Abstract
Clinical data that may be used in a secondary capacity to support research activities are regularly stored in three significantly different formats: (1) structured, codified data elements; (2) semi-structured or unstructured narrative text; and (3) multi-modal images. In this manuscript, we will describe the design of a computational system that is intended to support the ontology-anchored query and integration of such data types from multiple source systems. Additional features of the described system include (1) the use of Grid services-based electronic data interchange models to enable the use of our system in multi-site settings and (2) the use of a software framework intended to address both potential security and patient confidentiality concerns that arise when transmitting or otherwise manipulating potentially privileged personal health information. We will frame our discussion within the specific experimental context of the concept-oriented query and integration of correlated structured data, narrative text, and images for cancer research.
Similar content being viewed by others
References
Cimino JJ: From data to knowledge through concept-oriented terminologies: experience with the Medical Entities Dictionary. J Am Med Inform Assoc 7(3):288–297, 2000
Sujansky W: Heterogeneous database integration in biomedicine. J Biomed Inform 34(4):285–298, 2001
Kamal J, et al: Information warehouse as a tool to analyze computerized physician order entry order set utilization: opportunities for improvement. AMIA Annu Symp Proc 2003:336–340, 2003
Prather JC, et al: Medical data mining: knowledge discovery in a clinical data warehouse. Proc AMIA Annu Fall Symp 1997:101–105, 1997
Brown M, et al: CAD in clinical trials: current role and architectural requirements. Comput Med Imaging Graph 31(4–5):332–337, 2007
Kamauu AW, et al: Informatics in radiology (infoRAD): vendor-neutral case input into a server-based digital teaching file system. Radiographics 26(6):1877–1885, 2006
NCIA: Reference Image Database to Evaluate Response (RIDER). Available at http://ncia.nci.nih.gov/ncia/collections. Cited 2007
Sigal R: PACS as an e-academic tool International Congress series 2005, 1281, CARS 2005: Computer Assisted Radiology and Surgery, pp. 900–904
Boochever SS: HIS/RIS/PACS integration: getting to the gold standard. Radiol Manage 26:16–24, 2004
Gruber TR: Toward principles for the design of ontologies used for knowledge sharing. In: Guarino N, Poli R Eds. Formal Ontology in Conceptual Analysis and Knowledge RepresentationNorwell: Kluwer, 1993
Joseph P, Bruce GB: Ontology-guided knowledge discovery in databases. In: Proceedings of the international conference on knowledge capture. Victoria, British Columbia, Canada: ACM Press, 2001
Smith B, Kumar A: On controlled vocabularies in bioinformatics: a case study in the gene ontology. Biosilico: Drug Discovery Today 2(1):246–252, 2004
Gurcan MN, et al: Lung nodule detection on thoracic computed tomography images: preliminary evaluation of a computer-aided diagnosis system. Med Phys 29(11):2552–2558, 2002
Ebbert JO, Dupras DM, Erwin PJ: Searching the medical literature using PubMed: a tutorial. Mayo Clin Proc 78(1):87–91, 2003
Olson GM, et al: Collaboratories to support distributed science: the example of international HIV/AIDS research. In: Proceedings of SAICSIT, South Africa. Victoria, British Columbia, Canada: ACM Press, 2002
Butler D: Data, data, everywhere. Nature 414(6866):840–841, 2001
Marks RG, Conlon M, Ruberg SJ: Paradigm shifts in clinical trials enabled by information technology. Stat Med 20(17–18):2683–2696, 2001
Payne PR, Greaves AW, Kipps TJ: CRC clinical trials management system (CTMS): an integrated information management solution for collaborative clinical research. AMIA Annu Symp Proc 2003:967, 2003
Kuchenbecker J, et al: Use of internet technologies for data acquisition in large clinical trials. Telemed J E Health 7(1):73–76, 2001
Marks L, Power E: Using technology to address recruitment issues in the clinical trial process. Trends Biotechnol 20(3):105–109, 2002
Bates DW, et al: A proposal for electronic medical records in U.S. primary care. J Am Med Inform Assoc 10(1):1–10, 2003
Sung NS, et al: Central challenges facing the national clinical research enterprise. JAMA 289(10):1278–1287, 2003
Bates DW, et al: Effect of computerized physician order entry and a team intervention on prevention of serious medication errors. JAMA 280(15):1311–1316, 1998
Huang H, et al: Picture archiving and communication systems (PACS) in medicine, New York: Springer, 1991
Duerinckx AJ, Pisa EJ: Filmless picture archiving and communication system (PACS) in diagnostic radiology. Proc SPIE 318:9–18, 1982
Gurcan MN, et al: GridImage: a novel use of grid computing to support interactive human and computer-assisted detection decision support. J Digit Imaging 20:160–171, 2007
Craver JM, Gold RS: Research collaboratories: their potential for health behavior researchers. Am J Health Behav 26(6):504–509, 2002
Kukafka R, et al: Grounding a new information technology implementation framework in behavioral science: a systematic analysis of the literature on IT use. J Biomed Inform 36(3):218–227, 2003
Johnson MS, Gonzales MN, Bizila S: Responsible conduct of radiology research part V. The health insurance portability and accountability act and research. Radiology 237(3):757–764, 2005
Liu BJ, Zhou Z, Huang HK: A HIPAA-compliant architecture for securing clinical images. J Digit Imaging 19(2):172–180, 2006
Amendolia SR, et al: MammoGrid: a service oriented architecture based medical grid application. In: 3rd International Conference on Grid and Cooperative Computing, Wuhan, China, 2004
Blanquer I, et al: A Middleware grid for storing, retrieving and processing DICOM medical images. In: Workshop on Distributed Databases and Processing in Medical Image Computing (DIDAMIC), Rennes, France, 2004
Espert IB, Garcaa VH, Quilis JD: An OGSA middleware for managing medical images using ontologies. J Clin Monit Comput 19(4–5):295–305, 2005
Montagnat J, et al: Medical image content-based queries using the grid. In: HealthGrid’03, France, Lyon, 2003
Power D, et al: A relational approach to the capture of DICOM files for Grid-enabled medical imaging databases. In: ACM symposium on applied computing, Cyprus, Nicosia, 2004, pp 272–279
Foster I, Kesselman C: The Grid 2: blueprint for a new computing infrastructure, 2nd edition. New York: Morgan Kaufman, 2003, p. 748
Payne PR, et al: Conceptual knowledge acquisition in biomedicine: a methodological review. J Biomed Inform 40:582–602, 2007
NLM: Unified Medical Language System. Available at http://www.nlm.nih.gov/research/umls/meta2.html. Cited 2007
Bodenreider O: Using UMLS semantics for classification purposes. Proc AMIA Symp 2000:86–90, 2000
Campbell KE, et al: Representing thoughts, words, and things in the UMLS. J Am Med Inform Assoc 5(5):421–431, 1998
Thomas BJ, et al: Automated computer-assisted categorization of radiology reports. Am J Roentgenol 184(2):687–690, 2005
Tsui F-C, et al: Value of ICD-9-coded chief complaints for detection of epidemics. J Am Med Inform Assoc 9:S41–S47, 2002
Friedman C, et al: Automated encoding of clinical documents based on natural language processing. J Am Med Inform Assoc 11(5):392–402, 2004
Srinivasan S, et al: Finding UMLS Metathesaurus concepts in MEDLINE. In: American Medical Informatics Association Annual Symposium, 2002, pp 727–731
Taira RK, Soderland SG, Jakobovits RM: Automatic structuring of radiology free-text reports. Radiographics 21:237–245, 2001
Zou Q, et al: IndexFinder: a method of extracting key concepts from clinical texts for indexing. In: American Medical Informatics Association Annual Symposium, 2003, pp 763–767
Alonso O, et al: Oracle text white paper. Available at http://www.oracle.com/technology/products/text/index.html. Cited 2006
International Business Machines Corporation: DB2 text extender. Available at ftp://ftp.software.ibm.com/software/data/db2/extenders/text/db2tewkspecsheet.pdf. Cited 2002
Microsoft Corporation: SQL Server 2000 full-text search deployment white paper. Available at http://www.support.microsoft.com/kb/323739. Cited 2004
Ferrucci D, Lally A: Building an example application with the unstructured information management architecture. IBM Syst J 43(3):455–475, 2004
Baecker R, Small I, Mander R: Bringing icons to life. Proceedings of the SIGCHI conference on human factors in computing systems: reaching through technology. New Orleans, Louisiana, USA: ACM Press, 1991, pp 1–6
NEMA: Digital imaging and communications in medicine. Available at http://www.medical.nema.org/. Cited 2007
Armato III, SG, et al: Lung image database consortium: developing a resource for the medical imaging research community. Radiology 232:739–748, 2004
Sigal R: PACS as an e-academic tool. In CARS 2005: computer assisted radiology and surgery. 2005
Toms AP, et al: Building an anonymized catalogued radiology museum in PACS: a feasibility study. Br J Radiol 79:661–671, 2006
Cohen S, Gilboa F, Uri S: PACS and electronic health records, San Diego, CA: SPIE, 2002
Lehmann T, Wein B, Greenspan H: Integration of content-based image retrieval to picture archiving and communication systems. In: Medical Informatics Europe Conference, 2003
Traina A, Rosa NA, Traina C. Integrating images to patient electronic medical records through content-based retrieval techniques. In: 16th IEEE Symposium on Computer-Based Medical Systems, 2003
Leoni L, et al: A virtual data grid architecture for medical data using SRB. In: EuroPACS-MIR 2004, Trieste, Italy, 2004
Erdal S, et al: Flexible patient information search and retrieval framework: pilot implementation. In: Proceedings of the SPIE Medical Imaging, San Diego, CA, 2007
Erdal S, et al: Information warehouse application of caGrid: a prototype implementation. In: caBIG 2007 Annual Meeting, Washington, DC, 2007
Erdal S, et al: Integrating a PACS system to grid: a de-identification and integration framework. In: Annual Meeting of the Society for Imaging Informatics in Medicine (SIIM) 2007, Providence, RI, 2007
Lindberg C: The unified medical language system (UMLS) of the national library of medicine. J Am Med Rec Assoc 61(5):40–42, 1990
Lindberg DA, Humphreys BL, McCray AT: The unified medical language system. Methods Inf Med 32(4):281–291, 1993
Cancer Biomedical Informatics Grid (caBIGä). Available ttps://cabig.nci.nih.gov/workspaces/Architecture/caGrid/, https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. Cited 2006
Eckerson WW: Three tier client/server architecture: achieving scalability, performance, and efficiency in client server applications. Open Inf Syst 10:1–12, 1995
Gallaugher J, Ramanathan S: Choosing a client/server architecture. A comparison of two-tier and three-tier systems. Inf Syst Manage Mag 13(2):7–13
Clunie DA: DICOM structured reporting, Bangor, Pennsylvania: PixelMed, 2000
Payne PR, et al: Breaking the translational barriers: the value of integrating biomedical informatics and translational research. J Investig Med 53(4):192–200, 2005
Acknowledgments
Authors would like to thank Jason Buskirk, Felix Liu, Scott Silvey, Tremayne Smith, Ty Tolley and Herb Smaltz.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Erdal, S., Catalyurek, U.V., Payne, P.R.O. et al. A Knowledge-Anchored Integrative Image Search and Retrieval System. J Digit Imaging 22, 166–182 (2009). https://doi.org/10.1007/s10278-007-9086-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10278-007-9086-8