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INVESTIGATING IMPLICIT KNOWLEDGE IN ONTOLOGIES WITH APPLICATION TO THE ANATOMICAL DOMAIN

S. ZHANG, O. BODENREIDER
2003 Biocomputing 2004  
This paper investigates implicit knowledge in two ontologies of anatomy: the Foundational Model of Anatomy and GALEN.  ...  The application of these findings to ontology auditing, validation, and maintenance is discussed, as well as the application to ontology integration.  ...  Thanks also to Pieter Zanstra at Kermanog for providing us with an extended license for the GALEN server.  ... 
doi:10.1142/9789812704856_0024 fatcat:nhfgfuta6bhb7aux5jv2istexq

Investigating implicit knowledge in ontologies with application to the anatomical domain

S Zhang, O Bodenreider
2004 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
This paper investigates implicit knowledge in two ontologies of anatomy: the Foundational Model of Anatomy and GALEN.  ...  The application of these findings to ontology auditing, validation, and maintenance is discussed, as well as the application to ontology integration.  ...  Thanks also to Pieter Zanstra at Kermanog for providing us with an extended license for the GALEN server.  ... 
pmid:14992508 pmcid:PMC4351965 fatcat:vaqyoj4alnft7civb74x4bb63e

Desiderata for domain reference ontologies in biomedicine

Anita Burgun
2006 Journal of Biomedical Informatics  
Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain.  ...  ii) to infer new knowledge in ontologies of more complex entities, and (iii) to manage and help reasoning about individual data.  ...  Acknowledgment The author thanks Olivier Bodenreider and Olivier Dameron for providing valuable insight.  ... 
doi:10.1016/j.jbi.2005.09.002 pmid:16266830 fatcat:rs266b2rh5bo5dvyccqzrgkcrq

NLM Anatomical Ontology Alignment System. Results of the 2006 Ontology Alignment Contest

Songmao Zhang, Olivier Bodenreider
2006 International Semantic Web Conference  
National Library of Medicine, we have developed domain knowledge-based techniques for aligning large anatomical ontologies, with the objective of exploring approaches to aligning representations of anatomy  ...  When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with and reasoning across these  ...  Here, domain knowledge was required to assess what relations can be automatically extracted with high accuracy in the particular context of anatomical terms.  ... 
dblp:conf/semweb/ZhangB06 fatcat:saorbo5zi5cznd2zkq3fqzq5gu

Intelligent Medical Image SearchIntelligente Bildsuche in der Medizin

Sonja Zillner, Martin Huber
2009 it - Information Technology  
In this article we present the project MEDICO that strives to implement intelligent medical image search by means of machine learning algorithms and semantic technologies.  ...  Zusammenfassung Mit dem technologischen Forschritt in der medizinischen Bildgebung gewinnen medizinische Bilder in der Früherkennung, Diagnose, Behandlungsplanung und bei Nachfolgeuntersuchungen zunehmend  ...  Based on the comprehensive representation of the domain knowledge, hidden and implicit knowledge can be derived and enhance medical image search.  ... 
doi:10.1524/itit.2009.0553 fatcat:343lq4l55rcc3crmadpthfweyu

An Intelligent System Approach for Integrating Anatomical Ontologies

Peter Petrov, Milko Krachunov, Elena Todorovska, Dimitar Vassilev
2012 Biotechnology & Biotechnological Equipment  
To achieve the degree of intelligence that is needed, the AnatOM program utilizes the large amount of high-quality data (knowledge) available in several widely popular and generally recognized knowledge  ...  Anatomical (phenotypic) ontologies of various species nowadays typically contain from few thousands to few tens of thousands of terms and relations (which is a very small number compared to the count of  ...  When considering simple, limited application domains and developing Ai systems and Ai agent for them, the choice of a knowledge representation model is not that important as it is easy to come up with  ... 
doi:10.5504/bbeq.2012.0010 fatcat:x4pixqcqqfehdgbe2dwmdrti5i

A Semi-automated Method for Domain-Specific Ontology Creation from Medical Guidelines [article]

Omar ElAssy and Rik de Vendt and Fabiano Dalpiaz and Sjaak Brinkkemper
2022 arXiv   pre-print
A key component in automated conversation summarization is the matching of the knowledge graph of the consultation transcript with a medical domain ontology for the interpretation of the consultation conversation  ...  The automated capturing and summarization of medical consultations has the potential to reduce the administrative burden in healthcare.  ...  We make a step in this direction by laying down the formal foundations for the construction of semi-automated systems that support the interpretation of conversations using ontologies.  ... 
arXiv:2111.15338v2 fatcat:hjteclezprdqlcxuzwvpqorkhq

Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy

Songmao Zhang, Olivier Bodenreider
2006 Computers in Biology and Medicine  
As a case study, we investigate the degree to which the Foundational Model of Anatomy (FMA)-a large ontology of anatomy-complies with these 15 principles.  ...  Implicit relations-embedded in concept names or inferred from a combination of explicit relations-are used in this process in addition to the relations explicitly represented.  ...  The authors would like to thank Anand Kumar for suggesting this study and for helpful discussions.  ... 
doi:10.1016/j.compbiomed.2005.04.007 pmid:16144698 pmcid:PMC1784072 fatcat:3k5nipxlyvctrmvf33ukrjgazy

Aligning representations of anatomy using lexical and structural methods

Songmao Zhang, Olivier Bodenreider
2003 AMIA Annual Symposium Proceedings  
The importance of taking advantage of implicit domain knowledge acquired through complementation,augmentation, and inference is discussed.  ...  The objective of this experiment is to develop methods for aligning two representations of anatomy (the Foundational Model of Anatomy and GALEN) at the lexical and structural level.  ...  Thanks also to Pieter Zanstra at Kermanog for providing us with an extended license for the GALEN server.  ... 
pmid:14728274 pmcid:PMC1480279 fatcat:3avua5dwpbbjxhn2gxftwu4yce

The Foundational Model of Anatomy in OWL 2 and its use

Christine Golbreich, Julien Grosjean, Stefan Jacques Darmoni
2013 Artificial Intelligence in Medicine  
The main strength of the method is to leverage OWL 2 expressiveness and to rely on the naming conventions of the FMA, to make explicit some implicit semantics, while improving its ontological model and  ...  The method designed to represent the FMA ontology in OWL 2 presented in this article is general and may be extended to other ontologies.  ...  We want to thank the anonymous reviewers for their comments, very helpful to improve that document. The authors thank Leslie Block for her valuable advice in the editing of this manuscript.  ... 
doi:10.1016/j.artmed.2012.11.002 pmid:23273493 fatcat:bwk5qypsqnhzramjvd2eu46ajq

Image metadata reasoning for improved clinical decision support

Sonja Zillner, Daniel Sonntag
2012 Network Modeling Analysis in Health Informatics and Bioinformatics  
The resulting combined data serve as input to an automatic reasoning process in order to stage lymphoma patients automatically.  ...  In this article we describe how we made use of reasoning technologies to post-process medical image annotations in the context of the automated staging process of lymphoma patients.  ...  The responsibility for this publication lies with the authors.  ... 
doi:10.1007/s13721-012-0003-9 dblp:journals/netmahib/ZillnerS12 fatcat:4w4h36vgozfdpcpx3yu3phmpk4

Reasoning-Based Patient Classification for Enhanced Medical Image Annotation [chapter]

Sonja Zillner
2010 Lecture Notes in Computer Science  
We will exemplify the reasoning steps of the methodology along a use case for automatic lymphoma patient staging.  ...  Medical imaging plays an important role in today's clinical daily tasks, such as patient screening, diagnosis, treatment planning and follow up.  ...  The responsibility for this publication lies with the author. We are also thankful to Kamal Najib for his support with implementation tasks.  ... 
doi:10.1007/978-3-642-13486-9_17 fatcat:j27bobkf3bet7kt4ypaesi435i

A Case Study in Ontologies for Probabilistic Networks [chapter]

Eveline M. Helsper, Linda C. van der Gaag
2002 Research and Development in Intelligent Systems XVIII  
Building a probabilistic network for a real-life domain of application is a hard and time-consuming process, which is generally performed with the help of domain experts.  ...  To study the usefulness of ontologies for this purpose, we have constructed an ontology for the domain of oesophageal cancer, based upon a real-life probabilistic network for the staging of cancer of the  ...  We are grateful to Babs Taal and Berthe Aleman from the Netherlands Cancer Institute, Antoni van Leeuwenhoekhuis, who provided the domain knowledge for the construction of the oesophagus network.  ... 
doi:10.1007/978-1-4471-0119-2_18 fatcat:37lmiyey6zcxnab74likdamlii

Foundational model of neuroanatomy: implications for the Human Brain Project

R F Martin, J L Mejino, D M Bowden, J F Brinkley, C Rosse
2001 Proceedings. AMIA Symposium  
In order to meet the need for a controlled terminology in neuroinformatics, we have integrated the extensive terminology of NeuroNames into the Foundational Model of anatomy.  ...  We illustrate the application of foundational principles for the establishment of an inheritance hierarchy, which accommodates anatomical attributes of neuroanatomical concepts and provides the foundation  ...  Acknowledgements This work was supported in part by NIH contract LM13506 and grants LM06316 and Human Brain Project grant DC02310.  ... 
pmid:11825226 pmcid:PMC2243655 fatcat:t6kubyl2mnbchlc2j6qdm36nwe

Experience in Aligning AnatomicalOntologies

Songmao Zhang, Olivier Bodenreider
2007 International Journal on Semantic Web and Information Systems (IJSWIS)  
When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with these ontologies and reasoning  ...  The four anatomical ontologies under investigation are the Foundational Model of Anatomy, GALEN, the Adult Mouse Anatomical Dictionary and the NCI Thesaurus.  ...  of the GALEN at the University of Manchester, UK; to Martin Ringwald's group at the Jackson Laboratory for help with the Adult Mouse Anatomical Dictionary; and to Sherri de Coronado at  ... 
doi:10.4018/jswis.2007040101 pmid:18974854 pmcid:PMC2575410 fatcat:ppvoham76fbe3hynhiipvvw3da
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