Entity/quality-based logical definitions for the human skeletal phenome using PATO

Georgios V Gkoutos; Chris Mungall; Sandra Dolken; Michael Ashburner; Suzanna Lewis; John Hancock; Paul Schofield; Sebastian Kohler; Peter N Robinson

doi:10.1109/IEMBS.2009.5333362

Entity/quality-based logical definitions for the human skeletal phenome using PATO

Georgios V Gkoutos, Chris Mungall, Sandra Dolken, Michael Ashburner, Suzanna Lewis, John Hancock, Paul Schofield, Sebastian Kohler, Peter N Robinson

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (Non-Journal item)

70 Citations (Scopus)

Abstract

This paper describes an approach to providing computer-interpretable logical definitions for the terms of the Human Phenotype Ontology (HPO) using PATO, the ontology of phenotypic qualities, to link terms of the HPO to the anatomic and other entities that are affected by abnormal phenotypic qualities. This approach will allow improved computerized reasoning as well as a facility to compare phenotypes between different species. The PATO mapping will also provide direct links from phenotypic abnormalities and underlying anatomic structures encoded using the Foundational Model of Anatomy, which will be a valuable resource for computational investigations of the links between anatomical components and concepts representing diseases with abnormal phenotypes and associated genes.

Original language	English
Title of host publication	Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE
Publisher	IEEE Press
Pages	7069-7072
Number of pages	4
ISBN (Electronic)	978-1-4244-3296-7
ISBN (Print)	978-1-4244-3296-7
DOIs	https://doi.org/10.1109/IEMBS.2009.5333362
Publication status	Published - 2009
Event	Annual International conference of the IEEE, Engineering in Medicine and Biology Society - , United Kingdom of Great Britain and Northern Ireland Duration: 03 Sept 2009 → 06 Sept 2009

Conference

Conference	Annual International conference of the IEEE, Engineering in Medicine and Biology Society
Country/Territory	United Kingdom of Great Britain and Northern Ireland
Period	03 Sept 2009 → 06 Sept 2009

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1109/IEMBS.2009.5333362

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Gkoutos, G. V., Mungall, C., Dolken, S., Ashburner, M., Lewis, S., Hancock, J., Schofield, P., Kohler, S., & Robinson, P. N. (2009). Entity/quality-based logical definitions for the human skeletal phenome using PATO. In Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE (pp. 7069-7072). IEEE Press. https://doi.org/10.1109/IEMBS.2009.5333362

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title = "Entity/quality-based logical definitions for the human skeletal phenome using PATO",

abstract = "This paper describes an approach to providing computer-interpretable logical definitions for the terms of the Human Phenotype Ontology (HPO) using PATO, the ontology of phenotypic qualities, to link terms of the HPO to the anatomic and other entities that are affected by abnormal phenotypic qualities. This approach will allow improved computerized reasoning as well as a facility to compare phenotypes between different species. The PATO mapping will also provide direct links from phenotypic abnormalities and underlying anatomic structures encoded using the Foundational Model of Anatomy, which will be a valuable resource for computational investigations of the links between anatomical components and concepts representing diseases with abnormal phenotypes and associated genes.",

author = "Gkoutos, {Georgios V} and Chris Mungall and Sandra Dolken and Michael Ashburner and Suzanna Lewis and John Hancock and Paul Schofield and Sebastian Kohler and Robinson, {Peter N}",

year = "2009",

doi = "10.1109/IEMBS.2009.5333362",

language = "English",

isbn = "978-1-4244-3296-7",

pages = "7069--7072",

booktitle = "Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE",

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address = "United States of America",

note = "Annual International conference of the IEEE, Engineering in Medicine and Biology Society ; Conference date: 03-09-2009 Through 06-09-2009",

}

Gkoutos, GV, Mungall, C, Dolken, S, Ashburner, M, Lewis, S, Hancock, J, Schofield, P, Kohler, S & Robinson, PN 2009, Entity/quality-based logical definitions for the human skeletal phenome using PATO. in Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE. IEEE Press, pp. 7069-7072, Annual International conference of the IEEE, Engineering in Medicine and Biology Society, United Kingdom of Great Britain and Northern Ireland, 03 Sept 2009. https://doi.org/10.1109/IEMBS.2009.5333362

Entity/quality-based logical definitions for the human skeletal phenome using PATO. / Gkoutos, Georgios V; Mungall, Chris; Dolken, Sandra et al.
Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE. IEEE Press, 2009. p. 7069-7072.

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (Non-Journal item)

TY - GEN

T1 - Entity/quality-based logical definitions for the human skeletal phenome using PATO

AU - Gkoutos, Georgios V

AU - Mungall, Chris

AU - Dolken, Sandra

AU - Ashburner, Michael

AU - Lewis, Suzanna

AU - Hancock, John

AU - Schofield, Paul

AU - Kohler, Sebastian

AU - Robinson, Peter N

PY - 2009

Y1 - 2009

N2 - This paper describes an approach to providing computer-interpretable logical definitions for the terms of the Human Phenotype Ontology (HPO) using PATO, the ontology of phenotypic qualities, to link terms of the HPO to the anatomic and other entities that are affected by abnormal phenotypic qualities. This approach will allow improved computerized reasoning as well as a facility to compare phenotypes between different species. The PATO mapping will also provide direct links from phenotypic abnormalities and underlying anatomic structures encoded using the Foundational Model of Anatomy, which will be a valuable resource for computational investigations of the links between anatomical components and concepts representing diseases with abnormal phenotypes and associated genes.

AB - This paper describes an approach to providing computer-interpretable logical definitions for the terms of the Human Phenotype Ontology (HPO) using PATO, the ontology of phenotypic qualities, to link terms of the HPO to the anatomic and other entities that are affected by abnormal phenotypic qualities. This approach will allow improved computerized reasoning as well as a facility to compare phenotypes between different species. The PATO mapping will also provide direct links from phenotypic abnormalities and underlying anatomic structures encoded using the Foundational Model of Anatomy, which will be a valuable resource for computational investigations of the links between anatomical components and concepts representing diseases with abnormal phenotypes and associated genes.

UR - http://hdl.handle.net/2160/12088

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DO - 10.1109/IEMBS.2009.5333362

M3 - Conference Proceeding (Non-Journal item)

C2 - 19964203

SN - 978-1-4244-3296-7

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EP - 7072

BT - Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE

PB - IEEE Press

T2 - Annual International conference of the IEEE, Engineering in Medicine and Biology Society

Y2 - 3 September 2009 through 6 September 2009

ER -

Entity/quality-based logical definitions for the human skeletal phenome using PATO

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