medline
Vizenor L, Bodenreider O
Proceddings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM-2006) 2006:76-83
(Abstract) (PDF)
Using WordNet to Improve the Mapping of Data Elements to UMLS for Data Sources Integration
Mougin F, Burgun A, Bodenreider O
Proc AMIA Symp 2006:574-578.
(Abstract) (PDF)
Word Sense Disambiguation by Selecting the Best Semantic Type Based on Journal Descriptor Indexing: Preliminary Experiment
Humphrey SM, Rogers WJ, Kilicoglu H, Demner-Fushman D, Rindflesch TC
Journal of the American Society for Information Science and Technology. 2006 Jan 1;57(1):96-113.
(Abstract) (PDF)
 
Year 2005Back to top
A Consumer Health Informatics (CHI) Toolbox: Challenges and Implications
Bakker TA, Ryce AN, Logan RA, Tse T, Hutcherson L
Proceedings of AMIA Symposium 2005: 21-5.
(Abstract) (PDF)
A Consumer Health Informatics (CHI) Toolbox: Challenges and Implications
Bakker TA, Ryce AN, Logan RA, Tse T, Hutcherson LY
Proc. AMIA 2005: 21-25
(Abstract) (PDF)
Alignment of Multiple Ontologies of Anatomy: Deriving Indirect Mappings from Direct Mappings to a Reference
Zhang S, Bodenreider O
Proceedings of AMIA Annual Symposium 2005:864-868.
(Abstract) (PDF)
An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis
Wang H, Azuaje F, Bodenreider O
Proceedings of the 18th IEEE International Symposium on Computer-Based Medical Systems 2005:389-394.
(Abstract) (PDF)
An ontology of chemical entities helps identify dependence relations among Gene Ontology terms
Bergun A, Bodenreider O
Proceedings of the First International Symposium on Semantic Mining in Biomedicine (SMBM-2005) 2005.
(Abstract) (PDF)
Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal
Mougin F, Bodenreider O
Proceedings of AMIA Annual Symposium 2005:550-554.
(Abstract) (PDF)
Assessment of the National Library of Medicine's Health Disparities Plan: A Focus on Native American Outreach
Siegel ER, Wood FB, Dutcher GA, Ruffin A, Logan RA, Scott J
Journal of the Medical Library Association. 93:4 (October 2005): 10-20
(Abstract) (PDF)
A Text Corpora-Based Estimation of the Familiarity of Health Terminology
Zeng Q, Kin E, Crowell J, Tse T
VI International Symposium on Biological and Medical Data Analysis (ISBMDA), Aveiro, Portugal, 10-11 November 2005:184-92.
(Abstract) (PDF)
A Web Application to Support Consumer Health Vocabulary Development
Crowell J, Zeng QT, Tse T
Proceedings of AMIA Symposium Poster 2005: 932.
(Abstract) (PDF)
Biomedical Ontologies
Bodenreider O, Burgun A
In: Chen H, Fuller S, Jersh WR, Friedman C, editors. Medical Informatics: Advances in Knowledge Management and Data Mining in Biomedicine: Springer-Verlag; 2005. p. 211-236.
(Abstract) (PDF)
Classifying diseases with respect to anatomy: a study in SNOMED CT
Bergun A, Bodenreider O, Mougin F
Proceedings of AMIA Annual Symposium 2005:91-95.
(Abstract) (PDF)
Determining Prominent Subdomains in Medicine
Bernhardt PJ, Humphrey SM, Rindflesch TC
Proceedings of the AMIA Annual Symposium. 2005;:46-50.
(Abstract) (PDF)
Effects of Information and Machine Learning Algorithms on Word Sense Disambiguation with Small Datasets
Leroy G, Rindflesch TC
International Journal of Medical Informatics. 2005 Aug;74(7-8):573-85.
(Abstract) (PDF)
Enhancing Access to Patient Education Information: A Pilot Usability Study
Beaudoin DE, Rocha RA, Tse T
Proceedings of AMIA Symposium Poster 2005:892.
(Abstract) (PDF)
Evaluation of French and English MeSH Indexing Systems with a Parallel Corpus
Neveol A, Mork JG, Aronson AR, Darmoni SJ
AMIA Annu Symp Proc. 2005;:565-9
(Abstract) (PDF)
Fusion of Knowledge-intensive and Statistical Approaches for Retrieving and Annotating Textual Genomics Documents
Aronson AR, Demner-Fushman D, Humphrey SM, Lin J, Liu H, Ruch P, Ruiz ME, Smith LH, Tanabe LK, Wilbur WJ
Proc TREC 2005, 36-45
(Abstract) (PDF)
GenesTrace: Phenomic Knowledge Discovery Via Structured Terminologies
Cantor MN, Sarkar INK, Bodenreider O, Lussier YA
Pacific Symposium on Biocomputing 2005: World Scientific. 2005;:103-114.
(Abstract) (PDF)
Identifying Consumer-Friendly Display (CFD) Names for Health Concepts
Zeng QT, Tse T, Crowell J, Divita G, Roth L, Browne AC
Proceedings of AMIA Symposium 2005: 859-63.
(Abstract) (PDF)
Implementing RxNav, a RxNorm Browser
Zeng K, Bodenreider O, Nelson SJ
Proceedings of Medical Informatics Europe 2005 (CD-ROM) 2005:1268.
(Abstract) (PDF)
Issues in the Classification of Disease Instances with Ontologies
Bergun A, Bodenreider O, Jacquelinet C
Stud Health Technol Inform 2005;116:695-700.
(Abstract) (PDF)
Knowledge Integration for Bio-Threat Response
Backer A, Bodenreider O, Karp P, Kelly H, Loranger S, Musen M, Sriram R, Wroe C
Los Alamos White Paper
(Abstract) (PDF)
Linking the Gene Ontology to other biological ontologies
Bodenreider O, Burgun A
Proceedings of the ISMB'2005 SIG meeting on Bio-ontologies 2005:17-18.
(Abstract) (PDF)
Medical Facts to Support Inferencing in Natural Language Processing
Rindflesch TC, Pakhomov SV, Fiszman M, Kilicoglu H, Sanchex VR
Proceedings of the AMIA Annual Symposium. 2005;:634-38.
(Abstract) (PDF)
MedPost: A Part of Speech Tagger for BioMedical Text
Smith L, Rindflesch TC, Wilbure WJ
Bioinformatics. 2004 Sep 22;20(14):2320-1.
(Abstract) (PDF)
MedTag: A Collection of Biomedical Annotations
Smith L, Rindflesch TC, Wilbure WJ
Bioinformatics. 2004 Sep 22;20(14):2320-1.
(Abstract) (PDF)
Migrating the FMA from Protege to OWL
Golbreich C, Zhang S, Bodenreider O
Proceedings of the Eighth International Protege Conference 2005:108-111.
(Abstract) (PDF)
Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology
Bodenreider O, Aubry M, Burgun A
Pacific Symposium on Biocomputing 2005: World Scientific. 2005;:91-102.
(Abstract) (PDF)
Of Mice and Men: Aligning Mouse and Human Anatomies
Bodenreider O, Hayamizu TF, Ringwald M, De Coronado S, Zhang S
Proceedings of AMIA Annual Symposium 2005:61-65.
(Abstract) (PDF)
Ontology-driven Similarity Approaches to Supporting Gene Functional Assessment
Azuaje F, Wang H, Bodenreider O
Proceedings of the ISMB'2005 SIG meeting on Bio-ontologies 2005:9-10.
(Abstract) (PDF)
RxNav: A Progress Report
Zeng K, Bodenreider O, Nelson SJ
Proceedings of AMIA Annual Symposium 2005:1168.
(Abstract) (PDF)
Semantic Characteristics of MEDLINE Citations Useful for Therapeutic Decision-making
Sneiderman C, Demner-Fushman D, Fiszman M, Rindflesch TC
Proceedings of AMIA Annual Symposium, 2005;:1117.
(Abstract) (PDF)
Semantic Interpretation for the Biomedical Research Literature
Rindflesch TC, Fiszman M, Bisharah L
In Hsinchun C, Fuller S, Friedman C, Hersh w (eds.) Medical Informatics: Knowledge Management and Data Mining in Biomedicine. Springer: New York, pp. 399-422, 2005.
(Abstract) (PDF)
Semantic Representation of Consumer Questions and Physician Answers
Slaughter LA, Soergel D, Rindflesch TC
International Journal of Medical Informatics. August 23, 2005.
(Abstract) (PDF)
Semi-Automatic Indexing of Full Text Biomedical Articles
Gay CW, Kayaalp M, Aronson AR
AMIA Annu Symp Proc. 2005;:271-5
(Abstract) (PDF)
Supporting Access to Consumer Health Information Across Languages
Rosemblat G, Tse T, Gemoets D, Gillen JE, Ide NC
Proceedings of the 9th World Congress on Health Information and Libraries (ICML-9), September 20-23, 2005; Salvador, Bahia, Brazil.
(Abstract) (PDF)
The Foundational Model of Anatomy in OWL: experience and perspectives
Golbreich C, Zhang S, Bodenreider O
Proceedings of the Workshop on OWL: Experiences and Directions 2005.
(Abstract) (PDF)
The Importance of the Lexicon in Tagging Biological Text
Smith LH, Rindflesch TC, Wilbur WJ
Natural Language Engineering 2005.
(Abstract) (PDF)
The National Library of Medicine's Native American Outreach Portfolio: A Descriptive Overview
Wood FB, Siegel ER, Dutcher GA, Ruffin A, Logan RA
Journal of the Medical Library Association. 93:4 (October 2005): 21-34
(Abstract) (PDF)
Trial Registration at ClinicalTrials.gov between May and October 2005
Zarin DA, Tse T, Ide NC
New England Journal of Medicine 2005 December 29,353(26):2779-87.
(Abstract) (PDF)
Utilizing the UMLS for Semantic Mapping between Terminologies
Fung KW, Bodenreider O
Proceedings of AMIA Annual Symposium 2005:266-270.
(Abstract) (PDF)
Why Do We Need Probabilistic Approaches to Ontologies and the Associated Data?
Kayaalp M
Proc AMIA Symposium 2005
(Abstract) (PDF)
 
Year 2004Back to top
Abstraction Summarization for Managing the Biomedical Research Literature
Fiszman M, Rindflesch TC, Kilicoglu H
Proceedings of the HLT-NAACL Workshop on Computational Lexical Semantics. 2004;:76-83.
(Abstract) (PDF)
Adapting A Monolingual Consumer Health System for Cross-Language Information Retrieval
Rosemblat G, Tse T, Gemoets D
Advances in Knowledge Organization, Proceedings of the Eighth International ISKO Conference. 2004 July;9:315-321.
(Abstract) (PDF)
Aligning Knowledge Sources in the UMLS: Methods, Quantitative Results, and Applications
Bodenreider O, Burgun A
Medinfo. 2004 Sept.;2004:327-331.
(Abstract) (PDF)
Application of a Medical Text Indexer to an Online Dermatology Atlas
Kim GR , Aronson AR, Mork JG, Cohen BA, Lehmann CU
MedInfo. 2004 Sept.;2004:.
(Abstract) (PDF)
Assessing Readability of Consumer Health Information: An Exploratory Study
Gemoets D, Rosemblat G, Tse T, Logan R
Medinfo. 2004 Sept.;2004:869-73.
(Abstract) (PDF)
Comparing Associative Relationships Among Equivalent Concepts Across Ontologies
Zhang S, Bodenreider O
MedInfo. 2004 Sept.;2004: 459-463.
(Abstract) (PDF)
Design, Implementation and Management of a Web-based Data Entry System for ClinicalTrials.gov
Gillen JE, Tse T, Ide NC, McCray AT
Medinfo. 2004 Sept.;2004:1466-70.
(Abstract) (PDF)
Design of Genetics Home Reference: A New NLM Consumer Health Resource
Mitchell JA, Fun J, McCray AT
Journal of the American Medical Informatics Association. 2004 Nov.;11(6):439-447.
(Abstract) (PDF)
Development of a Test Collection of Manually Extracted Semantic Relationships in Health Consumer Texts
Slaughter LA, Rindflesch TC
MedInfo. 2004 Sept.;2004: 1865.
(Abstract) (PDF)
Evaluating Consumer Informatics: Learning from Health Campaign Research
Logan RA
Medinfo. 2004;2004:1147-51.
(Abstract) (PDF)
Failure Analysis of MetaMap Transfer (MMTx)
Divita G, Tse T, Roth L
Medinfo. 2004 Sept.;2004:763-7.
(Abstract) (PDF)
From Functional Similarity Among Gene Products to Dependence Relations Among Gene Ontology Terms (Abstract)
Bodenreider O, Aubry M, Burgun A
Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:53.
(Abstract) (PDF)
Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships
Wang H, Azuaje F, Bodenreider O, Dopazo J
Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'2004) 2004:25-31.
(Abstract) (PDF)
Gene Ontology-Driven Similarity for Gene Expression Correlation Analysis
Azuaje FJ, Bodenreider O, Wang H, Dopazo J
Proceedings of the second conference on Standards and Ontologies for Functional Genomics (SOFG 2) 2004:47.
(Abstract)
GenesTraceTM: Biological Knowledge Discovery via Structured Terminology
Sarkar IN, Cantor MN, Bodenreider O, Lussier YA
MedInfo.
(Abstract) (PDF)
Gene Terms and English Words: An Ambiguous Mix
Sehgal AK, Srinivasan P, Bodenreider O
Proceedings of the SIGIR 2004 Workshop on Search and Discovery in Bioinformatics 2004.
(Abstract) (PDF)
Helping Healthcare Consumers Understand: An "Interpretive Layer" for Finding and Making Sense of Medical Information
Soergel D, Tse T, Slaughter L
Medinfo. 2004 Sept.;2004:931-5.
(Abstract) (PDF)
How Two Korean Newspapers Covered a Public Health Crisis
Logan RA, Park J, Shin JH
Science Communication. 25:4:365-389 (June 2004)
(Abstract) (PDF)
Identifying Anatomical Concepts in Biomedical Text for Automatic Selection of Images
Bernhardt PJ, Rindflesch TC, Kilicoglu H, Tringali M
Medinfo. 2004 Sept.;2004: 1521.
(Abstract) (PDF)
Identifying Respiratory Findings in Emergency Department Reports for Biosurveillance using MetaMap
Chapman WW, Fiszman M, Dowling JN, Chapman BE, Rindflesch TC
Medinfo. 2004 Sept.;2004: 487-491.
(Abstract) (PDF)
Incorporating Ontology-Driven Similarity Knowledge Into Functional Genomics: An Exploratory Study
Bodenreider O, Azuaje F
Proceedings of the 2004 IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE-2004) 2004:317-324.
(Abstract) (PDF)
Investigating Implicit Knowledge in Ontologies with Application to the Anatomical Domain
Zhang S , Bodenreider O
Altman RB, Dunker AK, Hunter L, Jung TA, Klein TE, editors. Pacific Symposium on Biocomputing 2004: World Scientific. 2004;: 250-261.
(Abstract) (PDF)
Knowledge-intensive and Statistical Approaches to the Retrieval and Annotation of Genomics MEDLINE Citations
Aronson AR, Demner-Fushman D, Humphrey SM, Ide NC, Kim W, Liu H, Loanne RR, Mork JG, Smith LH, Tanabe LK, Wilbur WJ, Xie N
Proc TREC 2004, 503-11
(Abstract) (PDF)
Lessons Learned from Aligning two Representations of Anatomy
Zhang S, Mork P, Bodenreider O
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.
(Abstract) (PDF)
Mapping the Gene Ontology Into the Unified Medical Language System
Lomax J, McCray AT
Comparative and Functional Genomics
(Abstract) (PDF)
Methods for Diagnosing Physiological Conditions of Human Subjects from Multivariate Time Series Biosensor Data
Kayaalp M
Physiological Data Modeling Contest, the Twenty-First International Conference on Machine Learning (ICML), 2004 July.
(Abstract) (PDF)
Prevailing Impressions of Social Actors in Korean News Coverage of a Public Health Crisis
Logan RA, Shin JH, Park J
Science Communication. 25:4:399-418 (June 2004)
(Abstract) (PDF)
RxNav: A Semantic Navigation Tool for Clinical Drugs
Bodenreider O, Nelson SJ
Medinfo. 2004 Sept.;2004: 1530.
(Abstract) (PDF)
Strategies for Mapping Concepts in Gastrointestinal Endoscopy Reports to the UMLS Metathesaurus
Tringali M, Rindflesch TC, Kilicoglu H, Fiszman M, Bodenreider O
Medinfo. 2004 Sept.;2004: 1885.
(Abstract) (PDF)
Strategies for Supporting Consumer Health Information Seeking
McCray AT, Ide NC, Loane RR, Tse T
Medinfo. 2004 Sept.;2004:1152-6.
(Abstract) (PDF)
Summarization of an Online Medical Encyclopedia
Fiszman M, Rindflesch TC, Kilicoglu H
MedInfo. 2004 Sept.;2004: 506-510.
(Abstract) (PDF)
The NLM Indexing Initiative's Medical Text Indexer
Aronson AR, Mork JG, Gay CW, Humphrey SM, Rogers WJ
Medinfo. 2004 Sept.;2004: 268-272.
(Abstract) (PDF)
The Ontology-Epistemology Divide: A Case Study in Medical Terminology
Bodenreider O, Smith B, Burugn A
Proceedings of the Third International Conference on Formal Ontology in Information Systems (FOIS2004): IOS Press; 2004. p. 185-195.
(Abstract) (PDF)
The Unified Medical Language System (UMLS): Integrating Biomedical Terminology
Bodenreider O
Nucleic Acids Res; Database Issue. 2004;32: 267-70.
(Abstract) (PDF)
Using Natural Languge Processing, Locus Link, and the Gene Ontology to Compare OMIM to MEDLINE
Libbus B, Kilicoglu H, Rindflesch TC, Mork JG, Aronson AR
Proceedings of the HLT-NAACL Workshop on Linking the Biological Literature, Ontologies and Databases: Tools for Users. 2004;:69-76.
(Abstract) (PDF)
Using Symbolic Knowledge in the UMLS to Disambiguate Words in Small Datasets with a Naive Bayes Classifier
Leroy G, Rindflesch TC
Medinfo. 2004 Sept.;2004: 381-385.
(Abstract) (PDF)
 
Year 2003Back to top
Aligning Representations of Anatomy Using Lexical and Structural Methods
Zhang S , Bodenreider O
Proc. AMIA Symposium. 2003 Nov;:753-757.
(Abstract) (PDF)
An Evaluation of Hybrid Methods for Matching Biomedical Terminologies: Mapping the Gene Ontology to the UMLS
Cantor MN, SI N, Hartel F, Bodenreider O, Lussier YA
Stud Health Technol Inform. 2003;:62-67.
(Abstract) (PDF)
An Upper Level Ontology for the Biomedical Domain
McCray AT
Comp Funct Genom. 2003;4:80-4.
(Abstract) (PDF)
Biomedical Ontologies
Bodenreider O, Mitchell JA, McCray AT
Pacific Symposium on Biocomputing: World Scientific. 2003;:562-564.
(Abstract) (PDF)
Developing and Evaluating Criteria to Help Reviewers of Biomedical Informatics Manuscripts: A Case Report
Ammenwerth E, Wolff AC, Knaup P, Ulmer H, Skonetzki S, Van Bemmel JH, McCray AT, Haux R, Kulikowski C
J Am Med Inform Assoc. 2003 June.
(Abstract) (PDF)
Evaluation of WordNet as a Source of Lay Knowledge for Molecular Biology and Genetic Diseases: A Feasibility Study
Bodenreider O, Burgun A, Mitchell JA
Stud Health Technol Inform. 2003;95:379-384.
(Abstract) (PDF)
Exploring Adjectival Modification in Biomedical Discourse Across Two Genres
Bodenreider O, Pakhomov S
Proc. of the ACL, 2003 Workshop, Natural Language Processing in Biomedicine. 2003;:105-112.
(Abstract) (PDF)
Exploring Medical Expressions Used by Consumers and the Media: An Emerging View of Consumer Health Vocabularies
Tse T, Soergel D
AMIA Annual Symposium. 2003.
(Abstract) (PDF)
Exploring Semantic Groups Through Visual Approaches
Bodenreider O , McCray AT
Journal of Biomedical Informatics. 2003;36(6):414-432
(Abstract) (PDF)
From Phenotype to Genotype: Issues in Navigating the Available Information Resources
Mitchell JA , McCray AT , Bodenreider O
Methods of Information in Medicine. 2003;42(5):557-563.
(Abstract) (PDF)
Gene Indexing: Characterization and Analysis of NLM's GeneRIFs
Mitchell JA , Aronson AR , Mork JG , Folk LC , Humphrey SM , Ward JM
Proc. AMIA Symposium. 2003 Nov;:460-464.
(Abstract) (PDF)
Generating Hypotheses by Discovering Implicit Associations in the Literature: A Case Report of a Search for New Potential Therapeutic Uses for Thalidomide
Weeber M, Vos R, Klein H, De Jong-Van Den Berg LT, Aronson AR, Molema G
J Am Med Inform Assoc. ;10(3):252-9.
(Abstract) (PDF)
Graphical Visualization and Navigation of Genetic Disease Information
Bodenreider O , Mitchell JA
Proc. AMIA Symposium. 2003 Nov;:792.
(Abstract) (PDF)
Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts
Fiszman M, Rindflesch TC, Kilicoglu H
Proc. AMIA Symposium. 2003 Nov;:239-243.
(Abstract) (PDF)
Interpreting Hypernymic Propositions in an Online Medical Encyclopedia
Fiszman M, Rindflesch TC, Kilicoglu H
Proc. AMIA Symposium. 2003 Nov;:840.
(Abstract) (PDF)
Knowledge Augmentation for Aligning Ontologies: An Evaluation in the Biomedical Domain
Zhang S , Bodenreider O
Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference. 2003: 109-114.
(Abstract) (PDF)
Language and Vocabulary Tools
Brown AC , Divita Guy , Aronson AR , McCray AT
Proc. AMIA Symposium. 2003 Nov;:.
(Abstract) (PDF)
Machine Translation-Supported Cross Language Information Retrieval for a Consumer Health Resource
Rosemblat G, Gemoets D, Browne AC, Tse T
AMIA Annual Symposium. 2003.
(Abstract) (PDF)
Methods for Accurate Retrieval of MEDLINE Citations in Functional Genomics
Kayaalp, Mehmet , Aronson, Alan R , Humphrey, Susanne M, Ide, Nicholas C, Tanabe, Lorraine K
Proceedings of the Text Retrieval Conference (TREC-2003). 2003;: 175-84.
(Abstract) (PDF)
Procedures for Mapping Vocabularies from Non-Professional Discourse and a Case Study from the Medical Domain
Tse T, Soergel D
ASIST Annual Meeting. 2003.
(Abstract) (PDF)
Search Failures in Consumer Health Information Systems
McCray AT, Tse Tony
Proc. AMIA Symposium Proceedings. 2003 November; :431-434.
(Abstract) (PDF)
Semantic Integration in Biomedicine
Bodenreider O , Zhang S
Proceedings of the Semantic Integration Workshop at the Second International Semantic Web Conference. 2003;: 156-157.
(Abstract) (PDF)
Semantic Relations Asserting the Etiology of Genetic Diseases
Rindflesch TC , Libbus B , Hristovski D , Aronson AR , Kilicoglu H
Proc. AMIA Symposium. 2003 Nov;:554-558.
(Abstract) (PDF)
Strength in Numbers: Exploring Redundancy in Hierarchical Relations Across Biomedical Terminologies
Bodenreider O
Proc. AMIA Symposium. 2003 Nov;101-105:.
(Abstract) (PDF)
The Genetics Home Reference: A New NLM Consumer Health Resource
Mitchell JA , McCray AT
Proc. AMIA Symposium. 2003 Nov;:936.
(Abstract) (PDF)
The Interaction of Domain Knowledge and Linguistic Structure in Natural Language Processing: Interpreting Hypernymic Propositions in Biomedical Text
Rindflesch TC , Fiszman M
Journal of Biomedical Informatics. 2003;36(6):462-77.
(Abstract) (PDF)
The UMLS Knowledge Source Server: An Object Model For Delivering UMLS Data
Bangalore A , Thorn KE , Tilley C , Peters L
Proc. AMIA Symposium. 2003 Nov;:51-55.
(Abstract) (PDF)
The UMLS Semantic Network and the Semantic Web
Kashyap V
Proc. AMIA Symposium. 2003 Nov;:351-355.
(Abstract) (PDF)
Towards Linking Patients and Clinical Information: Detecting UMLS Concepts in E-mail
Brennan PF, Rindflesch TC
J Biomed Inform. 2003 Aug-Oct;36(4-5):334-41
(Abstract) (PDF)
Towards Semi-Automatic Generation of Biomedical Ontologies
Kashyap V , Ramakrishan C , Rindflesch TC
Proc. AMIA Symposium. 2003 Nov;:886.
(Abstract) (PDF)
 
Year 2002Back to top
A Conceptual Framework for the Biomedical Domain
McCray AT, Bodenreider O
The Semantics of Relationships: An Interdisciplinary Perspective. Boston: Kluwer Academic Publishers. 2002;:181-198.
(Abstract) (PDF)
Assessing the Consistency of a Biomedical Terminology Through Lexical Knowledge
Bodenreider O, Burgun A, Rindflesch TC
Int J Med Inf. 2002 Dec 4;67(1-3):85-95.
(Abstract) (PDF)
Assessing the Consistency of a Biomedical Terminology Through Lexical Knowledge
Bodenreider O, Burgun A, Rindflesch TC
Proc. of the Workshop on Natural Language Processing in Biomedical Applications. 2002;:77-83.
(Abstract) (PDF)
A Study of Abbreviations in MEDLINE Abstracts
Liu H, Aronson AR, Friedman C
Proc AMIA Symp. 2002 ;():464-8.
(Abstract) (PDF)
Characterizing the Definitions of Anatomical Concepts in WordNet and Specialized Sources
Bodenreider O, Burgun A
Proc. of the First Global WordNet Conference. 2002;:223-230.
(Abstract) (PDF)
Clinicaltrials.gov: Linking Patients to Medical Research
McCray AT
Cancer Informatics: Essential Technologies for Clinical Trials. New York: Springer Verlag. 2002;:302-307.
(Abstract) (PDF)
Discovering Protein Similarity Using Natural Language Processing
Sarkar IN, Rindflesch TC
Proc AMIA Symp. 2002 ;():677-81.
(Abstract) (PDF)
Evaluation of the UMLS as a Terminology and Knowledge Resource for Biomedical Informatics
Bodenreider O, Mitchell JA, McCray AT
Proc. of AMIA Annual Symposium. 2002;:61-65.
(Abstract) (PDF)
Experiences in Visualizing and Navigating Biomedical Ontologies and Knowledge Bases
Bodenreider O
Proc. of the ISMB'SIG meeting; Bio-ontologies. 2002;:29-32.
(Abstract) (PDF)
Exploring Text Mining from MEDLINE
Srinivasan P, Rindflesch T
Proc AMIA Symp. 2002 ;():722-6.
(Abstract) (PDF)
Finding UMLS Metathesaurus Concepts in MEDLINE
Srinivasan S, Rindflesch TC, Hole WT, Aronson AR, Mork JG
Proc AMIA Symp. 2002 ;():727-31.
(Abstract) (PDF)
From Phenotype to Genotype: Navigating the Available Information Resources
Mitchell JA, McCray AT, Bodenreider O
Proc. of AMIA Annual Symposium. 2002;:1109.
(Abstract) (PDF)
NLP-Based Information Extraction for Managing the Molecular Biology Literature
Libbus B, Rindflesch TC
Proc AMIA Symp. 2002 ;():445-9.
(Abstract) (PDF)
Overcoming Impediments to Effective Health and Biomedical Digital Libraries, JCDL
Hersh WJ, Velterop J, McCray AT, Eynsenbach G, Boguski M
JCDL. 2002;: 360.
(Abstract) (PDF)
Panel on Digital Preservation, JCDL
Ray J, Dale R, Moore R, Reich V, Underwood W, McCray AT
Panel on Digital Preservation, JCDL. 2002;: 365-367.
(Abstract) (PDF)
Representation of Roles in Biomedical Ontologies: A Case Study in Functional Genomics
Burgun A, Bodenreider O, Le Duff F, Moussouni F, Loreal O
Proc AMIA Symp. 2002 ;():86-90.
(Abstract) (PDF)
Semantic Processing for Enhanced Access to Biomedical Knowledge
Rindflesch TC, Aronson AR
Real World Semantic Web Applications, IOS Press. 2002;:157-72.
(Abstract) (PDF)
The Lexical Properties of the Gene Ontology (GO)
McCray AT, Browne AC, Bodenreider O
Proc. of AMIA Annual Symposium. 2002;:504-508.
(Abstract) (PDF)
Unsupervised, Corpus-Based Method for Extending a Biomedical Terminology
Bodenreider O, Rindflesch TC, Burgun A
Proc. of the ACL Workshop; Natural Language Processing in the Biomedical Domain. 2002;:53-60.
(Abstract) (PDF)
Web Crawling Agents for Retrieving Biomedical Information
Srinivasan P, Mitchell JA, Bodenreider O, Pant G, Menczer F
Proc. of the International Workshop on Bioinformatics and Multi-Agent Systems (BIXMAS). 2002 Jul.
(Abstract) (PDF)
 
Year 2001Back to top
'Ome Sweet 'Omics - A Genealogical Treasury of Words
Lederberg J, McCray AT
Genealogical Treasury of Words. Scientist. 2001;15(7):8.
(Abstract) (PDF)
Aggregating UMLS Semantic Types for Reducing Conceptual Complexity
McCray AT, Burgun A, Bodenreider O
Medinfo. 2001 ;10(Pt 1):216-20.
(Abstract) (PDF)
An Object-Oriented Model for Representing Semantic Locality in the UMLS
Bodenreider O
Medinfo. 2001 ;10(Pt 1):161-5.
(Abstract) (PDF)
Aspects of the Taxonomic Relation in the Biomedical Domain
Burgun A, Bodenreider O
FOIS. 2001;: 222-233
(Abstract) (PDF)
Automatic Indexing by Discipline and High-Level Categories: Methodology and Potential Applications
Humphrey SM, Rindflesch TC, Aronson AR
Advances in classification research. Proc. of the 11th ASIST SIG/CR Classification Research Workshop. 2001.
(Abstract) (PDF)
Automatic MeSH Term Assignment and Quality Assessment
Kim W, Aronson AR, Wilbur WJ
Proc AMIA Symp. 2001 ;():319-23.
(Abstract) (PDF)
Circular Hierarchical Relationships in the UMLS: Etiology, Diagnosis, Treatment, Complications, and Prevention
Bodenreider O
Proc AMIA Symp. 2001 ;():57-61.
(Abstract) (PDF)
Comparing Terms, Concepts and Semantic Classes in WordNet and the Unified Medical Language System
Burgun A, Bodenreider O
Proc. of the NAACL'2001 Workshop; WordNet and Other Lexical Resources: Applications, Extensions and Customizations. 2001;:77-82.
(Abstract) (PDF)
Developing a Test Collection for Biomedical Word Sense Disambiguation
Weeber M, Mork JG, Aronson AR
Proc AMIA Symp. 2001 ;():746-50.
(Abstract) (PDF)
Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program
Aronson AR
Proc AMIA Symp. 2001 ;():17-21.
(Abstract) (PDF)
Evaluating UMLS Strings for Natural Language Processing
McCray AT, Bodenreider O, Malley JD, Browne AC
Proc AMIA Symp. 2001 ;():448-52.
(Abstract) (PDF)
Lexically-Suggested Hyponymic Relations Among Medical Terms and Their Representation in the UMLS
Bodenreider O, Burgun A, Rindflesch TC
Proc. of TIA'2001; Terminology and Artificial Intelligence. 2001;:11-21.
(Abstract) (PDF)
Mapping the UMLS Semantic Network into General Ontologies
Burgun A, Bodenreider O
Proc AMIA Symp. 2001 ;():81-5.
(Abstract) (PDF)
Methods for Exploring the Semantics of the Relationships Between Co-Occurring UMLS Concepts
Burgun A, Bodenreider O
Medinfo. 2001 ;10(Pt 1):171-5.
(Abstract) (PDF)
Principles for Digital Library Development
McCray AT, Gallagher ME
Communications of the ACM. 2001 May; 44(5): 48-54.
(Abstract) (PDF)
Relationships Among Knowledge Structures: Vocabulary Integration Within a Subject Domain
Bodenreider O, Bean CA
Relationships in the organization of knowledge: Kluwer. 2001;:81-98.
(Abstract) (PDF)
 
Year 2000Back to top
Argument Identification for Arterial Branching Predications Asserted in Cardiac Catheterization Reports
Rindflesch TC, Bean CA, Sneiderman CA
Proc AMIA Symp. 2000 ;():704-8.
(Abstract) (PDF)
A Semantic Navigation Tool for the UMLS
Bodenreider O
Proc. of AMIA Annual Symposium. 2000;: 971.
(Abstract) (PDF)
Automatic Indexing by Discipline and High-Level Category: Methodology and Potential Applications
Humphrey S, Rindflesch TC, Aronson AR
Proc. of the 11th SIG/CR Classification Research Workshop. 2000;:103-16.
(Abstract) (PDF)
Better Access to Information About Clinical Trials
McCray AT
Ann Intern Med. 2000 Oct 17;133(8):609-14.
(Abstract) (PDF)
Comment les Usagers Accedent a l'Information Medicale Aux USA: l'Exemple de MEDLINEplus [How Consumers Access Health Information in the USA: The MEDLINEplus Example]
Bodenreider O
Innovation et Technologie en Biologie et Medecine. 2000;21(5):286-90.
(Abstract) (PDF)
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]
Botti G, Bodenreider O, Burgun A, Le Beux P, Fieschi M
Innovation et Technologie en Biologie et Médecine. 2000;21(5):291-97.
Design and Implementation of a National Clinical Trials Registry
McCray AT, Ide NC
J Am Med Inform Assoc. ;7(3):313-23.
(Abstract) (PDF)
Developing Web Browser Recording Tools Using Server-Side Programming Technology
Lu CJ, Bangalore A, Tse T
Proc. of WebNet 2000, World conference on WWW and Internet: Association for the Advancement of Computing in Education. 2000;:372-7.
(Abstract) (PDF)
EDGAR: Extraction of Drugs, Genese, and Relations from the Biomedical Literature
Rindflesch TC, Tanabe L, Weinstein JN, Hunter L
Pac Symp Biocomput. 2000 ;():517-28.
(Abstract) (PDF)
Extracting Molecular Binding Relationships from Biomedical Text
Rindflesch TC, Rajan J, Hunter L
Proc. of the 6th Applied Natural Language Processing Conference. 2000;: 188-95.
(Abstract) (PDF)
Extracting the Lowest-Frequency Words: Pitfalls and Possibilities
Weeber M, Vos R
Computational Linguistics. 2000;26(3):301-17.
(Abstract) (PDF)
Identifying Proper Names in Parallel Medical Terminologies
Bodenreider O, Zweigenbaum P
Stud Health Technol Inform. 2000 ;77():443-7.
(Abstract) (PDF)
Modelling Syllepse in Medical Knowledge Bases with Application in the Domain of Organ Failure and Transplantation
Jacquelinet C, Bodenreider O, Burgun A
Proc. of OntoLex; Workshop on Ontologies and Lexical Knowledge Bases 2000.
(Abstract) (PDF)
Strategies d'Identification des Noms Propres a Partir de Nomenclatures Medicales Paralleles
Bodenreider O, Zweigenbaum P
Traitement Automatique des Langues. 2000;41(3):727-757.
(Abstract) (PDF)
System Expansion and Integration with Agents in HSTAT
Xiaocheng L, Prettyman M, Antonucci R
Proc. of the World Multiconference on Systemics, Cybernetics, and Informatics. 2000 Jul.;: 2000.
Text-Based Discovery in Biomedicine: The Architecture of the DAD-System
Weeber M, Klein H, Aronson AR, Mork JG, de Jong-van den Berg LT, Vos R
Proc AMIA Symp. 2000 ;():903-7.
(Abstract) (PDF)
The NLM Indexing Initiative
Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ
Proc AMIA Symp. 2000 ;():17-21.
(Abstract) (PDF)
Towards Efficient XML Query Processing, XML
Shin DW
Developer Day in XML 2000: Graphic Communications Association. 2000;:1-45.
Usability Issues in Developing a Web-Based Consumer Health Site
McCray AT, Dorfman E, Ripple A, Ide NC, Jha M, Katz DG, Loane RF, Tse T
Proc AMIA Symp. 2000 ;():556-60.
(Abstract) (PDF)
Using UMLS Semantics for Classification Purposes
Bodenreider O
Proc AMIA Symp. 2000 ;():86-90.
(Abstract) (PDF)