SIABO: Semantic Information Access through Biomedical Ontologies

Troels Andreasen, Sine Zambach, Tine Lassen, Jørgen Fischer Nilsson, Bodil Nistrup Madsen, Per Anker Jensen, Hanne Erdman Thomsen, Bartlomiej Antoni Szymczak

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

The scientific aim of the project presented in this paper is to provide an approach to representing, organizing, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontologies', i.e., ontologies providing increasingly specialized concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so-called ‘ontological semantics' which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form of data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project is unique in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.
Original languageEnglish
Title of host publicationKEOD 2009 : 1st International Conference on Knowledge Engeneering and Ontology Development
EditorsJan L. G. Dietz
Number of pages6
PublisherInstitute for Systems and Technologies of Information, Control and Communication
Publication date2009
Pages171-176
ISBN (Print)978-989-674-012-2
Publication statusPublished - 2009
EventInternational Conference on Knowledge Engeneering and Ontology Development (KEOD) - Funchal, Portugal
Duration: 6 Oct 20098 Oct 2009

Conference

ConferenceInternational Conference on Knowledge Engeneering and Ontology Development (KEOD)
CountryPortugal
CityFunchal
Period06/10/200908/10/2009

Keywords

  • Domain modelling
  • Ontology engeneering
  • NLP
  • Ontological, Content-oriented text search

Cite this

Andreasen, T., Zambach, S., Lassen, T., Nilsson, J. F., Madsen, B. N., Jensen, P. A., ... Szymczak, B. A. (2009). SIABO: Semantic Information Access through Biomedical Ontologies. In J. L. G. Dietz (Ed.), KEOD 2009: 1st International Conference on Knowledge Engeneering and Ontology Development (pp. 171-176). Institute for Systems and Technologies of Information, Control and Communication.
Andreasen, Troels ; Zambach, Sine ; Lassen, Tine ; Nilsson, Jørgen Fischer ; Madsen, Bodil Nistrup ; Jensen, Per Anker ; Thomsen, Hanne Erdman ; Szymczak, Bartlomiej Antoni. / SIABO : Semantic Information Access through Biomedical Ontologies. KEOD 2009: 1st International Conference on Knowledge Engeneering and Ontology Development. editor / Jan L. G. Dietz. Institute for Systems and Technologies of Information, Control and Communication, 2009. pp. 171-176
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title = "SIABO: Semantic Information Access through Biomedical Ontologies",
abstract = "The scientific aim of the project presented in this paper is to provide an approach to representing, organizing, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontologies', i.e., ontologies providing increasingly specialized concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so-called ‘ontological semantics' which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form of data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project is unique in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.",
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author = "Troels Andreasen and Sine Zambach and Tine Lassen and Nilsson, {J{\o}rgen Fischer} and Madsen, {Bodil Nistrup} and Jensen, {Per Anker} and Thomsen, {Hanne Erdman} and Szymczak, {Bartlomiej Antoni}",
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language = "English",
isbn = "978-989-674-012-2",
pages = "171--176",
editor = "Dietz, {Jan L. G.}",
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Andreasen, T, Zambach, S, Lassen, T, Nilsson, JF, Madsen, BN, Jensen, PA, Thomsen, HE & Szymczak, BA 2009, SIABO: Semantic Information Access through Biomedical Ontologies. in JLG Dietz (ed.), KEOD 2009: 1st International Conference on Knowledge Engeneering and Ontology Development. Institute for Systems and Technologies of Information, Control and Communication, pp. 171-176, Funchal, Portugal, 06/10/2009.

SIABO : Semantic Information Access through Biomedical Ontologies. / Andreasen, Troels; Zambach, Sine; Lassen, Tine; Nilsson, Jørgen Fischer; Madsen, Bodil Nistrup; Jensen, Per Anker; Thomsen, Hanne Erdman; Szymczak, Bartlomiej Antoni.

KEOD 2009: 1st International Conference on Knowledge Engeneering and Ontology Development. ed. / Jan L. G. Dietz. Institute for Systems and Technologies of Information, Control and Communication, 2009. p. 171-176.

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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T1 - SIABO

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AU - Lassen, Tine

AU - Nilsson, Jørgen Fischer

AU - Madsen, Bodil Nistrup

AU - Jensen, Per Anker

AU - Thomsen, Hanne Erdman

AU - Szymczak, Bartlomiej Antoni

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N2 - The scientific aim of the project presented in this paper is to provide an approach to representing, organizing, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontologies', i.e., ontologies providing increasingly specialized concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so-called ‘ontological semantics' which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form of data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project is unique in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.

AB - The scientific aim of the project presented in this paper is to provide an approach to representing, organizing, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontologies', i.e., ontologies providing increasingly specialized concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so-called ‘ontological semantics' which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form of data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project is unique in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.

KW - Domæne modellering

KW - Ontologi-konstruktion

KW - Natursprogsanalyse

KW - Ontologisk, indholdsbaseret søgning

KW - Domain modelling

KW - Ontology engeneering

KW - NLP

KW - Ontological, Content-oriented text search

M3 - Article in proceedings

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BT - KEOD 2009

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Andreasen T, Zambach S, Lassen T, Nilsson JF, Madsen BN, Jensen PA et al. SIABO: Semantic Information Access through Biomedical Ontologies. In Dietz JLG, editor, KEOD 2009: 1st International Conference on Knowledge Engeneering and Ontology Development. Institute for Systems and Technologies of Information, Control and Communication. 2009. p. 171-176