Taxonomy and the Production of Semantic Phenotypes

Matthew J. Yoder; Michael B. Twidale; Andrea K. Thomer; Lars Vogt; Nico M. Franz; Jinlong Guo; Andrew R. Deans; James P. Balhoff

doi:10.3233/978-1-61499-854-9-53

Taxonomy and the Production of Semantic Phenotypes

Matthew J. Yoder, Michael B. Twidale, Andrea K. Thomer, Lars Vogt, Nico M. Franz, Jinlong Guo, Andrew R. Deans, James P. Balhoff

Prairie Research Institute

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

Abstract

Taxonomists produce a myriad of phenotypic descriptions. Traditionally these are provided in terse (telegraphic) natural language. As seen in parallel within other fields of biology researchers are exploring ways to formalize parts of the taxonomic process so that aspects of it are more computational in nature. The currently used data formalizations, mechanisms for persisting data, applications, and computing approaches related to the production of semantic descriptions (phenotypes) are reviewed, they, and their adopters are limited in number. In order to move forward we step back and characterize taxonomists with respect to their typical workflow and tendencies. We then use these characteristics as a basis for exploring how we might create software that taxonomists will find intuitive within their current workflows, providing interface examples as thought experiments.

Original language	English (US)
Title of host publication	Application of Semantic Technology in Biodiversity Science
Editors	A. E. Thessen
Pages	53--77
Volume	33
DOIs	https://doi.org/10.3233/978-1-61499-854-9-53
State	Published - 2018

Publication series

Name	Studies on the Semantic Web

Keywords

INHS

Access to Document

10.3233/978-1-61499-854-9-53

Link

Fingerprint Dive into the research topics of 'Taxonomy and the Production of Semantic Phenotypes'. Together they form a unique fingerprint.

Cite this

Yoder, M. J., Twidale, M. B., Thomer, A. K., Vogt, L., Franz, N. M., Guo, J., Deans, A. R., & Balhoff, J. P. (2018). Taxonomy and the Production of Semantic Phenotypes. In A. E. Thessen (Ed.), Application of Semantic Technology in Biodiversity Science (Vol. 33, pp. 53--77). (Studies on the Semantic Web). https://doi.org/10.3233/978-1-61499-854-9-53

Taxonomy and the Production of Semantic Phenotypes. / Yoder, Matthew J.; Twidale, Michael B.; Thomer, Andrea K.; Vogt, Lars; Franz, Nico M.; Guo, Jinlong; Deans, Andrew R.; Balhoff, James P.

Application of Semantic Technology in Biodiversity Science. ed. / A. E. Thessen. Vol. 33 2018. p. 53--77 (Studies on the Semantic Web).

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

@inbook{bbf7908f1d6149d7a9a468a1f5706abb,

title = "Taxonomy and the Production of Semantic Phenotypes",

abstract = "Taxonomists produce a myriad of phenotypic descriptions. Traditionally these are provided in terse (telegraphic) natural language. As seen in parallel within other fields of biology researchers are exploring ways to formalize parts of the taxonomic process so that aspects of it are more computational in nature. The currently used data formalizations, mechanisms for persisting data, applications, and computing approaches related to the production of semantic descriptions (phenotypes) are reviewed, they, and their adopters are limited in number. In order to move forward we step back and characterize taxonomists with respect to their typical workflow and tendencies. We then use these characteristics as a basis for exploring how we might create software that taxonomists will find intuitive within their current workflows, providing interface examples as thought experiments.",

keywords = "INHS",

author = "Yoder, {Matthew J.} and Twidale, {Michael B.} and Thomer, {Andrea K.} and Lars Vogt and Franz, {Nico M.} and Jinlong Guo and Deans, {Andrew R.} and Balhoff, {James P.}",

note = "WOS:000474507700004",

year = "2018",

doi = "10.3233/978-1-61499-854-9-53",

language = "English (US)",

volume = "33",

series = "Studies on the Semantic Web",

pages = "53----77",

editor = "Thessen, {A. E.}",

booktitle = "Application of Semantic Technology in Biodiversity Science",

}

TY - CHAP

T1 - Taxonomy and the Production of Semantic Phenotypes

AU - Yoder, Matthew J.

AU - Twidale, Michael B.

AU - Thomer, Andrea K.

AU - Vogt, Lars

AU - Franz, Nico M.

AU - Guo, Jinlong

AU - Deans, Andrew R.

AU - Balhoff, James P.

N1 - WOS:000474507700004

PY - 2018

Y1 - 2018

N2 - Taxonomists produce a myriad of phenotypic descriptions. Traditionally these are provided in terse (telegraphic) natural language. As seen in parallel within other fields of biology researchers are exploring ways to formalize parts of the taxonomic process so that aspects of it are more computational in nature. The currently used data formalizations, mechanisms for persisting data, applications, and computing approaches related to the production of semantic descriptions (phenotypes) are reviewed, they, and their adopters are limited in number. In order to move forward we step back and characterize taxonomists with respect to their typical workflow and tendencies. We then use these characteristics as a basis for exploring how we might create software that taxonomists will find intuitive within their current workflows, providing interface examples as thought experiments.

AB - Taxonomists produce a myriad of phenotypic descriptions. Traditionally these are provided in terse (telegraphic) natural language. As seen in parallel within other fields of biology researchers are exploring ways to formalize parts of the taxonomic process so that aspects of it are more computational in nature. The currently used data formalizations, mechanisms for persisting data, applications, and computing approaches related to the production of semantic descriptions (phenotypes) are reviewed, they, and their adopters are limited in number. In order to move forward we step back and characterize taxonomists with respect to their typical workflow and tendencies. We then use these characteristics as a basis for exploring how we might create software that taxonomists will find intuitive within their current workflows, providing interface examples as thought experiments.

KW - INHS

UR - http://ebooks.iospress.nl/volumearticle/49540

U2 - 10.3233/978-1-61499-854-9-53

DO - 10.3233/978-1-61499-854-9-53

M3 - Chapter

VL - 33

T3 - Studies on the Semantic Web

SP - 53

EP - 77

BT - Application of Semantic Technology in Biodiversity Science

A2 - Thessen, A. E.

ER -