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Knowledge retrieval in the anatomical domain

Published:11 November 2010Publication History

ABSTRACT

The information requirement in the health area and the increase difficult for knowledge retrieval inside this domain, demands the existence of tools to support the processing of large amount of existing texts in the information repositories sources. Addressing this problem this work introduces an architecture aiming to support knowledge retrieval process from databases using annotated images in the anatomical domain. The architecture was implemented using five layers (the domain ontology, the annotation, the support, the retrieval and visualization layers) based on the Foundational Model of Anatomy and the Unified Medical Language System, reference ontologies in the biomedical domain. This architecture improves substantially the knowledge retrieval due to the use of images that link its regions with concepts of biomedical ontologies. The architecture proposed can be generalized and applied in other domains employing other reference ontologies.

References

  1. A. Aronson. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. In Proceedings of the AMIA Symposium, pages 17--21. American Medical Informatics Association, 2001.Google ScholarGoogle Scholar
  2. R. A. Baeza-Yates and B. A. Ribeiro-Neto. Modern Information Retrieval. ACM Press/Addison-Wesley, 1999. Google ScholarGoogle ScholarDigital LibraryDigital Library
  3. S. Bechhofer. Ontoweb report: Ontology language standardization efforts. Technical report, Technical report, IST Project, IST-2000-29243, 2002. 60, 2002.Google ScholarGoogle Scholar
  4. A. Betin-Can and N. Baykal. Medicoport: A medical search engine for all. Computer Methods and Programs in Biomedicine, 86(1):73--86, 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  5. O. Bodenreider. The unified medical language system (umls): integrating biomedical terminology. Nucleic Acids Research, 32(Database Issue):267--270, 2004.Google ScholarGoogle Scholar
  6. O. Bodenreider. From terminology integration to information integration: Unified medical language system (umls). In BioRDF Teleconference, W3C Semantic Web Health Care and Life Sciences Interest Group, 2006.Google ScholarGoogle Scholar
  7. O. Bodenreider. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. IMIA Yearbook of Medical Informatics, pages 67--79, 2008.Google ScholarGoogle Scholar
  8. P. Bottoni, R. Civica, S. Levialdi, L. Orso, E. Panizzi, and R. Trinchese. Storing and retrieving multimedia web notes. In Databases in Networked Information Systems, volume 3433 of Lecture Notes in Computer Science, pages 119--137. Springer Berlin / Heidelberg, 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  9. J. Brinkley, D. Suciu, L. Detwiler, J. Gennari, C. Rosse, et al. A framework for using reference ontologies as a foundation for the semantic web. In AMIA Annual Symposium Proceedings, volume 2006, pages 96--100. American Medical Informatics Association, 2006.Google ScholarGoogle Scholar
  10. R. A. Burkhard. Learning from architects: The difference between knowledge visualization and information visualization. Eighth International Conference on Information Visualisation (IV'04), pages 519--524, 2004. Google ScholarGoogle ScholarDigital LibraryDigital Library
  11. R. A. Burkhard. Knowledge Visualization -- The Use of Complementary Visual Representations for the Transfer of Knowledge. A Model, a Framework, and Four New Approaches. PhD thesis, Swiss Federal Institute of Technology Zurich, Switzerland, 2005.Google ScholarGoogle Scholar
  12. R. A. Burkhard. Towards a framework and a model for knowledge visualization: synergies between information and knowledge visualization. In Knowledge and Information Visualization, volume 3426, pages 238--255. Springer, Berlin/Heidelberg, 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  13. R. A. Burkhard and M. Meier. Tube map visualization: evaluation of a novel knowledge visualization application for the transfer of knowledge in long-term projects. Journal of Universal Computer Science, 11(4):473--494, 2005.Google ScholarGoogle Scholar
  14. G. Canfora and L. Cerulo. A taxonomy of information retrieval models and tools. Journal of Computing and Information Technology - CIT, 12(3):175--194, 2004.Google ScholarGoogle Scholar
  15. C. Chronaki, X. Zabulis, and S. Orphanoudakis. Ic2 net medical image annotation service. Informatics for Health and Social Care, 22(4):337--347, 1997.Google ScholarGoogle Scholar
  16. O. Corcho. Ontology based document annotation: trends and open research problems. International Journal of Metadata, Semantics and Ontologies, 1(1):47--57, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  17. M. Eppler and R. A. Burkhard. Knowledge Visualization Towards a New Discipline and its Fields of Application. 2004.Google ScholarGoogle Scholar
  18. M. Eppler and R. A. Burkhard. Knowledge Visualization. Encyclopedia of Knowledge Management, 2005.Google ScholarGoogle Scholar
  19. J.-D. Fekete, J. J. Wijk, J. T. Stasko, and C. North. The value of information visualization. In Information Visualization: Human-Centered Issues and Perspectives, pages 1--18. Springer-Verlag, 2008. Google ScholarGoogle ScholarDigital LibraryDigital Library
  20. K. Fenstermacher. Process-aware knowledge retrieval. In Proceedings of the 35th Hawaii International Conference on System Sciences, volume 7, page 209. 2, 2002. Google ScholarGoogle ScholarDigital LibraryDigital Library
  21. E. Greengrass. Information retrieval: A survey, 2001.Google ScholarGoogle Scholar
  22. M. Guah. Today's health care demands knowledge management strategy. 26th International Conference on Information Technology Interfaces, 1: 461--467, June 2004.Google ScholarGoogle Scholar
  23. C. Halaschek-Wiener, J. Golbeck, B. Parsia, J. Hendler, A. Schain, and M. Grove. A flexible approach for managing digital images on the semantic web. In Proceedings of the 5th International Workshop on Knowledge Markup and Semantic Annotation, 2005.Google ScholarGoogle Scholar
  24. C. Halaschek-Wiener, J. Golbeck, A. Schain, M. Grove, B. Parsia, and J. Hendler. Photostuff--an image annotation tool for the semantic web. In Proceedings of the 4th International Semantic Web Conference, 2005.Google ScholarGoogle Scholar
  25. C. Halaschek-Wiener, J. Golbeck, A. Schain, M. Grove, B. Parsia, and J. Hendler. Annotation and provenance tracking in semantic web photo libraries. In Provenance and Annotation of Data, volume 4145 of Lecture Notes in Computer Science, pages 82--89. Springer Berlin / Heidelberg, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  26. C. Halaschek-Wiener, A. Schain, M. Grove, B. Parsia, and J. Hendler. Management of digital images on the semantic web. In Proceedings of the 4th International Semantic Web Conference, 2005.Google ScholarGoogle Scholar
  27. A. Hanbury. A survey of methods for image annotation. Journal of Visual Languages & Computing, 19(5):617--627, 2008. Google ScholarGoogle ScholarDigital LibraryDigital Library
  28. R. Haux. Health information systems-past, present, future. International Journal of Medical Informatics, 75(3--4): 268--281, 2006.Google ScholarGoogle ScholarCross RefCross Ref
  29. L. Hollink, G. Schreiber, J. Wielemaker, and B. Wielinga. Semantic annotation of image collections. In S. Handschuh, M. Koivunen, R. Dieng, and S. Staab, editors, Proc. of the 4th Int'l. Workshop on Knowledge Markup and Semantic Annotation, Knowledge Capture 2003, 2003.Google ScholarGoogle Scholar
  30. J. Hou and S. Pai. A spatial knowledge sharing platform. using the visualization approach. International Journal of Production Research, 47(1): 25--50, 2009.Google ScholarGoogle ScholarCross RefCross Ref
  31. W. Hsu, S. Antani, L. R. Long, L. Neve, and G. R. Thoma. Spirs: A web-based image retrieval system for large biomedical databases. International Journal of Medical Informatics, 78(Supplement 1): S13--S24, 2009.Google ScholarGoogle ScholarCross RefCross Ref
  32. P. W. Hung, S. B. Johnson, D. R. Kaufman, and E. A. Mendon¸ca. A multi-level model of information seeking in the clinical domain. Journal of Biomedical Informatics, 41(2): 357--370, 2008. Google ScholarGoogle ScholarDigital LibraryDigital Library
  33. E. Hyvönen and A. Styrman. Ontology-based image retrieval. In E. Hyvönen and M. Klemettinen, editors, Proceedings of the XML Finland 2002 Conference, 2002.Google ScholarGoogle Scholar
  34. P. Ingwersen. Information Retrieval Interaction. Taylor Graham, 1992. Google ScholarGoogle ScholarDigital LibraryDigital Library
  35. W. Jinhong and W. Huiling. Study on semantic knowledge retrieval based context. In IEEE International Symposium on Knowledge Acquisition and Modeling Workshop, pages 1006--1009, 2008.Google ScholarGoogle Scholar
  36. A. Kiryakov, B. Popov, I. Terziev, D. Manov, and D. Ognyanoff. Semantic annotation, indexing, and retrieval. Web Semantics: Science, Services and Agents on the World Wide Web, 2(1): 49--79, 2004. Google ScholarGoogle ScholarDigital LibraryDigital Library
  37. W. Lober, L. Trigg, D. Bliss, and J. Brinkley. Iml: An image markup language. In Proceedings, American Medical Informatics Association Fall Symposium, pages 403--407. American Medical Informatics Association, 2001.Google ScholarGoogle Scholar
  38. P. Martin and P. W. Eklund. Knowledge retrieval and the world wide web. Intelligent Systems and their Applications, IEEE, 15(3): 18--25, 2000. Google ScholarGoogle ScholarDigital LibraryDigital Library
  39. M. Möller and M. Sintek. A generic framework for semantic medical image retrieval. In T. Bürger, S. Dasiopoulou, C. Eckes, S. J. Perantonis, J. Pereira, and V. Tzouvaras, editors, KAMC, volume 253 of CEUR Workshop Proceedings. CEUR-WS.org, 2007.Google ScholarGoogle Scholar
  40. J. Osborne, J. Flatow, M. Holko, S. Lin, W. Kibbe, L. Zhu, M. Danila, G. Feng, and R. Chisholm. Annotating the human genome with disease ontology. BMC Genomics, 10(Suppl 1): S6, 2009.Google ScholarGoogle ScholarCross RefCross Ref
  41. T. Osman, D. Thakker, G. Schaefer, and P. Lakin. An integrative semantic framework for image annotation and retrieval. In Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence, pages 366--373. IEEE Computer Society, 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  42. J. Paralic and I. Kostial. Ontology-based information retrieval. In Proceedings of the 14th International Conference on Information and Intelligent systems (IIS 2003), Varazdin, Croatia, pages 23--28, 2003.Google ScholarGoogle Scholar
  43. L. Reeve and H. Han. Survey of semantic annotation platforms. In SAC '05: Proceedings of the 2005 ACM symposium on Applied computing, pages 1634--1638, New York, NY, USA, 2005. ACM. Google ScholarGoogle ScholarDigital LibraryDigital Library
  44. D. Revere and S. Fuller. Building a Customizable Knowledge Management Environment to Support Public Health Practice: Design Strategies. Hawaii International Conference on System Sciences, Proceedings of the 41st Annual, 2008. Google ScholarGoogle ScholarDigital LibraryDigital Library
  45. D. Revere, A. Turner, A. Madhavan, N. Rambo, P. Bugni, A. Kimball, and S. Fuller. Understanding the information needs of public health practitioners: A literature review to inform design of an interactive digital knowledge management system. Journal of Biomedical Informatics, 40(4): 410--421, 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  46. C. Rosse and J. Mejino. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Journal of Biomedical Informatics, 36(6): 478--500, 2003. Google ScholarGoogle ScholarDigital LibraryDigital Library
  47. C. Rosse and J. Mejino. The foundational model of anatomy ontology. In Anatomy Ontologies for Bioinformatics, volume 6 of Computational Biology, pages 59--117. Springer London, 2008.Google ScholarGoogle Scholar
  48. C. Rosse, L. Shapiro, and J. Brinkley. The Digital Anatomist Foundational Model: Principles for Defining and Structuring its Concept Domain. In American Medical Informatics Association Fall Symposium, pages 820--824, 1998.Google ScholarGoogle Scholar
  49. D. Rubin, P. Mongkolwat, V. Kleper, K. Supekar, and D. Channin. Medical imaging on the semantic web: Annotation and image markup. In AAAI Spring Symposium - Technical Report SS-08-05, pp. 93--98, 2008.Google ScholarGoogle Scholar
  50. D. Rubin, C. Rodriguez, P. Shah, and C. Beaulieu. ipad: Semantic annotation and markup of radiological images. In AMIA Annu Symp Proc, volume 2008, pages 626--630. American Medical Informatics Association, 2008.Google ScholarGoogle Scholar
  51. D. L. Rubin, P. Mongkolwat, V. Kleper, K. Supekar, and D. S. Channin. Annotation and image markup: Accessing and interoperating with the semantic content in medical imaging. Intelligent Systems, IEEE, 24(1):57--65, 2009. Google ScholarGoogle ScholarDigital LibraryDigital Library
  52. J. Sandars and R. Heller. Improving the implementation of evidence-based practice: a knowledge management perspective. Journal of Evaluation in Clinical Practice, 12(3): 341--346, 2006.Google ScholarGoogle ScholarCross RefCross Ref
  53. A. T. Schreiber, B. Dubbeldam, J. Wielemaker, and B. Wielinga. Ontology-based photo annotation. Intelligent Systems, IEEE, 16(3): 66--74, 2001. Google ScholarGoogle ScholarDigital LibraryDigital Library
  54. G. Schreiber, I. Blok, D. Carlier, W. van Gent, J. Hokstam, and U. Roos. A mini-experiment in semantic annotation. In I. Horrocks and J. Hendler, editors, The Semantic Web - ISWC 2002, pages 404--408. Springer Berlin / Heidelberg, 2002. Google ScholarGoogle ScholarDigital LibraryDigital Library
  55. K. Seki and J. Mostafa. Literature-based discovery by an enhanced information retrieval model. In V. Corruble, M. Takeda, and E. Suzuki, editors, Discovery Science, volume 4755 of Lecture Notes in Computer Science, pages 185--196. Springer, 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  56. P. Sondhi, P. Raj, V. Kumar, and A. Mittal. Question Processing and Clustering in INDOC: A Biomedical Question Answering System. EURASIP Journal on Bioinformatics and Systems Biology, 2007(3), 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  57. D. Sonntag and M. Möller. A multimodal dialogue mashup for medical image semantics. In Proceeding of the 14th international conference on Intelligent user interfaces, pages 381--384, Hong Kong, China, 2010. ACM. Google ScholarGoogle ScholarDigital LibraryDigital Library
  58. S. Steffen, M. Er, and H. Siegfried. An annotation framework for the semantic web. In S. Isjizaki, editor, Proceedings of the First Workshop on Multimedia Annotation, Tokyo, Japan, 2001.Google ScholarGoogle Scholar
  59. R. Studer, V. Benjamins, and D. Fensel. Knowledge engineering: Principles and methods. Data & Knowledge Engineering, 25(1--2): 161--197, 1998. Google ScholarGoogle ScholarDigital LibraryDigital Library
  60. R. Studer, S. Decker, D. Fensel, and S. Staab. Situation and perspective of knowledge engineering. In J. Cuena, Y. Demazeau, A. G. Serrano, and J. Treur, editors, Knowledge Engineering and Agent Technology, pages 237--232. IOS Press, Amsterdan, The Netherlands, 2000.Google ScholarGoogle Scholar
  61. T. Theodosiou, L. Angelis, and A. Vakali. Non-linear correlation of content and metadata information extracted from biomedical article datasets. Journal of Biomedical Informatics, 41(1): 202--216, 2008. Google ScholarGoogle ScholarDigital LibraryDigital Library
  62. V. Uren, P. Cimiano, J. Iria, S. Handschuh, M. Vargas-Vera, E. Motta, and F. Ciravegna. Semantic annotation for knowledge management: Requirements and a survey of the state of the art. Web Semantics: Science, Services and Agents on the World Wide Web, 4(1): 14--28, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  63. C. Ware. Information visualization: perception for design. Morgan Kaufmann Publishers Inc., 2000. Google ScholarGoogle ScholarDigital LibraryDigital Library
  64. W. Xiao-yue. Visualization based on concept maps: An efficient way to knowledge sharing and knowledge discovery in e-science environment. In M. Yan, editor, Fourth International Conference on Fuzzy Systems and Knowledge Discovery, FSKD 2007, volume 2, pages 144--147, Haikou, Hainan, China, 2009. Google ScholarGoogle ScholarDigital LibraryDigital Library
  65. T. Xiaohui, L. Yuefeng, Z. Ning, and R. Nayak. An ontology-based framework for knowledge retrieval. In IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology, volume 1, pages 510--517, 2008. Google ScholarGoogle ScholarDigital LibraryDigital Library

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        cover image ACM Other conferences
        IHI '10: Proceedings of the 1st ACM International Health Informatics Symposium
        November 2010
        886 pages
        ISBN:9781450300308
        DOI:10.1145/1882992

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