한국정보과학회논문지:소프트웨어및응용 (Journal of KIISE:Software and Applications)

한국정보과학회 (Korean Institute of Information Scientists and Engineers)
권호 표지

OWL 기반 그래픽 바이오 온톨로지 관리 시스템의 설계 및 구현

Design and Implementation of a Graphical Bio-Ontology Management System based on OWL

  • 김기헌 (전북대학교 전산통계학과) ;
  • 최재훈 (한국전자통신연구원) ;
  • 양재동 (전북대학교전자정보공학부) ;
  • 박천수 (한국전자통신연구원 지능형로봇연구단)
  • 발행 : 2005.06.01
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

본 논문에서는 OWL(Web Ontology Language) 기반 그래픽 바이오 온톨로지 관리 시스템을 설계하고 구현하였다 이 시스템은 생물학 용어들 사이의 복잡한 의미 관계들로 구성되는 바이오 온톨로지를 본 논문에서 정의한 그래픽 표기를 이용하여 표현한다. 또한, 시각화된 환경에서 수행되는 상속과 역상 속 메커니즘은 이미 구축된 방대한 용어들 사이의 관계를 시스템이 구조적으로 파악할 수 있게 함으로써, 전문가가 새로 추가되는 용어에 대한 관계를 의미적으로 일관성 있게 반자동으로 구축할 수 있다. 구축된 온톨로지는 기본적으로 OWL로 기술되며, 다른 여러 표준 온톨로지 언어(RDF/RDFS, DAML+OIL 등)로 의미적 손실 없이 변환된다. 본 시스템의 중요한 특징은 OWL의 강력한 의미적 표현력과 이를 잘 정의할 수 있는 그래픽 표기법을 채택함으로써 시각화된 메커니즘을 통해 바이오 온톨로지를 정교하게 모델링할 수 있다는 점이다.

In this paper, we design and implement a graphical bio-ontology management system based on OWL(Web Ontology Language). It allows domain experts to easily manage sophisticated bio-ontologies in which biological knowledge is encoded. The knowledge can be seamlessly modeled into the ontology by well defined graphical notations, which capture most of subtle semantics inherently existing between biological terms. Our system provides a new construction mechanism, which can determine a considerable part of relationships between terms by their inheritance and inverse-inheritance. For keeping their semantics to be consistent, the mechanism supplies domain experts with information available from relationships being constructed or already constructed. The constructed ontology is basically formatted by OWL, which may benefit from its powerful semantic expressiveness. Additionally, it can be automatically translated into other standard languages without semantic loss, such as RDF/RDFS, DAML+OIL and so on. The main characteristics of our system is that it enables domain experts to delicately model the bio-ontology by the visualized construction mechanisms adopting well-defined graphical notations based on OWL.

키워드

참고문헌

  1. Gruber, T., 'A Translation Approach to Portable Ontology Specifications,' in Knowledge Acquisition Journal, Vol. 5, pp. 199-220, 1993 https://doi.org/10.1006/knac.1993.1008
  2. Lambrix, P., Habbouche, M. and Perez, M., 'Evaluation of ontology development tools for bioinformatics,' Bioinformatics, Vol. 19, pp. 1564-1571, 2003 https://doi.org/10.1093/bioinformatics/btg194
  3. Rosse, C. and Megino, J.L.V., 'A reference ontology for bioinformatics : the Foundational Model of Anatomy,' Journal of Biomedical Informatics, Inpress, 2003
  4. Stevens, R., Goble, C., Horrocks, I. and Bechhofer, S., 'Building a Bioinformatics Ontology Using OIL,' IEEE Transactions on Information Technology in Biomedicine, Vol. 6, pp. 135-141, 2002 https://doi.org/10.1109/TITB.2002.1006301
  5. Jensen, L.J., Gupta, R., Starfeldt, H.-H. and Brunak, S., 'Prediction of Human Protein Function According to Gene Ontology Categories,' Bioinformatics, Vol. 19, pp. 653-642, 2003 https://doi.org/10.1093/bioinformatics/btg036
  6. Karp, P.D., 'An Ontology for Biological function based on molecular interactions,' Bioinformatics, Vol. 16, pp. 269-285, 2000 https://doi.org/10.1093/bioinformatics/16.3.269
  7. Westbrook, J.D. and Bourne, P.E., 'STAR/mmCIF: Anontology for macromolecular structure,' Bioinformatics Ontology, Vol. 16, pp. 159-168, 1999
  8. Kumar A., Smith B., 'The Unified Medical Language System and the Gene Ontology: Some Critical Reflections,' Proc KI 2003, pp. 135-148, 2003
  9. Noy, N. F., Sintek, M., Decker, S., Crubezy, M., Fergerson, R. W. and Musen, M. A., 'Creating Semantic Web Contents with Protege-2000,' IEEE Intelligent Systems 16(2), pp. 60-71, 2001 https://doi.org/10.1109/5254.920601
  10. Bechhofer, S., Horrocks, I., Goble, C. and Stevens, R., 'OilEd: a Reason-able Ontology Editor for the Semantic Web,' Proceedings of KI2001, LNAI Vol. 2174, pp. 396-408, 2001
  11. Horrocks, I., 'Reasoning with Expressive Description Logics:Theory and Practice,' Proceedings of CADE-02, Springer-Velag Lecture Notes in Artificial Intelligence, LNAI 2393, pp. 1-15, 2002
  12. DagEdit,
  13. ezOWL
  14. OWLViz
  15. TGVizTab
  16. Dean, M. and Schreiber, G., 'Web Ontology Language (OWL) Reference Version 1.0,' , 2002
  17. Smith, M., McGuinness, D. and Welth, C., 'Web Ontology Language (OWL) Guide Version 1.0,' , 2002
  18. Kim, W., Introduction to Object-Oriented Databases, The MIT Press, 1990
  19. Choi, J.H., Yang, J.D. and Lee, D.G., 'An object-based Approach to Managing Domain Specific Thesauri : Semiautomatic Thesaurus Construction and Query-based Browsing,' International Journal of Software Engineering & Knowledge Engineering, Vol. 10, pp. 1-27, 2002
  20. TouchGraph, http://www.touchgraph.com
  21. JENA 2 - A Semantic Web Framework,