OME core ontology: An OWL-based life science imaging data model

Norio Kobayashi; Josh Moore; Shuichi Onami; Jason R. Swedlow

OME core ontology: An OWL-based life science imaging data model

Norio Kobayashi
, Josh Moore
, Shuichi Onami
, Jason R. Swedlow

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

Abstract

The Open Microscopy Environment (OME) is a consortium that produces open-source tools and format standards for microscopy data. The OME model is a specification for sharing biological imaging data in two parts: metadata as OME-XML and binary data as OMETIFF. We built an OWL ontology translation of the OME-XML specification called OME core ontology so as to catch up with the rapid progress and diversification of imaging technology and to facilitate integrated analysis with various life science data. This poster presents the details and status of the ontology, associated tools, and future plans.

Original language	English
Pages (from-to)	149-150
Number of pages	2
Journal	CEUR Workshop Proceedings
Volume	2849
Publication status	Published - Dec 2019
Event	12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2019 - Edinburgh, United Kingdom Duration: 10 Dec 2019 → 11 Dec 2019

Keywords

Imaging ontology
Microscopy imaging
Open microscopy environment
Semantic integration

ASJC Scopus subject areas

General Computer Science

Cite this

@article{461974379afa4439a94f490fda19a178,

title = "OME core ontology: An OWL-based life science imaging data model",

abstract = "The Open Microscopy Environment (OME) is a consortium that produces open-source tools and format standards for microscopy data. The OME model is a specification for sharing biological imaging data in two parts: metadata as OME-XML and binary data as OMETIFF. We built an OWL ontology translation of the OME-XML specification called OME core ontology so as to catch up with the rapid progress and diversification of imaging technology and to facilitate integrated analysis with various life science data. This poster presents the details and status of the ontology, associated tools, and future plans.",

keywords = "Imaging ontology, Microscopy imaging, Open microscopy environment, Semantic integration",

author = "Norio Kobayashi and Josh Moore and Shuichi Onami and Swedlow, \{Jason R.\}",

note = "Funding Information: This work has been supported by JSPS KAKENHI grant numbers 17K00434, 17K00424 and 18K19766, and Japan Science and Technology Agency (JST) Core Research for Evolutionary Science and Technology (CREST) Grant Number JPMJCR1511. Publisher Copyright: Copyright {\textcopyright} 2019 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).; 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2019 ; Conference date: 10-12-2019 Through 11-12-2019",

year = "2019",

month = dec,

language = "English",

volume = "2849",

pages = "149--150",

journal = "CEUR Workshop Proceedings",

issn = "1613-0073",

publisher = "CEUR-WS",

}

TY - JOUR

T1 - OME core ontology

T2 - 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2019

AU - Kobayashi, Norio

AU - Moore, Josh

AU - Onami, Shuichi

AU - Swedlow, Jason R.

N1 - Funding Information: This work has been supported by JSPS KAKENHI grant numbers 17K00434, 17K00424 and 18K19766, and Japan Science and Technology Agency (JST) Core Research for Evolutionary Science and Technology (CREST) Grant Number JPMJCR1511. Publisher Copyright: Copyright © 2019 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).

PY - 2019/12

Y1 - 2019/12

N2 - The Open Microscopy Environment (OME) is a consortium that produces open-source tools and format standards for microscopy data. The OME model is a specification for sharing biological imaging data in two parts: metadata as OME-XML and binary data as OMETIFF. We built an OWL ontology translation of the OME-XML specification called OME core ontology so as to catch up with the rapid progress and diversification of imaging technology and to facilitate integrated analysis with various life science data. This poster presents the details and status of the ontology, associated tools, and future plans.

AB - The Open Microscopy Environment (OME) is a consortium that produces open-source tools and format standards for microscopy data. The OME model is a specification for sharing biological imaging data in two parts: metadata as OME-XML and binary data as OMETIFF. We built an OWL ontology translation of the OME-XML specification called OME core ontology so as to catch up with the rapid progress and diversification of imaging technology and to facilitate integrated analysis with various life science data. This poster presents the details and status of the ontology, associated tools, and future plans.

KW - Imaging ontology

KW - Microscopy imaging

KW - Open microscopy environment

KW - Semantic integration

UR - https://www.scopus.com/pages/publications/85104042926

UR - https://ceur-ws.org/Vol-2849/

M3 - Conference article

AN - SCOPUS:85104042926

SN - 1613-0073

VL - 2849

SP - 149

EP - 150

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

Y2 - 10 December 2019 through 11 December 2019

ER -

OME core ontology: An OWL-based life science imaging data model

Abstract

Keywords

ASJC Scopus subject areas

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