Aligning the human phenotype and mammalian phenotype ontology using dead simple ontology design patterns

Nicole Vasilevsky; James P. Balhoff; Christopher J. Mungall; David Osumi-Sutherland; Sebastian Kohler; Susan Bello; Cynthia Smith; Peter Robinson; Melissa Haendel

Aligning the human phenotype and mammalian phenotype ontology using dead simple ontology design patterns

Nicole Vasilevsky, James P. Balhoff, Christopher J. Mungall, David Osumi-Sutherland, Sebastian Kohler, Susan Bello, Cynthia Smith, Peter Robinson, Melissa Haendel

Research output: Contribution to journal › Conference article › peer-review

Abstract

The Human Phenotype Ontology (HP) and Mammalian Phenotype (MP) Ontology represent information about abnormal phenotypes encountered in human diseases and mammalian organisms, respectively. It is a goal to co-develop these ontologies and align the terminology and logical axioms to increase interoperability of the two ontologies. Towards this end, we have worked to develop consistent design patterns for commonly used types of classes, such as morphological phenotypes or abnormal anatomical structures. We are currently implementing ‘dead simple ontology design patterns’ (DOSDP), which are design patterns that can be specified in a YAML text file and can be used to generate new terms, documentation, retrofit old terms, and allows for reuse of patterns. This paper describes the development and implementation of the DOSDP in the HP and MP.

Original language	English (US)
Journal	CEUR Workshop Proceedings
Volume	2137
State	Published - 2017
Event	8th International Conference on Biomedical Ontology, ICBO 2017 - Newcastle-upon-Tyne, United Kingdom Duration: Sep 13 2017 → Sep 15 2017

ASJC Scopus subject areas

General Computer Science

Cite this

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title = "Aligning the human phenotype and mammalian phenotype ontology using dead simple ontology design patterns",

abstract = "The Human Phenotype Ontology (HP) and Mammalian Phenotype (MP) Ontology represent information about abnormal phenotypes encountered in human diseases and mammalian organisms, respectively. It is a goal to co-develop these ontologies and align the terminology and logical axioms to increase interoperability of the two ontologies. Towards this end, we have worked to develop consistent design patterns for commonly used types of classes, such as morphological phenotypes or abnormal anatomical structures. We are currently implementing {\textquoteleft}dead simple ontology design patterns{\textquoteright} (DOSDP), which are design patterns that can be specified in a YAML text file and can be used to generate new terms, documentation, retrofit old terms, and allows for reuse of patterns. This paper describes the development and implementation of the DOSDP in the HP and MP.",

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AU - Vasilevsky, Nicole

AU - Balhoff, James P.

AU - Mungall, Christopher J.

AU - Osumi-Sutherland, David

AU - Kohler, Sebastian

AU - Bello, Susan

AU - Smith, Cynthia

AU - Robinson, Peter

AU - Haendel, Melissa

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N2 - The Human Phenotype Ontology (HP) and Mammalian Phenotype (MP) Ontology represent information about abnormal phenotypes encountered in human diseases and mammalian organisms, respectively. It is a goal to co-develop these ontologies and align the terminology and logical axioms to increase interoperability of the two ontologies. Towards this end, we have worked to develop consistent design patterns for commonly used types of classes, such as morphological phenotypes or abnormal anatomical structures. We are currently implementing ‘dead simple ontology design patterns’ (DOSDP), which are design patterns that can be specified in a YAML text file and can be used to generate new terms, documentation, retrofit old terms, and allows for reuse of patterns. This paper describes the development and implementation of the DOSDP in the HP and MP.

AB - The Human Phenotype Ontology (HP) and Mammalian Phenotype (MP) Ontology represent information about abnormal phenotypes encountered in human diseases and mammalian organisms, respectively. It is a goal to co-develop these ontologies and align the terminology and logical axioms to increase interoperability of the two ontologies. Towards this end, we have worked to develop consistent design patterns for commonly used types of classes, such as morphological phenotypes or abnormal anatomical structures. We are currently implementing ‘dead simple ontology design patterns’ (DOSDP), which are design patterns that can be specified in a YAML text file and can be used to generate new terms, documentation, retrofit old terms, and allows for reuse of patterns. This paper describes the development and implementation of the DOSDP in the HP and MP.

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Aligning the human phenotype and mammalian phenotype ontology using dead simple ontology design patterns

Abstract

ASJC Scopus subject areas

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