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Towards an upper level ontology for molecular biology

Stefan Schulz, Elena Beisswanger, Joachim Wermter, Udo Hahn
2006 AMIA Annual Symposium Proceedings  
There is a growing need for the general-purpose description of the basic conceptual entities in the life sciences.  ...  As an alternative,we here present BioTop, a description-logic-based top level ontology for molecular biology, which we consider as an ontologically conscious redesign of the GENIA ontology.  ...  Acknowledgments: This work was supported by the EU Network of Excellence 'Semantic Interoperability and Data Mining in Biomedicine' (NoE 507505) (, as well as the EC STREP  ... 
pmid:17238430 pmcid:PMC1839533 fatcat:4yvcia7rcjdnriyqxvmjloww3u

An Ontology of Therapies [chapter]

Claudio Eccher, Antonella Ferro, Domenico M. Pisanelli
2010 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
Ontologies are the essential glue to build interoperable systems and the talk of the day in the medical community.  ...  In this paper we present the ontology of medical therapies developed in the course of the Oncocure project, aimed at building a guideline based decision support integrated with a legacy Electronic Patient  ...  Ontologies are the talk of the day in the medical informatics community. Their relevant role in the design and implementation of information systems in health care is now widely acknowledged.  ... 
doi:10.1007/978-3-642-11745-9_22 fatcat:nhhuexvnsfamnak5kpl635d2re

An Ontology for Task World Models [chapter]

Martijn van Welie, Gerrit C. van der Veer, Anton Eliëns
1998 Eurographics  
Such an ontology helps to understand the different task modeling methods and it can also be operationalized for use in tools.  ...  In this paper, we discuss 1) ingredients common to most task models, 2) how task modeling relates to the design of user interfaces, and 3) our proposed ontology for task analysis.  ...  Schofield and Steve P. Guest for their enthusiastic help and invaluable suggestions.  ... 
doi:10.1007/978-3-7091-3693-5_5 fatcat:viyjyjty2zh6jljk7sndswm5hi

A Semantic Similarity Measure for Expressive Description Logics [article]

Claudia d'Amato, Nicola Fanizzi, Floriana Esposito
2009 arXiv   pre-print
A totally semantic measure is presented which is able to calculate a similarity value between concept descriptions and also between concept description and individual or between individuals expressed in  ...  Considering that Description Logics stand as the theoretic framework for the ontological knowledge representation and reasoning, the proposed measure can be effectively used for agglomerative and divisional  ...  and roles to their extension.  ... 
arXiv:0911.5043v1 fatcat:idk5k7thr5bmxc7vvgf5ktqpya

GALEN based formal representation of ICD10

Gergely Héja, György Surján, Gergely Lukácsy, Péter Pallinger, Miklós Gergely
2007 International Journal of Medical Informatics  
The constructed ontology has been converted to OWL, and a test system has been implemented in Prolog to verify the feasibility of the approach.  ...  The formal representation of the first two chapters of ICD10 has been almost completed. The paper presents the main aspects of the modelling, and the experienced problems.  ...  IKTA 00126/2002 and by the Hungarian Ministry of Health. The kind help of dr. Gábor Csongor Kovács is highly appreciated. References  ... 
doi:10.1016/j.ijmedinf.2006.07.008 pmid:17023201 fatcat:un7o3nimmfgilnmvealsriqwzq

A strategy for improving and integrating biomedical ontologies

Cornelius Rosse, Anand Kumar, Jose L V Mejino, Daniel L Cook, Landon T Detwiler, Barry Smith
2005 AMIA Annual Symposium Proceedings  
When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored.  ...  OBR is designed to facilitate inference across the boundaries of domain ontologies in anatomy, physiology and pathology.  ...  Acknowledgements This work was supported in part by a grant from the DARPA Virtual Soldier Project, Contract # W81XWH-04-2-0012, the Wolfgang Paul Program of the Alexander Von Humboldt Foundation and the  ... 
pmid:16779118 pmcid:PMC1560467 fatcat:hwokggqljvc6pofs3pcf4sqwxi

Document annotation and ontology population from linguistic extractions

Florence Amardeilh, Philippe Laublet, Jean-Luc Minel
2005 Proceedings of the 3rd international conference on Knowledge capture - K-CAP '05  
The rules instantiate these concepts, attributes and relations in the knowledge base constrained by the domain ontology.  ...  In this paper, we present a workbench for semi-automatic ontology population from textual documents.  ...  Also we parse the topics with regards to their attributes and the associations wrt their roles in order to take advantage of the constraints modeled in the ontology.  ... 
doi:10.1145/1088622.1088651 dblp:conf/kcap/AmardeilhLM05 fatcat:jvbgumndwvei5gulihlloe6m2m

COVID-19: Disease Pattern Study based on Semantic-Web Approach using Description Logic

Ria Rawal, Kartik Goel, Charu Gupta
2020 2020 IEEE International Conference for Innovation in Technology (INOCON)  
Description logic combined with semantics, forms the treasured Description logic ontology. Several studies have depicted semantics of Description Logic, using concepts and roles.  ...  The main aim of our paper is to use Description Logic ontologies and the semantic web-based approach to remove ambiguity developed around spread of COVID-19.  ...  Brother Sibling i.e. brother belongs to the subset of siblings. RBox or relational axioms are used to represent the different properties assigned to roles.  ... 
doi:10.1109/inocon50539.2020.9298278 fatcat:sdnhie76zfbi5fwsilgxpmta6i

An overview of the ONIONS project: Applying ontologies to the integration of medical terminologies

Aldo Gangemi, Domenico M. Pisanelli, Geri Steve
1999 Data & Knowledge Engineering  
Current results of our research include the integration of some top-level ontologies in the ON9.2 ontology library, and the formalization of the terminological knowledge in the UMLS Metathesaurus.  ...  This is followed by several case studies concerning lexical polysemy, the interface between ontologies and lexicon, and other special problems encountered in the specification of the ontologies.  ...  Acknowledgements We wish to thank Nicola Guarino for his precious suggestions and useful hints and the anonymous referees whose remarks gave us the opportunity of improving our paper.  ... 
doi:10.1016/s0169-023x(99)00023-3 fatcat:etakndnymjg7vgsbfb5h3ojrne

Semantic Grounding Strategies for Tagbased Recommender Systems

Frederico Durao, Peter Dolog
2011 International journal of Web & Semantic Technology  
Therefore, similarities computed without their semantic groundings might lead to less relevant recommendations. In this paper, we study a semantic grounding used for tag similarity calculus.  ...  The study besides other things reveals that currently available OWL ontologies are very narrow and the percentage of the similarity expansions is rather small.  ...  ACKNOWLEDGEMENTS The research leading to these results is part of the project "KiWi -Knowledge in a Wiki" and has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013  ... 
doi:10.5121/ijwest.2011.2405 fatcat:pq6aff52izgcjkx2sdv6jpinbm

The Theory of Top-Level Ontological Mappings and Its Application to Clinical Trial Protocols [chapter]

Barbara Heller, Heinrich Herre, Kristin Lippoldt
2004 Lecture Notes in Computer Science  
We outline a framework consisting of a system of formal tools designed to support the development of data dictionaries, taxonomies and knowledge systems.  ...  This method is based on ontological mappings using reference top-level ontologies, and is inspired by rigorous logico-philosophical principles.  ...  Acknowledgements We want to thank our medical experts of the Competence Network Malignant Lymphoma and the Coordination Centers for Clinical Trials, Cologne and Leipzig for their support in creating and  ... 
doi:10.1007/978-3-540-30202-5_1 fatcat:kktcltzppnfqbh7yhjd3bormsu

Using ontology databases for scalable query answering, inconsistency detection, and data integration

Paea LePendu, Dejing Dou
2010 Journal of Intelligent Information Systems  
We have applied our methods to two case studies in biomedicine, using ontologies and data from genetics and neuroscience to illustrate two important applications: first, ontology databases answer ontology-based  ...  An ontology database is a basic relational database management system that models an ontology plus its instances.  ...  We thank Doug Howe and Jiawei Rong for their contributions on our GO and NEMO case studies. We also thank the ZFIN group, Zena M. Ariola and Gwen A. Frishkoff for their feedback on and contributions.  ... 
doi:10.1007/s10844-010-0133-4 pmid:22163378 pmcid:PMC3230227 fatcat:y7bbj5ktgbbwhg66jemta57gim

NanoParticle Ontology for cancer nanotechnology research

Dennis G. Thomas, Rohit V. Pappu, Nathan A. Baker
2011 Journal of Biomedical Informatics  
In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language  ...  Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools.  ...  The authors would also like to thank the anonymous referees for their valuable comments and suggestions, which has greatly affected the development of NPO.  ... 
doi:10.1016/j.jbi.2010.03.001 pmid:20211274 pmcid:PMC3042056 fatcat:3yialhmeljas3ficjh2zx45wta

Ontology Driven Concept Approximation [chapter]

Sinh Hoa Nguyen, Trung Thanh Nguyen, Hung Son Nguyen
2006 Lecture Notes in Computer Science  
This paper investigates the concept approximation problem using ontology as an domain knowledge representation model and rough set theory.  ...  In this paper we consider the extended model for knowledge representation where the concept hierarchies are embedded with additional knowledge in a form of relations or constrains among sub-concepts.  ...  The Role of Ontology in Inductive Learning Ontology is defined in literature as a formal description of concept names and relation types organized in a partial ordering by the concept-subconcept relation  ... 
doi:10.1007/11908029_57 fatcat:xbtgapca3ba3zgzz6b5f2kfh3q

Modularisation of domain ontologies implemented in description logics and related formalisms including OWL

Alan L. Rector
2003 Proceedings of the international conference on Knowledge capture - K-CAP '03  
Modularity is a key requirement for large ontologies in order to achieve re-use, maintainability, and evolution. Mechanisms for 'normalisation' to achieve analogous aims are standard for databases.  ...  This paper proposes initial criteria for a two-step normalisation of ontologies implemented using OWL or related DL based formalisms.  ...  In Guarino and welty they correspond to "types", "quasi-types" and certain concepts used to construct representation of "formal and material roles".  ... 
doi:10.1145/945649.945664 fatcat:iiknejtvoza3li363p6b3xnwra
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