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  • McCray AT, Bodenreider O. A Conceptual Framework for the Biomedical Domain The Semantics of Relationships: An Interdisciplinary Perspective. Boston: Kluwer Academic Publishers. 2002;:181-198.
  • Jaeger S. A geomedical approach to Chinese medicine: The origin of the yin-yang symbol. Recent Advances in Theories and Practice of Chinese Medicine, Haixue Kuang (Ed.), ISBN: 978-953-307-903-5, InTech, 2012.
  • Borovikov E, Zavorin I. A multi-stage document processing approach To Arabic text recognition. Guide to OCR for Arabic Scripts. 2012:55-78.
  • Rajaraman S, Candemir S, Xue Z, Alderson P, Thoma G, Antani SK. A Novel Stacked Model Ensemble for Improved TB Detection in Chest Radiographs. In Santosh KC et al. (Eds.). Medical Imaging: Artificial Intelligence, Image Recognition, and Machine Learning Techniques. (pp. 1-26). New York, NY: CRC Press, Taylor & Francis Group.
  • Zweigenbaum P, Demner-Fushman D. Advanced Literature-Mining Tools. In Edwards D, Stajich J, and Hansen D. (Editors). Bioinformatics: Tools and Applications. Springer 2009.
  • Almubarak H, Guo P, Stanley RJ, Long LR, Antani SK, Thoma GR. Algorithm Enhancements for Improvement of Localized Classification of Uterine Cervical Cancer Digital Histology Images. in Handbook of Research on Emerging Perspectives on Healthcare Information Systems and Informatics,. IGI Global (Hershey, PA).
  • Bodenreider O. API: NDF-RT
  • Bodenreider O. API: Prescribable
  • Aronson AR. API: Semantic Knowledge Representation
  • Demner-Fushman D, Elhadad N. Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing. IMIA Yearbook of Medical Informatics 2016.
  • Lindberg, DAB, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM (Editor). At the helm of the world's largest biomedical library: 2005 Interviews with Donald A.B. Lindberg, MD Conversations with Medical Informatics Pioneers: An oral history project.
  • Zweigenbaum P, Demner-Fushman D. Bioinformatics: Tools and Applications. Springer 2009.
  • Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11
  • 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): p. 67-79.
  • Simpson MS, Demner-Fushman D. Biomedical Text Mining: A Survey of Recent Progress. In Charu C. Aggarwal and ChengXiang Zhai, Editors. Mining Text Data. (Springer) 2011.
  • Jaeger S. Chest X-ray Screening System: Segmentation Module – v3
  • Mamlin BW, Overhage JM, Tierney WM, Dexter PR, McDonald CJ. Clinical decision support within the Regenstrief Medical Record System [Book//chapter] Health Informatics, Berner, Eta S. (Ed.) 2nd ed., 2007, 190-21.
  • 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.
  • Hristovski D, Kastrin A, Peterlin B, Rindflesch TC. Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation Lecture Notes in Bioinformatics. Springer
  • Thamizhvani TR, Lakshmanan S, Rajaraman S. Computer Aided Diagnosis of Skin Tumours from Dermal Images. Hemanth D., Smys S. (eds) Computational Vision and Bio Inspired Computing. Lecture Notes in Computational Vision and Biomechanics, vol 28. Springer, Cham
  • Tang P, McDonald CJ. Computer-Based Patient-Record Systems - Chapter 9. In Shortliffe E, Perreault L, eds. Medical Informatics. New York: springer. 2001:327-358. DOI: 10.1007/978-0-387-21721-5_9.
  • Long LR, Antani SK, Thoma GR, Deserno TM. Content-based Image Retrieval For Advancing Medical Diagnostics, Treatment, and Education New Technologies for Advancing Healthcare and Clinical Practices. June 2011:1-17.
  • Thoma GR, Razi A, Seamans J, Strupp-Adams A, Edwards L, Gao J, Ledoux MT. Dataset: AnatQuest
  • Demner-Fushman D, Kilicoglu H. Dataset: CHQA Named Entity Dataset
  • McDonald CJ, Abhyankar S, Taft L. Dataset: common units of measure - subset of the Unified Code for Units of Measure.
  • McDonald C. Dataset: LOINC Panels and Forms file
  • McDonald CJ, Vreeman D, Goodwin RM. Dataset: LOINC Top 2000+ Lab Observations and Mapper's Guide
  • McDonald C, Vreeman D, Goodwin RM. Dataset: LOINC Top 300+ Lab Orders
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: newborn screening LOINC codes (AHIC panel).
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: Newborn screening LOINC panel.
  • Abhyankar S, Goodwin RM, Zuckerman A, McDonald CJ. Dataset: newborn screening results annotated example HL7 electronic message guidance (v 5.2).
  • Demner-Fushman D, Roberts K. Dataset: Question Decomposition Data
  • Demner-Fushman D, Roberts K. Dataset: Question Type Data
  • Kilicoglu H. Dataset: Sortal Anaphora Dataset
  • Kilicoglu H. Dataset: Structured Drug Product Label (SPL) Coreference Dataset
  • Bodenreider O. Disease Ontologies In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H, editors. Encyclopedia of Systems Biology: Springer; 2013. p. 578-581.
  • McDonald CJ, Tang PC, Hripcsak G. Electronic Health Record Systems. . In: Shortliffe EH, Cimino JJ, editors. Biomedical Informatics: Computer Applications in Healthcare and Biomedicine 4th ED [Internet]. London: Springer London; 2014. p. 391–421. Available from: http://link.springer.com/10.1007/978-1-4471-4474-8.
  • Collen MF, Sittig DF (Interviewer and Editor), Ash JS (Editor), Goodwin RM (Editor). Engineering Computerized Multiphasic Health Screening: 2005 Interview of Morris F. Collen, MD. Conversations with Medical Informatics Pioneers: An oral history project.
  • Yao S, Yu H, AliAkbarpour H, Seetharaman G, Palaniappan K. EpiX: A 3D Measurement Tool for Heritage, Archeology, and Aerial Photogrammetry Heritage Preservation, pp. 47-66, 2018.
  • Ash J, Sittig D. Everything Electronic Medical Records: Systems, Standards and Studies Conversations with Medical Informatics Pioneers: An oral history project.
  • Borovikov E, Vajda S. FaceMatch: real-world face image retrieval. In: Santosh K., Hangarge M., Bevilacqua V., Negi A. (eds) Recent Trends in Image Processing and Pattern Recognition. RTIP2R 2016. Communications in Computer and Information Science, vol 709. Springer, Singapore. 405-419.
  • Detmer DE, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM (Editor). Fostering Health Policy and the Biomedical Informatics Profession: 2006 Interview of Don Detmer. Conversations with Medical Informatics Pioneers: An oral history project.
  • Warner HR, Sittig DF (Interviewer and Editor), Ash JS (Editor), Goodwin RM (Editor). Founder of the HELP System and the Utah Medical Informatics Program: 2005 Interview of Homer R. Warner, Sr. Conversations with Medical Informatics Pioneers: An oral history project.
  • Barnett GO, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM (Editor). From "Farm Boy" to Director of the Laboratory of Computer Science: 2004 Interview of G. Octo Barnett Conversations with Medical Informatics Pioneers: An oral history project.
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin R, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), Release 1, STU Release 4. US Realm, Chapter 5, Clinical Genomics Results Reporting. Published for May 2017 Ballot.
  • McCray AT. Informatics Research, Development, and Training at the Lister Hill National Center for Biomedical Communications In: Yearbook of Medical Informatics 03. Stuttgart: Schattauer Verlag; 2003. pp 193-203.
  • Ash JS (Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM (Editor). Introduction Conversations with Medical Informatics Pioneers: An oral history project.
  • McDonald CJ, Hill G. IUPAC Silver Book- Compendium of Terminology and Nomenclature of Properties in Clinical Laboratory Sciences - Chapter 8 - Kinds-of-Quantity of Dimension One. SI Unit 1. Royal Society of Chemistry; 2009. doi:10.1039/978178262245.1-00075.
  • Fung KW, Bodenreider O. Knowledge representation and ontologies. Richesson RL, Andrews JE (Eds.). Clinical Research Informatics, Health Informatics, DOI 10.1007/978-1-84882-448-5_14, Springer-Verlag London Limited Publishing 2012.
  • McDonald CJ. Logical Observation Identifiers Names and Codes for In Vitro Diagnostic Test; Guidance for Industry and Food and Drug Administration Staff. Silver Spring, Md: Center for Devices and Radiological Health, FDA, 2018.
  • Jaeger S. Malaria Datasets
  • Gill MJ, Pearson G, Neve L, Miernicki G, Antani SK, Thoma GR. Mobile App: ReUnite iOS app
  • Thoma GR. Mobile App: Turning the Pages
  • 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
  • Borovikov E, Vajda S, Lingappa G, Bonifant MC. Parallel Computing in Face Image Retrieval: Practical Approach to the Real-World Image Search. Multi-Core Computer Vision and Image Processing for Intelligent Applications. IGI Global, 2017. 155-189. Web. 12 Sep. 2016. doi:10.4018/978-1-5225-0889-2.ch006
  • Thoma GR. Public Access to Anatomic Images Chapter in: Medical Informatics: Knowledge Management and Data Mining in Biomedicine
  • Bodenreider O, Bean CA. Relationships Among Knowledge Structures: Vocabulary Integration Within a Subject Domain. In: Bean A, Green R, editors. Relationships in the organization of knowledge. Springer; 2001. pp. 81-98.
  • Kilicoglu H. Software: Bio-SCoRes
  • Neve L, Long LR, Antani SK. Software: Boundary Marking Tool 2 (BMT2)
  • Kayaalp M, Dodd Z, Browne AC, Sagan, P, McDonald CJ. Software: NLM-Scrubber
  • Thoma GR, Ford G, Demner-Fushman D, Antani SK, Chung M. Software: Panorama
  • Mork JG, Aronson AR. The Medical Text Indexer (MTI) system for indexing biomedical literature. book chapter submitted to monograph Indexing Specialities: Medicine. Edited by L. Pilar Wyman. Medford, NJ: Information Today, Inc., in association with the American Society of Indexers, Phoenix, AZ. 2010.
  • Tse T, Zarin D, Williams R, Ide N. The role and importance of clinical trial registries and results databases In: Gallin JI, Ognibene FP, eds, Principles and Practice of Clinical Research. 3rd ed. Amsterdam: Academic Press; 2012: 171-81.
  • Matheson NW, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM (Editor). The Woman Behind the NLM’s Integrated Advanced Information Management Systems (IAIMS) Initiative: 2005 Interview of Nina Matheson. Conversations with Medical Informatics Pioneers: An oral history project.
  • McDonald CJ. Top LOINC Codes – Orders and Observations
  • Antani SK. Tuberculosis Chest X-ray Image Data Sets
  • Williams RJ. Tutorial: ClinicalTrials.gov: Registration and Results Submission Requirements
  • Cimino JJ. Tutorial: meeting data access and reporting requirements with the NIH’s Biomedical Translational Research Information System (BTRIS).
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 14, Use Case – Clinical Genomics Code Systems. in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin RM, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. US Realm, Chapter 5, Use Case – Clinical Genomics Results Reporting in HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), DTSU3. HL7 International (Ann Arbor).
  • Morrison SM. Web Interface: Genetics Home Reference
  • Lingappa G, Thoma GR, Antani SK. Web Interface: MyMorph
  • Demner-Fushman D, Antani SK, Simpson M. Web Interface: Open-I
  • Bodenreider O. Web Interface: RxMix
  • Bodenreider O. Web Interface: RxNav