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Formalizing biomedical concepts from textual definitionsPetrova, Alina, Ma, Yue, Tsatsaronis, George, Kissa, Maria, Distel, Felix, Baader, Franz, Schroeder, Michael 07 January 2016 (has links) (PDF)
BACKGROUND:
Ontologies play a major role in life sciences, enabling a number of applications, from new data integration to knowledge verification. SNOMED CT is a large medical ontology that is formally defined so that it ensures global consistency and support of complex reasoning tasks. Most biomedical ontologies and taxonomies on the other hand define concepts only textually, without the use of logic. Here, we investigate how to automatically generate formal concept definitions from textual ones. We develop a method that uses machine learning in combination with several types of lexical and semantic features and outputs formal definitions that follow the structure of SNOMED CT concept definitions.
RESULTS:
We evaluate our method on three benchmarks and test both the underlying relation extraction component as well as the overall quality of output concept definitions. In addition, we provide an analysis on the following aspects: (1) How do definitions mined from the Web and literature differ from the ones mined from manually created definitions, e.g., MeSH? (2) How do different feature representations, e.g., the restrictions of relations' domain and range, impact on the generated definition quality?, (3) How do different machine learning algorithms compare to each other for the task of formal definition generation?, and, (4) What is the influence of the learning data size to the task? We discuss all of these settings in detail and show that the suggested approach can achieve success rates of over 90%. In addition, the results show that the choice of corpora, lexical features, learning algorithm and data size do not impact the performance as strongly as semantic types do. Semantic types limit the domain and range of a predicted relation, and as long as relations' domain and range pairs do not overlap, this information is most valuable in formalizing textual definitions.
CONCLUSIONS:
The analysis presented in this manuscript implies that automated methods can provide a valuable contribution to the formalization of biomedical knowledge, thus paving the way for future applications that go beyond retrieval and into complex reasoning. The method is implemented and accessible to the public from: https://github.com/alifahsyamsiyah/learningDL.
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Formalizing biomedical concepts from textual definitionsTsatsaronis, George, Ma, Yue, Petrova, Alina, Kissa, Maria, Distel, Felix, Baader , Franz, Schroeder, Michael 04 January 2016 (has links) (PDF)
Background
Ontologies play a major role in life sciences, enabling a number of applications, from new data integration to knowledge verification. SNOMED CT is a large medical ontology that is formally defined so that it ensures global consistency and support of complex reasoning tasks. Most biomedical ontologies and taxonomies on the other hand define concepts only textually, without the use of logic. Here, we investigate how to automatically generate formal concept definitions from textual ones. We develop a method that uses machine learning in combination with several types of lexical and semantic features and outputs formal definitions that follow the structure of SNOMED CT concept definitions.
Results
We evaluate our method on three benchmarks and test both the underlying relation extraction component as well as the overall quality of output concept definitions. In addition, we provide an analysis on the following aspects: (1) How do definitions mined from the Web and literature differ from the ones mined from manually created definitions, e.g., MeSH? (2) How do different feature representations, e.g., the restrictions of relations’ domain and range, impact on the generated definition quality?, (3) How do different machine learning algorithms compare to each other for the task of formal definition generation?, and, (4) What is the influence of the learning data size to the task? We discuss all of these settings in detail and show that the suggested approach can achieve success rates of over 90%. In addition, the results show that the choice of corpora, lexical features, learning algorithm and data size do not impact the performance as strongly as semantic types do. Semantic types limit the domain and range of a predicted relation, and as long as relations’ domain and range pairs do not overlap, this information is most valuable in formalizing textual definitions.
Conclusions
The analysis presented in this manuscript implies that automated methods can provide a valuable contribution to the formalization of biomedical knowledge, thus paving the way for future applications that go beyond retrieval and into complex reasoning. The method is implemented and accessible to the public from: https://github.com/alifahsyamsiyah/learningDL.
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Formalizing biomedical concepts from textual definitionsPetrova, Alina, Ma, Yue, Tsatsaronis, George, Kissa, Maria, Distel, Felix, Baader, Franz, Schroeder, Michael 07 January 2016 (has links)
BACKGROUND:
Ontologies play a major role in life sciences, enabling a number of applications, from new data integration to knowledge verification. SNOMED CT is a large medical ontology that is formally defined so that it ensures global consistency and support of complex reasoning tasks. Most biomedical ontologies and taxonomies on the other hand define concepts only textually, without the use of logic. Here, we investigate how to automatically generate formal concept definitions from textual ones. We develop a method that uses machine learning in combination with several types of lexical and semantic features and outputs formal definitions that follow the structure of SNOMED CT concept definitions.
RESULTS:
We evaluate our method on three benchmarks and test both the underlying relation extraction component as well as the overall quality of output concept definitions. In addition, we provide an analysis on the following aspects: (1) How do definitions mined from the Web and literature differ from the ones mined from manually created definitions, e.g., MeSH? (2) How do different feature representations, e.g., the restrictions of relations' domain and range, impact on the generated definition quality?, (3) How do different machine learning algorithms compare to each other for the task of formal definition generation?, and, (4) What is the influence of the learning data size to the task? We discuss all of these settings in detail and show that the suggested approach can achieve success rates of over 90%. In addition, the results show that the choice of corpora, lexical features, learning algorithm and data size do not impact the performance as strongly as semantic types do. Semantic types limit the domain and range of a predicted relation, and as long as relations' domain and range pairs do not overlap, this information is most valuable in formalizing textual definitions.
CONCLUSIONS:
The analysis presented in this manuscript implies that automated methods can provide a valuable contribution to the formalization of biomedical knowledge, thus paving the way for future applications that go beyond retrieval and into complex reasoning. The method is implemented and accessible to the public from: https://github.com/alifahsyamsiyah/learningDL.
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Formalizing biomedical concepts from textual definitions: Research ArticleTsatsaronis, George, Ma, Yue, Petrova, Alina, Kissa, Maria, Distel, Felix, Baader, Franz, Schroeder, Michael 04 January 2016 (has links)
Background
Ontologies play a major role in life sciences, enabling a number of applications, from new data integration to knowledge verification. SNOMED CT is a large medical ontology that is formally defined so that it ensures global consistency and support of complex reasoning tasks. Most biomedical ontologies and taxonomies on the other hand define concepts only textually, without the use of logic. Here, we investigate how to automatically generate formal concept definitions from textual ones. We develop a method that uses machine learning in combination with several types of lexical and semantic features and outputs formal definitions that follow the structure of SNOMED CT concept definitions.
Results
We evaluate our method on three benchmarks and test both the underlying relation extraction component as well as the overall quality of output concept definitions. In addition, we provide an analysis on the following aspects: (1) How do definitions mined from the Web and literature differ from the ones mined from manually created definitions, e.g., MeSH? (2) How do different feature representations, e.g., the restrictions of relations’ domain and range, impact on the generated definition quality?, (3) How do different machine learning algorithms compare to each other for the task of formal definition generation?, and, (4) What is the influence of the learning data size to the task? We discuss all of these settings in detail and show that the suggested approach can achieve success rates of over 90%. In addition, the results show that the choice of corpora, lexical features, learning algorithm and data size do not impact the performance as strongly as semantic types do. Semantic types limit the domain and range of a predicted relation, and as long as relations’ domain and range pairs do not overlap, this information is most valuable in formalizing textual definitions.
Conclusions
The analysis presented in this manuscript implies that automated methods can provide a valuable contribution to the formalization of biomedical knowledge, thus paving the way for future applications that go beyond retrieval and into complex reasoning. The method is implemented and accessible to the public from: https://github.com/alifahsyamsiyah/learningDL.
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Polynomial-Time Reasoning Support for Design and Maintenance of Large-Scale Biomedical OntologiesSuntisrivaraporn, Boontawee 05 February 2009 (has links) (PDF)
Description Logics (DLs) belong to a successful family of knowledge representation formalisms with two key assets: formally well-defined semantics which allows to represent knowledge in an unambiguous way and automated reasoning which allows to infer implicit knowledge from the one given explicitly. This thesis investigates various reasoning techniques for tractable DLs in the EL family which have been implemented in the CEL system. It suggests that the use of the lightweight DLs, in which reasoning is tractable, is beneficial for ontology design and maintenance both in terms of expressivity and scalability. The claim is supported by a case study on the renown medical ontology SNOMED CT and extensive empirical evaluation on several large-scale biomedical ontologies.
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Polynomial-Time Reasoning Support for Design and Maintenance of Large-Scale Biomedical OntologiesSuntisrivaraporn, Boontawee 21 January 2009 (has links)
Description Logics (DLs) belong to a successful family of knowledge representation formalisms with two key assets: formally well-defined semantics which allows to represent knowledge in an unambiguous way and automated reasoning which allows to infer implicit knowledge from the one given explicitly. This thesis investigates various reasoning techniques for tractable DLs in the EL family which have been implemented in the CEL system. It suggests that the use of the lightweight DLs, in which reasoning is tractable, is beneficial for ontology design and maintenance both in terms of expressivity and scalability. The claim is supported by a case study on the renown medical ontology SNOMED CT and extensive empirical evaluation on several large-scale biomedical ontologies.
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