Ontology modularization to improve semantic medical image annotation

Journal of Biomedical Informatics

Volumn 44, Issue 1, 2011, Pages 155-162

  Wennerberg, Pinar ^a   Schulz, Klaus ^b   Buitelaar, Paul ^c  

^a SIEMENS AG   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

Medical knowledge engineering; Ontology modularization

Indexed keywords

ACTIVE FIELD; CLINICAL ENVIRONMENTS; CLINICAL SETTINGS; DATA SETS; LABOR INTENSIVE; MANUAL ANNOTATION; MEDICAL IMAGE ANNOTATION; MEDICAL IMAGES; MEDICAL KNOWLEDGE ENGINEERING; MEDICAL ONTOLOGY; MODULARIZATIONS; SEARCH ALGORITHMS; SEMANTIC DESCRIPTIONS; SEMANTIC IMAGES; SEMANTIC SEARCH ENGINES; TEXT ANNOTATIONS; WEALTH OF INFORMATION;

IMAGE ANALYSIS; KNOWLEDGE ENGINEERING; MEDICAL IMAGING; MODULAR CONSTRUCTION; SEARCH ENGINES; SEMANTICS;

ONTOLOGY;

ALGORITHM; ARTICLE; HUMAN; IMAGE ANALYSIS; IMAGE PROCESSING; LYMPHOMA; MEDICAL RECORD; PRIORITY JOURNAL;

ALGORITHMS; CHI-SQUARE DISTRIBUTION; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; DIAGNOSTIC IMAGING; DOCUMENTATION; HUMANS; LYMPHOMA; SEMANTICS;

EID: 79952016971     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2010.12.005     Document Type: Article

References (34)

1. Wennerberg P, Zillner S, Moeller M, Buitelaar P, Sintek M. KEMM: a knowledge engineering methodology in the medical domain. In: Proceedings of the 5th international conference on formal ontology in information systems (FOIS); 2008.
2. Wennerberg P, Zillner S, Buitelaar P. Interactive clinical query derivation and evaluation. In: AAAI 2009 spring symposium on technosocial predictive analytics (TPAI), Stanford, San Francisco USA; 2009.
3. Buitelaar P, Wennerberg P, Zillner S. Statistical term profiling for query pattern mining. In: Proceedings of ACL 2008 BioNLP workshop; 2008.
4. Wennerberg P, Buitelaar P, Zillner S. Towards a human anatomy data set for query pattern mining based on Wikipedia and domain semantic resources. In: Proceedings of a workshop on building and evaluating resources for biomedical text mining (LREC); 2008.
5. Rosse C., Mejino J. A reference ontology for biomedical informatics: the foundational model of anatomy. J Biomed Inform 2003, 36(6):478-500.
6. Johnson HL, Cohen K, Baumgartner JW, Lu Z, Bada M, Kester T. Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. In: Pacific symposium on biocomputing; 2006. p. 28-39.
7. Pinto H, Martins J. Ontology integration: how to perform the process. In: Proceedings of international joint conference on artificial intelligence; 2001.
8. Moeller M, Sintek M, Buitelaar P, Mukherjee S, Zhou X, Freund J. Medical image understanding through the integration of cross-modal object recognition with formal domain knowledge. In: Proceedings of Healthinf; 2008.
9. Moeller M, Regel S, Sintek M. Radsem: semantic annotation and retrieval for medical images. In: Proceedings of the 6th annual European semantic web conference (ESWC), Hersonissos, Crete; 2009.
10. Wittekind C., Meyer H., Bootz F. TNM Klassifikation maligner Tumoren 2005, Springer Medizin Verlag, Heidelberg.
11. Dameron O, Roques E, Rubin D, Marquet G, Burgun A. Grading lung tumors using OWL-DL based reasoning. In: Proceedings of 9th international protege conference; 2006.
12. Uschold M. Building ontologies: towards a unified methodology. In: 16th annual conference of the British Computer Society Specialist Group on expert systems, Cambridge, UK; 1996.
13. Jones D, Bench-Capon T, Visser P. Methodologies for ontology development. In: Proceedings of IT& KNOWS conference, XV IFIP world computer congress, Budapest; August 1998.
14. Lopez MF, Gomez-Perez A, Juristo N. Methontology: from ontological art towards ontological engineering. In: Proceedings of AAAI97 spring symposium series, workshop on ontological engineering; 1997. p. 3340.
15. Gruninger M, Fox MS. The design and evaluation of ontologies for enterprise engineering. In: Proceedings of the workshop on implemented ontologies, European conference on artificial intelligence (ECAI); 1994.
16. Sure Y, Studer R. To-knowledge methodology - final version. Institute AIFB, University of Karlsruhe, On-to-knowledge deliverable; 18, 2002.
17. Schreiber G., Akkermans H., Anjewierden A., Dehoog R., Shadbolt N., Vandevelde W., et al. Knowledge engineering and management: the CommonKADS methodology 1999, The MIT Press.
18. Rector A. Modularisation of domain ontologies implemented in description logics and related formalisims including OWL. In: Proceedings of the K-Cap 2003 conference; 2003. p. 121-8.
19. Parent C, Spaccapietra S. An overview of modularity. In: Stuckenschmidt H, Parent C, Spaccapietra S, editors. Modular ontologies. Springer; 2009. p. 5-23.
20. Cuenca G, Horrocks I, Kazakov Y, Sattler U. Just the right amount: extracting modules from ontologies. In: Proceedings of the 16th international conference on WWW; 2007. p. 717-26.
21. Stuckenschmidt H, Schlicht A. Structure-based partitioning of large ontologies. In: Stuckenschmidt H, Parent C, Spaccapietra S, editors. Modular ontologies. Springer; 2009. p. 5-23.
22. Stuckenschmidt H., Parent C., Spaccapietra S. Modular ontologies concepts, theories and techniques for knowledge modularization 2009, Springer.
23. Mungall C. Obol: integrating language and meaning in bio-ontologies. Comp Functional Genomics 2004, 5:509.
24. Marquet G, Dameron O, Saikali S, Mosser J, Burgun A. Grading glioma tumors using OWL-DL and NCI-Thesaurus. In: Proceedings of the American Medical Informatics Association conference AMIA; 2007.
25. C. Goldbreich, O. Dameron, O. Bierlaire, B. Gibaud, What reasoning support for ontology and rules? The brain anatomy case study. In: Proceedings of the Workshop on OWL experiences and directions; 2005.
26. Zillner S, Hauer T, Rogulin D, Tsymbal A, Huber M, Solomonides T. Semantic visualization of patient information. In: Proceedings of the 21th IEEE international symposium on computer-based medical systems (CBMS); 2008.
27. Horridge M, Bechhofer S. The OWL API: a Java API for working with OWL 2 ontologies. In: Proceedings of the 6th OWL experienced and directions workshop (OWLED2009); 2009.
28. Baader F., Calvanese D., McGuinness D.L., Nardi D., Patel-Schneider P.F. The description logic handbook: theory, implementation, and applications. Description logic handbook 2003, Cambridge University Press.
29. Wennerberg P, Zillner S, Schulz K. Context driven modularization of a representation of human anatomy. In: Proceedings of the AMIA 2009 summit on translational bioinformatics (AMIA), San Francisco, USA; 2010.
30. Schreiber G., Akkermans H., Anjewierden A., Dehoog R., Shadbolt N., Vandevelde W., et al. Knowledge engineering and management: the CommonKADS methodology 1999, The MIT Press.
31. Kendal S.L., Creen M. An introduction to knowledge engineering 2007, Springer.
32. Kastrin A, Hristovski D. A fast document classification algorithm for gene symbol disambiguation in the BITOLA literature-based discovery support system. In: AMIA 2008 annual symposium. Washington (DC): American Medical Informatics Association; 2008.
33. Kleinberg J. Authoritative sources in a hyperlinked environment. J ACM 1999, 46(5):604-632.
34. Seidel C. Christian Seidel - System zur dynamischen Erfassung domaenenspezifischer Texteinheiten und Texte mit Hilfe von Eigenvektormethoden. Muenchen: Verlag Dr. Hut; 2010.