On bringing bioimaging data into the open (World)

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

On bringing bioimaging data into the open (World)

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

School of Life Sciences

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

3 Citations (Scopus)

20 Downloads (Pure)

Abstract

For over 15 years, the Open Microscopy Environment (OME) Data Model has provided a basis for the storage, exchange and re-use of bioimaging data. During that time, XML Schema and XSL Transformations have provided a reliable mechanism to support the yearly updates to the model, keeping valuable data accessible by the research community. However, the acceleration of developments in the bioimaging domain now demand a more flexible, collaborative representation without the loss of versioning control. The OME Consortium proposes to adopt the semantic web stack for a next generation of data formats.

Original language	English
Article number	6
Pages (from-to)	44-53
Number of pages	10
Journal	CEUR Workshop Proceedings
Volume	2849
Publication status	Published - 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

Bioimaging
Domain model
FAIR data principles
Linked open data
Semantic framework

ASJC Scopus subject areas

General Computer Science

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Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
Final published version, 693 KBLicence: CC BY

Cite this

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title = "On bringing bioimaging data into the open (World)",

abstract = "For over 15 years, the Open Microscopy Environment (OME) Data Model has provided a basis for the storage, exchange and re-use of bioimaging data. During that time, XML Schema and XSL Transformations have provided a reliable mechanism to support the yearly updates to the model, keeping valuable data accessible by the research community. However, the acceleration of developments in the bioimaging domain now demand a more flexible, collaborative representation without the loss of versioning control. The OME Consortium proposes to adopt the semantic web stack for a next generation of data formats.",

keywords = "Bioimaging, Domain model, FAIR data principles, Linked open data, Semantic framework",

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

note = "Funding Information: NK was supported by JSPS KAKENHI (17K00434, 17K00424, 18K19766). SK was supported by the Deutsche Forschungsgemeinschaft (SFB944-INF). SO was supported by Core Research for Evolutionary Science and Technology (JST-CREST) (JPMJCR1511). Work on OME by JM and JRS is supported by awards from the BBSRC (BB/R015384/1) and the Wellcome Trust (212962/Z/18/Z). 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",

language = "English",

volume = "2849",

pages = "44--53",

journal = "CEUR Workshop Proceedings",

issn = "1613-0073",

publisher = "CEUR-WS",

}

TY - JOUR

T1 - On bringing bioimaging data into the open (World)

AU - Moore, Josh

AU - Kobayashi, Norio

AU - Kunis, Susanne

AU - Onami, Shuichi

AU - Swedlow, Jason R.

N1 - Funding Information: NK was supported by JSPS KAKENHI (17K00434, 17K00424, 18K19766). SK was supported by the Deutsche Forschungsgemeinschaft (SFB944-INF). SO was supported by Core Research for Evolutionary Science and Technology (JST-CREST) (JPMJCR1511). Work on OME by JM and JRS is supported by awards from the BBSRC (BB/R015384/1) and the Wellcome Trust (212962/Z/18/Z). 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

Y1 - 2019

N2 - For over 15 years, the Open Microscopy Environment (OME) Data Model has provided a basis for the storage, exchange and re-use of bioimaging data. During that time, XML Schema and XSL Transformations have provided a reliable mechanism to support the yearly updates to the model, keeping valuable data accessible by the research community. However, the acceleration of developments in the bioimaging domain now demand a more flexible, collaborative representation without the loss of versioning control. The OME Consortium proposes to adopt the semantic web stack for a next generation of data formats.

AB - For over 15 years, the Open Microscopy Environment (OME) Data Model has provided a basis for the storage, exchange and re-use of bioimaging data. During that time, XML Schema and XSL Transformations have provided a reliable mechanism to support the yearly updates to the model, keeping valuable data accessible by the research community. However, the acceleration of developments in the bioimaging domain now demand a more flexible, collaborative representation without the loss of versioning control. The OME Consortium proposes to adopt the semantic web stack for a next generation of data formats.

KW - Bioimaging

KW - Domain model

KW - FAIR data principles

KW - Linked open data

KW - Semantic framework

UR - http://www.scopus.com/inward/record.url?scp=85104041488&partnerID=8YFLogxK

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

M3 - Conference article

AN - SCOPUS:85104041488

SN - 1613-0073

VL - 2849

SP - 44

EP - 53

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

M1 - 6

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

Y2 - 10 December 2019 through 11 December 2019

ER -

On bringing bioimaging data into the open (World)

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

The Image Data Resource: Making Biological Imaging Data FAIR (Joint with EMBL-EBI) (Biomedical Resources Grant)

BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)

Cite this

On bringing bioimaging data into the open (World)

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Projects

The Image Data Resource: Making Biological Imaging Data FAIR (Joint with EMBL-EBI) (Biomedical Resources Grant)

BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)

Cite this