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ViBrism DB

General Information

ViBrism DB is a database for anatomical gene expression maps and topological co-expression network graphs created with original techniques of microtomy-based gene expression measurements, Transcriptome Tomography. The DB is equipped with a WebGL-based 2D/3D visualization platform, BAH viewer, and a network viewer. Users can access a total of 172,022 datasets of coding/non-coding transcripts and lncRNAs, present in the mouse brains at four post-natal stages. Expression maps are seen in the whole anatomical context of 3D MR images of the brains. In situ hybridization images and anatomical area maps are browsable in the same space of 3D expression maps. Created images are shareable using URLs, including scene-setting parameters. The DB is expandable by community activity.

Homepage http://vibrism.neuroinf.jp/

Countries that developed this resource Japan

Created in 2012

Taxonomic range

Mus musculus

Knowledge Domains

Subjects

User-defined Tags

Neuroinformatics

How to cite this record FAIRsharing.org: ViBrism DB; ViBrism DB; DOI: https://doi.org/10.25504/FAIRsharing.EJFNZn; Last edited: March 19, 2021, 1:05 p.m.; Last accessed: Aug 02 2021 1:19 a.m.

This record is maintained by yukooho

Record added: Nov. 7, 2018, 2:46 p.m.
Record updated: Feb. 24, 2021, 11:09 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.EJFNZn' by 'The FAIRsharing Team' at 11:09, 24 Feb 2021 (approved):

	'grants' has been modified:
		Before:
			JSPS KAKENHI 25560428, 26280110, 268032, 15HP8038, 16HP8032, 17HP8082, JP15H05954, 23300137, 258057, 25330342, 16J09788
		After:
			JSPS KAKENHI 15HP8038
			JSPS KAKENHI 16HP8032 
			JSPS KAKENHI 16J09788
			JSPS KAKENHI 17HP8082 
			JSPS KAKENHI 23300137
			JSPS KAKENHI 25330342 
			JSPS KAKENHI 25560428
			JSPS KAKENHI 258057
			JSPS KAKENHI 26280110 
			JSPS KAKENHI 268032
			JSPS KAKENHI JP15H05954 
		Added:
			JSPS KAKENHI 15HP8038
			JSPS KAKENHI 16HP8032 
			JSPS KAKENHI 16J09788
			JSPS KAKENHI 17HP8082 
			JSPS KAKENHI 23300137
			JSPS KAKENHI 25330342 
			JSPS KAKENHI 25560428
			JSPS KAKENHI 258057
			JSPS KAKENHI 26280110 
			JSPS KAKENHI 268032
			JSPS KAKENHI JP15H05954 
		Removed:
			JSPS KAKENHI 25560428, 26280110, 268032, 15HP8038, 16HP8032, 17HP8082, JP15H05954, 23300137, 258057, 25330342, 16J09788

Edits to 'https://fairsharing.org/FAIRsharing.EJFNZn' by 'The FAIRsharing Team' at 13:58, 12 Nov 2018 (approved):

	'organizations' has been modified:
		Before:
			Japan Society for the Promotion of Science|https://www.jsps.go.jp/english/e-grants/|Funds
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Funds
		After:
			Japan Society for the Promotion of Science|https://www.jsps.go.jp/english/e-grants/|Funds
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Maintains,Funds
		Added:
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Maintains,Funds
		Removed:
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Funds

	'supportLinks' has been modified:
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			email|site-editor@brent-research.org
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			email|site-editor@brent-research.org
			help|http://vibrism.neuroinf.jp/instruction.html
			online documentation|http://vibrism.neuroinf.jp/about.html
			online documentation|http://vibrism.neuroinf.jp/examples.html
		Added:
			help|http://vibrism.neuroinf.jp/instruction.html
			online documentation|http://vibrism.neuroinf.jp/about.html
			online documentation|http://vibrism.neuroinf.jp/examples.html
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	'licences' has been modified:
		Before:
		After:
			Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)|https://creativecommons.org/licenses/by-sa/4.0/|Data
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			Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)|https://creativecommons.org/licenses/by-sa/4.0/|Data
		Removed:

	'dataProcesses' has been modified:
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			GEO Series accession numbers GSE118176
			GEO Series accession numbers GSE118177
			GEO Series accession numbers GSE118178
			GEO Series accession numbers GSE36408
		After:
			GEO Series accession numbers GSE118176
			GEO Series accession numbers GSE118177
			GEO Series accession numbers GSE118178
			GEO Series accession numbers GSE36408
			Expression Similarity Search and Network Viewer
			Expression Density Search in Anatomical Areas
			BAH Viewer
			3D Expression Map (Search by Gene ID)
		Added:
			Expression Similarity Search and Network Viewer
			Expression Density Search in Anatomical Areas
			BAH Viewer
			3D Expression Map (Search by Gene ID)
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	'domains' has been modified:
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			Gene expression
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			Gene expression
			Life Science
			Magnetic resonance imaging (MRI)
			Neuroinformatics
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			Life Science
			Magnetic resonance imaging (MRI)
			Neuroinformatics
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	'taxonomies' has been modified:
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			Mus musculus
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			Mus musculus
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Edits to 'https://fairsharing.org/FAIRsharing.EJFNZn' by 'yukooho' at 15:42, 07 Nov 2018 (approved):

	'organizations' has been modified:
		Before:
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Undefined
			Japan Society for the Promotion of Science|https://www.jsps.go.jp/english/e-grants/|Funds
		After:
			Japan Society for the Promotion of Science|https://www.jsps.go.jp/english/e-grants/|Funds
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Funds
		Added:
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Funds
		Removed:
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Undefined

Edits to 'https://fairsharing.org/FAIRsharing.EJFNZn' by 'yukooho' at 15:37, 07 Nov 2018 (approved):

	'organizations' has been modified:
		Before:
		After:
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Undefined
			Japan Society for the Promotion of Science|https://www.jsps.go.jp/english/e-grants/|Funds
		Added:
			Neuroinformatics Unit, RIKEN Center for Brain Science|http://www.riken.jp/en/research/labs/cbs/integr_comput_brainsci_collab/neuroinf/|Undefined
			Japan Society for the Promotion of Science|https://www.jsps.go.jp/english/e-grants/|Funds
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			email|site-editor@brent-research.org
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			email|site-editor@brent-research.org
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	'licences' has been modified:
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		After:
			Creative Commons Attribution-ShareAlike 4.0 International License.|https://creativecommons.org/licenses/by-sa/4.0/|Data
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			Creative Commons Attribution-ShareAlike 4.0 International License.|https://creativecommons.org/licenses/by-sa/4.0/|Data
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	'dataProcesses' has been modified:
		Before:
		After:
			GEO Series accession numbers GSE118176
			GEO Series accession numbers GSE118177
			GEO Series accession numbers GSE118178
			GEO Series accession numbers GSE36408
		Added:
			GEO Series accession numbers GSE118176
			GEO Series accession numbers GSE118177
			GEO Series accession numbers GSE118178
			GEO Series accession numbers GSE36408
		Removed:

	'grants' has been modified:
		Before:
		After:
			JSPS KAKENHI 25560428, 26280110, 268032, 15HP8038, 16HP8032, 17HP8082, JP15H05954, 23300137, 258057, 25330342, 16J09788
		Added:
			JSPS KAKENHI 25560428, 26280110, 268032, 15HP8038, 16HP8032, 17HP8082, JP15H05954, 23300137, 258057, 25330342, 16J09788
		Removed:

	'publications' has been modified:
		Before:
		After:
			ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks.|Morita M,Shimokawa K,Nishimura M,Nakamura S,Tsujimura Y,Takemoto S,Tawara T,Yokota H,Wemler S,Miyamoto D,Ikeno H,Sato A,Furuichi T,Kobayashi N,Okumura Y,Yamaguchi Y,Okamura-Oho Y|Nucleic Acids Res|2018
			Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain.|Okamura-Oho Y,Shimokawa K,Nishimura M,Takemoto S,Sato A,Furuichi T,Yokota H|Sci Rep|2014
			Transcriptome tomography for brain analysis in the web-accessible anatomical space.|Okamura-Oho Y,Shimokawa K,Takemoto S,Hirakiyama A,Nakamura S,Tsujimura Y,Nishimura M,Kasukawa T,Masumoto KH,Nikaido I,Shigeyoshi Y,Ueda HR,Song G,Gee J,Himeno R,Yokota H|PLoS One|2012
		Added:
			ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks.|Morita M,Shimokawa K,Nishimura M,Nakamura S,Tsujimura Y,Takemoto S,Tawara T,Yokota H,Wemler S,Miyamoto D,Ikeno H,Sato A,Furuichi T,Kobayashi N,Okumura Y,Yamaguchi Y,Okamura-Oho Y|Nucleic Acids Res|2018
			Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain.|Okamura-Oho Y,Shimokawa K,Nishimura M,Takemoto S,Sato A,Furuichi T,Yokota H|Sci Rep|2014
			Transcriptome tomography for brain analysis in the web-accessible anatomical space.|Okamura-Oho Y,Shimokawa K,Takemoto S,Hirakiyama A,Nakamura S,Tsujimura Y,Nishimura M,Kasukawa T,Masumoto KH,Nikaido I,Shigeyoshi Y,Ueda HR,Song G,Gee J,Himeno R,Yokota H|PLoS One|2012
		Removed:

Support

General

support email	ViBrism DB Committee
help	ViBrism Instructions
online documentation	About ViBrism
online documentation	Video Tutorials

Additional Information

Contact

Yuko Okamura-Oho ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)

Data Release

GEO Series accession numbers GSE118176	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118176
GEO Series accession numbers GSE118177	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118177
GEO Series accession numbers GSE118178	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118178
GEO Series accession numbers GSE36408	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36408

Data Access

Expression Similarity Search and Network Viewer	http://vibrism.neuroinf.jp/setsearch/search
Expression Density Search in Anatomical Areas	http://vibrism.neuroinf.jp/setsearch/anatomical
BAH Viewer	http://vibrism.neuroinf.jp/bahviewer.html
3D Expression Map (Search by Gene ID)	http://vibrism.neuroinf.jp/search.html

Publications

ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks.

Morita M,Shimokawa K,Nishimura M,Nakamura S,Tsujimura Y,Takemoto S,Tawara T,Yokota H,Wemler S,Miyamoto D,Ikeno H,Sato A,Furuichi T,Kobayashi N,Okumura Y,Yamaguchi Y,Okamura-Oho Y
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain.

Okamura-Oho Y,Shimokawa K,Nishimura M,Takemoto S,Sato A,Furuichi T,Yokota H
Sci Rep 2014

View Paper (PubMed) View Publication

Transcriptome tomography for brain analysis in the web-accessible anatomical space.

Okamura-Oho Y,Shimokawa K,Takemoto S,Hirakiyama A,Nakamura S,Tsujimura Y,Nishimura M,Kasukawa T,Masumoto KH,Nikaido I,Shigeyoshi Y,Ueda HR,Song G,Gee J,Himeno R,Yokota H
PLoS One 2012

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

No related databases defined

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by yukooho

Funds

Japan Society for the Promotion of Science, Tokyo, Japan (Consortium)
Neuroinformatics Unit, RIKEN Center for Brain Science (Research institute) Lead

Maintains

Neuroinformatics Unit, RIKEN Center for Brain Science (Research institute) Lead

Grant Number(s)

JSPS KAKENHI 15HP8038 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 16HP8032 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 16J09788 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 17HP8082 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 23300137 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 25330342 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 25560428 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 258057 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 26280110 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI 268032 (Japan Society for the Promotion of Science, Tokyo, Japan)
JSPS KAKENHI JP15H05954 (Japan Society for the Promotion of Science, Tokyo, Japan)

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