An advanced strategy for integration of biological measurement data

Hiroshi Masuya; Georgios V Gkoutos; Nobuhiko Tanaka; Kazunori Waki; Yoshihiro Okuda; Tatsuya Kushida; Norio Kobayashi; Koji Doi; Kouji Kozaki; Robert Hoehndorf

An advanced strategy for integration of biological measurement data

Hiroshi Masuya, Georgios V Gkoutos, Nobuhiko Tanaka, Kazunori Waki, Yoshihiro Okuda, Tatsuya Kushida, Norio Kobayashi, Koji Doi, Kouji Kozaki, Robert Hoehndorf

Cancer and Genomic Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

11 Citations (Scopus)

66 Downloads (Pure)

Abstract

Aiming at integration of measurement data across various biological experiments, we investigated a methodology for expanding the Phenotypic Quality Ontology (PATO), commonly used for descriptions of biological phenotypes, based on the YAMATO top-level ontology. The mapping of ontology terms from PATO to the YAMATO framework brings several benefits, including: introduction of a classification of quality values to represent measurement scales; distinction of different contexts in which comparisons of ordinal values are made; and establishment of interoperability of quality description formalisms based on different top-level ontologies. In this study, we propose an ontological basis for integrating cross-species and cross-experimental biological measurement data.

Original language	English
Title of host publication	ICBO-2011
Subtitle of host publication	Proceedings of the 2nd International Conference on Biomedical Ontology
Editors	Olivier Bodenreider , Maryann E. Martone, Alan Ruttenberg
Publisher	CEUR-WS.org
Pages	79-86
Publication status	Published - 2011
Event	International Conference on Biomedical Ontology 2011 - New York, Buffalo, United States Duration: 26 Jul 2011 → 30 Jul 2011

Publication series

Name	CEUR Workshop Proceedings
Volume	833
ISSN (Print)	1613-0073

Conference

Conference	International Conference on Biomedical Ontology 2011
Country/Territory	United States
City	Buffalo
Period	26/07/11 → 30/07/11

Keywords

Interoperability
top-level ontology
quality
phenotype

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Masuya_et_al_An_advanced_strategy_ICBO_2011
Open access article distributed under the terms of the Creative Commons Attribution License 3.0, which permits unrestricted use, distribution, and reproduction, provided the original work is properly cited.
Final published version, 4.65 MBLicence: Creative Commons: Attribution (CC BY)

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Masuya, H., Gkoutos, G. V., Tanaka, N., Waki, K., Okuda, Y., Kushida, T., Kobayashi, N., Doi, K., Kozaki, K., & Hoehndorf, R. (2011). An advanced strategy for integration of biological measurement data. In O. Bodenreider , M. E. Martone, & A. Ruttenberg (Eds.), ICBO-2011: Proceedings of the 2nd International Conference on Biomedical Ontology (pp. 79-86). (CEUR Workshop Proceedings; Vol. 833). CEUR-WS.org.

@inproceedings{4860b4f9d7bb4c2b8d9ed136e1df5e9f,

title = "An advanced strategy for integration of biological measurement data",

abstract = "Aiming at integration of measurement data across various biological experiments, we investigated a methodology for expanding the Phenotypic Quality Ontology (PATO), commonly used for descriptions of biological phenotypes, based on the YAMATO top-level ontology. The mapping of ontology terms from PATO to the YAMATO framework brings several benefits, including: introduction of a classification of quality values to represent measurement scales; distinction of different contexts in which comparisons of ordinal values are made; and establishment of interoperability of quality description formalisms based on different top-level ontologies. In this study, we propose an ontological basis for integrating cross-species and cross-experimental biological measurement data. ",

keywords = "Interoperability, top-level ontology, quality, phenotype",

author = "Hiroshi Masuya and Gkoutos, {Georgios V} and Nobuhiko Tanaka and Kazunori Waki and Yoshihiro Okuda and Tatsuya Kushida and Norio Kobayashi and Koji Doi and Kouji Kozaki and Robert Hoehndorf",

year = "2011",

language = "English",

series = "CEUR Workshop Proceedings",

publisher = "CEUR-WS.org",

pages = "79--86",

editor = "{Bodenreider }, Olivier and Martone, {Maryann E.} and Alan Ruttenberg",

booktitle = "ICBO-2011",

note = "International Conference on Biomedical Ontology 2011 ; Conference date: 26-07-2011 Through 30-07-2011",

}

Masuya, H, Gkoutos, GV, Tanaka, N, Waki, K, Okuda, Y, Kushida, T, Kobayashi, N, Doi, K, Kozaki, K & Hoehndorf, R 2011, An advanced strategy for integration of biological measurement data. in O Bodenreider , ME Martone & A Ruttenberg (eds), ICBO-2011: Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR Workshop Proceedings, vol. 833, CEUR-WS.org, pp. 79-86, International Conference on Biomedical Ontology 2011, Buffalo, United States, 26/07/11.

An advanced strategy for integration of biological measurement data. / Masuya, Hiroshi; Gkoutos, Georgios V; Tanaka, Nobuhiko et al.
ICBO-2011: Proceedings of the 2nd International Conference on Biomedical Ontology. ed. / Olivier Bodenreider ; Maryann E. Martone; Alan Ruttenberg. CEUR-WS.org, 2011. p. 79-86 (CEUR Workshop Proceedings; Vol. 833).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - An advanced strategy for integration of biological measurement data

AU - Masuya, Hiroshi

AU - Gkoutos, Georgios V

AU - Tanaka, Nobuhiko

AU - Waki, Kazunori

AU - Okuda, Yoshihiro

AU - Kushida, Tatsuya

AU - Kobayashi, Norio

AU - Doi, Koji

AU - Kozaki, Kouji

AU - Hoehndorf, Robert

PY - 2011

Y1 - 2011

N2 - Aiming at integration of measurement data across various biological experiments, we investigated a methodology for expanding the Phenotypic Quality Ontology (PATO), commonly used for descriptions of biological phenotypes, based on the YAMATO top-level ontology. The mapping of ontology terms from PATO to the YAMATO framework brings several benefits, including: introduction of a classification of quality values to represent measurement scales; distinction of different contexts in which comparisons of ordinal values are made; and establishment of interoperability of quality description formalisms based on different top-level ontologies. In this study, we propose an ontological basis for integrating cross-species and cross-experimental biological measurement data.

AB - Aiming at integration of measurement data across various biological experiments, we investigated a methodology for expanding the Phenotypic Quality Ontology (PATO), commonly used for descriptions of biological phenotypes, based on the YAMATO top-level ontology. The mapping of ontology terms from PATO to the YAMATO framework brings several benefits, including: introduction of a classification of quality values to represent measurement scales; distinction of different contexts in which comparisons of ordinal values are made; and establishment of interoperability of quality description formalisms based on different top-level ontologies. In this study, we propose an ontological basis for integrating cross-species and cross-experimental biological measurement data.

KW - Interoperability

KW - top-level ontology

KW - quality

KW - phenotype

M3 - Conference contribution

T3 - CEUR Workshop Proceedings

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EP - 86

BT - ICBO-2011

A2 - Bodenreider , Olivier

A2 - Martone, Maryann E.

A2 - Ruttenberg, Alan

PB - CEUR-WS.org

T2 - International Conference on Biomedical Ontology 2011

Y2 - 26 July 2011 through 30 July 2011

ER -

An advanced strategy for integration of biological measurement data

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Keywords

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