Literature-based knowledge discovery from relationship associations based on a dl ontology created from MeSH

Steven B. Kraines, Weisen Guo, Daisuke Hoshiyama, Takaki Makino, Haruo Mizutani, Yoshihiro Okuda, Yo Shidahara, Toshihisa Takagi

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

Abstract

Literature-based knowledge discovery generates potential discoveries from associations between specific concepts that have been previously reported in the literature. However, because the associations are generally between individual concepts, the knowledge of specific relationships between those concepts is lost. A description logic (DL) ontology adds a set of logically defined relationship types, called properties, to a classification of concepts for a particular knowledge domain. Properties can represent specific relationships between instances of concepts used to describe the things studied by a particular researcher. These relationships form a "triple" consisting of a domain instance, a range instance, and the property specifying the way those instances are related. A "relationship association" is a pair of relationship triples where one of the instances from each relationship can be determined to be semantically equivalent. In this paper, we report our work to structure a subset of more than 1300 terms from the Medical Subject Headings (MeSH) controlled vocabulary into a DL ontology, and to use that DL ontology to create a corpus of A-Boxes, which we call "semantic statements", each of which describes one of 392 research articles that we selected from MEDLINE. Relationship associations were extracted from the corpus of semantic statements using a previously reported technique. Then, by making the assumption of the transitivity of association used in literature-based knowledge discovery, we generate hypothetical relationship associations by combining pairs of relationship associations. We then evaluate the "interestingness" of those candidate knowledge discoveries from a life science perspective.

Original languageEnglish
Title of host publicationKnowledge Discovery, Knowledge Engineering and Knowledge Management - Second International Joint Conference, IC3K 2010, Revised Selected Papers
PublisherSpringer
Pages87-106
Number of pages20
Volume272 CCIS
ISBN (Print)9783642297632
DOIs
Publication statusPublished - 2013
Externally publishedYes
Event2nd International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management, IC3K 2010 - Valencia, Valencia, Spain
Duration: 25 Oct 201028 Oct 2010

Publication series

NameCommunications in Computer and Information Science
Volume272 CCIS
ISSN (Print)18650929

Conference

Conference2nd International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management, IC3K 2010
CountrySpain
CityValencia
Period25/10/1028/10/10

Fingerprint

Data mining
Ontology
Semantics
Thesauri

Cite this

Kraines, S. B., Guo, W., Hoshiyama, D., Makino, T., Mizutani, H., Okuda, Y., ... Takagi, T. (2013). Literature-based knowledge discovery from relationship associations based on a dl ontology created from MeSH. In Knowledge Discovery, Knowledge Engineering and Knowledge Management - Second International Joint Conference, IC3K 2010, Revised Selected Papers (Vol. 272 CCIS, pp. 87-106). (Communications in Computer and Information Science; Vol. 272 CCIS). Springer. https://doi.org/10.1007/978-3-642-29764-9-6
Kraines, Steven B. ; Guo, Weisen ; Hoshiyama, Daisuke ; Makino, Takaki ; Mizutani, Haruo ; Okuda, Yoshihiro ; Shidahara, Yo ; Takagi, Toshihisa. / Literature-based knowledge discovery from relationship associations based on a dl ontology created from MeSH. Knowledge Discovery, Knowledge Engineering and Knowledge Management - Second International Joint Conference, IC3K 2010, Revised Selected Papers. Vol. 272 CCIS Springer, 2013. pp. 87-106 (Communications in Computer and Information Science).
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abstract = "Literature-based knowledge discovery generates potential discoveries from associations between specific concepts that have been previously reported in the literature. However, because the associations are generally between individual concepts, the knowledge of specific relationships between those concepts is lost. A description logic (DL) ontology adds a set of logically defined relationship types, called properties, to a classification of concepts for a particular knowledge domain. Properties can represent specific relationships between instances of concepts used to describe the things studied by a particular researcher. These relationships form a {"}triple{"} consisting of a domain instance, a range instance, and the property specifying the way those instances are related. A {"}relationship association{"} is a pair of relationship triples where one of the instances from each relationship can be determined to be semantically equivalent. In this paper, we report our work to structure a subset of more than 1300 terms from the Medical Subject Headings (MeSH) controlled vocabulary into a DL ontology, and to use that DL ontology to create a corpus of A-Boxes, which we call {"}semantic statements{"}, each of which describes one of 392 research articles that we selected from MEDLINE. Relationship associations were extracted from the corpus of semantic statements using a previously reported technique. Then, by making the assumption of the transitivity of association used in literature-based knowledge discovery, we generate hypothetical relationship associations by combining pairs of relationship associations. We then evaluate the {"}interestingness{"} of those candidate knowledge discoveries from a life science perspective.",
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Kraines, SB, Guo, W, Hoshiyama, D, Makino, T, Mizutani, H, Okuda, Y, Shidahara, Y & Takagi, T 2013, Literature-based knowledge discovery from relationship associations based on a dl ontology created from MeSH. in Knowledge Discovery, Knowledge Engineering and Knowledge Management - Second International Joint Conference, IC3K 2010, Revised Selected Papers. vol. 272 CCIS, Communications in Computer and Information Science, vol. 272 CCIS, Springer, pp. 87-106, 2nd International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management, IC3K 2010, Valencia, Spain, 25/10/10. https://doi.org/10.1007/978-3-642-29764-9-6

Literature-based knowledge discovery from relationship associations based on a dl ontology created from MeSH. / Kraines, Steven B.; Guo, Weisen; Hoshiyama, Daisuke; Makino, Takaki; Mizutani, Haruo; Okuda, Yoshihiro; Shidahara, Yo; Takagi, Toshihisa.

Knowledge Discovery, Knowledge Engineering and Knowledge Management - Second International Joint Conference, IC3K 2010, Revised Selected Papers. Vol. 272 CCIS Springer, 2013. p. 87-106 (Communications in Computer and Information Science; Vol. 272 CCIS).

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

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Kraines SB, Guo W, Hoshiyama D, Makino T, Mizutani H, Okuda Y et al. Literature-based knowledge discovery from relationship associations based on a dl ontology created from MeSH. In Knowledge Discovery, Knowledge Engineering and Knowledge Management - Second International Joint Conference, IC3K 2010, Revised Selected Papers. Vol. 272 CCIS. Springer. 2013. p. 87-106. (Communications in Computer and Information Science). https://doi.org/10.1007/978-3-642-29764-9-6