Standardization of assay representation in the Ontology for Biomedical Investigations

Randi Vita; Jie Zheng; Rebecca Jackson; Damion Dooley; James A. Overton; Mark A. Miller; Daniel C. Berrios; Richard H. Scheuermann; Yongqun He; Hande Küçük Mcginty; Mathias Brochhausen; Aisyah Yu Lin; Sagar B. Jain; Marcus C. Chibucos; John Judkins; Michelle G. Giglio; Irene Y. Feng; Gully Burns; Matthew H. Brush; Bjoern Peters; Christian J. Stoeckert

doi:10.1093/database/baab040

Standardization of assay representation in the Ontology for Biomedical Investigations

Randi Vita, Jie Zheng, Rebecca Jackson, Damion Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Küçük Mcginty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern PetersChristian J. Stoeckert

Oregon Clinical and Translational Research Institute

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Abstract

The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

Original language	English (US)
Article number	baab040
Journal	Database
Volume	2021
DOIs	https://doi.org/10.1093/database/baab040
State	Published - 2021

ASJC Scopus subject areas

Information Systems
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

Access to Document

10.1093/database/baab040

Cite this

Vita, R., Zheng, J., Jackson, R., Dooley, D., Overton, J. A., Miller, M. A., Berrios, D. C., Scheuermann, R. H., He, Y., Mcginty, H. K., Brochhausen, M., Lin, A. Y., Jain, S. B., Chibucos, M. C., Judkins, J., Giglio, M. G., Feng, I. Y., Burns, G., Brush, M. H., ... Stoeckert, C. J. (2021). Standardization of assay representation in the Ontology for Biomedical Investigations. Database, 2021, Article baab040. https://doi.org/10.1093/database/baab040

Vita, R, Zheng, J, Jackson, R, Dooley, D, Overton, JA, Miller, MA, Berrios, DC, Scheuermann, RH, He, Y, Mcginty, HK, Brochhausen, M, Lin, AY, Jain, SB, Chibucos, MC, Judkins, J, Giglio, MG, Feng, IY, Burns, G, Brush, MH, Peters, B & Stoeckert, CJ 2021, 'Standardization of assay representation in the Ontology for Biomedical Investigations', Database, vol. 2021, baab040. https://doi.org/10.1093/database/baab040

@article{07ab0bc3192d4013a8c1f442297fe425,

title = "Standardization of assay representation in the Ontology for Biomedical Investigations",

abstract = "The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.",

author = "Randi Vita and Jie Zheng and Rebecca Jackson and Damion Dooley and Overton, {James A.} and Miller, {Mark A.} and Berrios, {Daniel C.} and Scheuermann, {Richard H.} and Yongqun He and Mcginty, {Hande K{\"u}{\c c}{\"u}k} and Mathias Brochhausen and Lin, {Aisyah Yu} and Jain, {Sagar B.} and Chibucos, {Marcus C.} and John Judkins and Giglio, {Michelle G.} and Feng, {Irene Y.} and Gully Burns and Brush, {Matthew H.} and Bjoern Peters and Stoeckert, {Christian J.}",

note = "Publisher Copyright: {\textcopyright} 2021 The Author(s). Published by Oxford University Press.",

year = "2021",

doi = "10.1093/database/baab040",

language = "English (US)",

volume = "2021",

journal = "Database",

issn = "1758-0463",

publisher = "Oxford University Press",

}

TY - JOUR

T1 - Standardization of assay representation in the Ontology for Biomedical Investigations

AU - Vita, Randi

AU - Zheng, Jie

AU - Jackson, Rebecca

AU - Dooley, Damion

AU - Overton, James A.

AU - Miller, Mark A.

AU - Berrios, Daniel C.

AU - Scheuermann, Richard H.

AU - He, Yongqun

AU - Mcginty, Hande Küçük

AU - Brochhausen, Mathias

AU - Lin, Aisyah Yu

AU - Jain, Sagar B.

AU - Chibucos, Marcus C.

AU - Judkins, John

AU - Giglio, Michelle G.

AU - Feng, Irene Y.

AU - Burns, Gully

AU - Brush, Matthew H.

AU - Peters, Bjoern

AU - Stoeckert, Christian J.

PY - 2021

Y1 - 2021

N2 - The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

AB - The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

UR - http://www.scopus.com/inward/record.url?scp=85112124023&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85112124023&partnerID=8YFLogxK

U2 - 10.1093/database/baab040

DO - 10.1093/database/baab040

M3 - Article

C2 - 34244718

AN - SCOPUS:85112124023

SN - 1758-0463

VL - 2021

JO - Database

JF - Database

M1 - baab040

ER -

Standardization of assay representation in the Ontology for Biomedical Investigations

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this