A guide to the BRAIN Initiative Cell Census Network data ecosystem

Michael Hawrylycz; Maryann E. Martone; Giorgio A. Ascoli; Jan G. Bjaalie; Hong Wei Dong; Satrajit S. Ghosh; Jesse Gillis; Ronna Hertzano; David R. Haynor; Patrick R. Hof; Yongsoo Kim; Ed Lein; Yufeng Liu; Jeremy A. Miller; Partha P. Mitra; Eran Mukamel; Lydia Ng; David Osumi-Sutherland; Hanchuan Peng; Patrick L. Ray; Raymond Sanchez; Aviv Regev; Alex Ropelewski; Richard H. Scheuermann; Shawn Zheng Kai Tan; Carol L. Thompson; Timothy Tickle; Hagen Tilgner; Merina Varghese; Brock Wester; Owen White; Hongkui Zeng; Brian Aevermann; David Allemang; Seth Ament; Thomas L. Athey; Cody Baker; Katherine S. Baker; Pamela M. Baker; Anita Bandrowski; Samik Banerjee; Prajal Bishwakarma; Ambrose Carr; Min Chen; Roni Choudhury; Jonah Cool; Heather Creasy; Florence D'Orazi; Kylee Degatano; Benjamin Dichter; Song Lin Ding; Tim Dolbeare; Joseph R. Ecker; Rongxin Fang; Jean Christophe Fillion-Robin; Timothy P. Fliss; James Gee; Tom Gillespie; Nathan Gouwens; Guo Qiang Zhang; Yaroslav O. Halchenko; Nomi L. Harris; Brian R. Herb; Houri Hintiryan; Gregory Hood; Sam Horvath; Bingxing Huo; Dorota Jarecka; Shengdian Jiang; Farzaneh Khajouei; Elizabeth A. Kiernan; Huseyin Kir; Lauren Kruse; Changkyu Lee; Boudewijn Lelieveldt; Yang Li; Hanqing Liu; Lijuan Liu; Anup Markuhar; James Mathews; Kaylee L. Mathews; Chris Mezias; Michael I. Miller; Tyler Mollenkopf; Shoaib Mufti; Christopher J. Mungall; Joshua Orvis; Maja A. Puchades; Lei Qu; Joseph P. Receveur; Bing Ren; Nathan Sjoquist; Staats; Daniel Tward; Cindy T.J. van Velthoven; Quanxin Wang; Fangming Xie; Hua Xu; Zizhen Yao; Zhixi Yun; Yun Renee Zhang; W. Jim Zheng; Brian Zingg

doi:10.1371/journal.pbio.3002133

A guide to the BRAIN Initiative Cell Census Network data ecosystem

Michael Hawrylycz, Maryann E. Martone, Giorgio A. Ascoli, Jan G. Bjaalie, Hong Wei Dong, Satrajit S. Ghosh, Jesse Gillis, Ronna Hertzano, David R. Haynor, Patrick R. Hof, Yongsoo Kim, Ed Lein, Yufeng Liu, Jeremy A. Miller, Partha P. Mitra, Eran Mukamel, Lydia Ng, David Osumi-Sutherland, Hanchuan Peng, Patrick L. RayRaymond Sanchez, Aviv Regev, Alex Ropelewski, Richard H. Scheuermann, Shawn Zheng Kai Tan, Carol L. Thompson, Timothy Tickle, Hagen Tilgner, Merina Varghese, Brock Wester, Owen White, Hongkui Zeng, Brian Aevermann, David Allemang, Seth Ament, Thomas L. Athey, Cody Baker, Katherine S. Baker, Pamela M. Baker, Anita Bandrowski, Samik Banerjee, Prajal Bishwakarma, Ambrose Carr, Min Chen, Roni Choudhury, Jonah Cool, Heather Creasy, Florence D'Orazi, Kylee Degatano, Benjamin Dichter, Song Lin Ding, Tim Dolbeare, Joseph R. Ecker, Rongxin Fang, Jean Christophe Fillion-Robin, Timothy P. Fliss, James Gee, Tom Gillespie, Nathan Gouwens, Guo Qiang Zhang, Yaroslav O. Halchenko, Nomi L. Harris, Brian R. Herb, Houri Hintiryan, Gregory Hood, Sam Horvath, Bingxing Huo, Dorota Jarecka, Shengdian Jiang, Farzaneh Khajouei, Elizabeth A. Kiernan, Huseyin Kir, Lauren Kruse, Changkyu Lee, Boudewijn Lelieveldt, Yang Li, Hanqing Liu, Lijuan Liu, Anup Markuhar, James Mathews, Kaylee L. Mathews, Chris Mezias, Michael I. Miller, Tyler Mollenkopf, Shoaib Mufti, Christopher J. Mungall, Joshua Orvis, Maja A. Puchades, Lei Qu, Joseph P. Receveur, Bing Ren, Nathan Sjoquist, Staats, Daniel Tward, Cindy T.J. van Velthoven, Quanxin Wang, Fangming Xie, Hua Xu, Zizhen Yao, Zhixi Yun, Yun Renee Zhang, W. Jim Zheng, Brian Zingg

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Abstract

Characterizing cellular diversity at different levels of biological organization and across AU data: Ple modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

Original language	English
Article number	e3002133
Journal	PLoS Biology
Volume	21
Issue number	6 June
DOIs	https://doi.org/10.1371/journal.pbio.3002133
State	Published - Jun 2023

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Hawrylycz, M., Martone, M. E., Ascoli, G. A., Bjaalie, J. G., Dong, H. W., Ghosh, S. S., Gillis, J., Hertzano, R., Haynor, D. R., Hof, P. R., Kim, Y., Lein, E., Liu, Y., Miller, J. A., Mitra, P. P., Mukamel, E., Ng, L., Osumi-Sutherland, D., Peng, H., ... Zingg, B. (2023). A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biology, 21(6 June), Article e3002133. https://doi.org/10.1371/journal.pbio.3002133

@article{ac5e80f3dafe465b98c7fc0845a62767,

title = "A guide to the BRAIN Initiative Cell Census Network data ecosystem",

abstract = "Characterizing cellular diversity at different levels of biological organization and across AU data: Ple modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.",

author = "Michael Hawrylycz and Martone, {Maryann E.} and Ascoli, {Giorgio A.} and Bjaalie, {Jan G.} and Dong, {Hong Wei} and Ghosh, {Satrajit S.} and Jesse Gillis and Ronna Hertzano and Haynor, {David R.} and Hof, {Patrick R.} and Yongsoo Kim and Ed Lein and Yufeng Liu and Miller, {Jeremy A.} and Mitra, {Partha P.} and Eran Mukamel and Lydia Ng and David Osumi-Sutherland and Hanchuan Peng and Ray, {Patrick L.} and Raymond Sanchez and Aviv Regev and Alex Ropelewski and Scheuermann, {Richard H.} and Tan, {Shawn Zheng Kai} and Thompson, {Carol L.} and Timothy Tickle and Hagen Tilgner and Merina Varghese and Brock Wester and Owen White and Hongkui Zeng and Brian Aevermann and David Allemang and Seth Ament and Athey, {Thomas L.} and Cody Baker and Baker, {Katherine S.} and Baker, {Pamela M.} and Anita Bandrowski and Samik Banerjee and Prajal Bishwakarma and Ambrose Carr and Min Chen and Roni Choudhury and Jonah Cool and Heather Creasy and Florence D'Orazi and Kylee Degatano and Benjamin Dichter and Ding, {Song Lin} and Tim Dolbeare and Ecker, {Joseph R.} and Rongxin Fang and Fillion-Robin, {Jean Christophe} and Fliss, {Timothy P.} and James Gee and Tom Gillespie and Nathan Gouwens and Zhang, {Guo Qiang} and Halchenko, {Yaroslav O.} and Harris, {Nomi L.} and Herb, {Brian R.} and Houri Hintiryan and Gregory Hood and Sam Horvath and Bingxing Huo and Dorota Jarecka and Shengdian Jiang and Farzaneh Khajouei and Kiernan, {Elizabeth A.} and Huseyin Kir and Lauren Kruse and Changkyu Lee and Boudewijn Lelieveldt and Yang Li and Hanqing Liu and Lijuan Liu and Anup Markuhar and James Mathews and Mathews, {Kaylee L.} and Chris Mezias and Miller, {Michael I.} and Tyler Mollenkopf and Shoaib Mufti and Mungall, {Christopher J.} and Joshua Orvis and Puchades, {Maja A.} and Lei Qu and Receveur, {Joseph P.} and Bing Ren and Nathan Sjoquist and Staats and Daniel Tward and {van Velthoven}, {Cindy T.J.} and Quanxin Wang and Fangming Xie and Hua Xu and Zizhen Yao and Zhixi Yun and Zhang, {Yun Renee} and Zheng, {W. Jim} and Brian Zingg",

note = "Publisher Copyright: Copyright: {\textcopyright} 2023 Hawrylycz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2023",

month = jun,

doi = "10.1371/journal.pbio.3002133",

language = "English",

volume = "21",

journal = "PLoS Biology",

issn = "1544-9173",

publisher = "Public Library of Science",

number = "6 June",

}

Hawrylycz, M, Martone, ME, Ascoli, GA, Bjaalie, JG, Dong, HW, Ghosh, SS, Gillis, J, Hertzano, R, Haynor, DR, Hof, PR, Kim, Y, Lein, E, Liu, Y, Miller, JA, Mitra, PP, Mukamel, E, Ng, L, Osumi-Sutherland, D, Peng, H, Ray, PL, Sanchez, R, Regev, A, Ropelewski, A, Scheuermann, RH, Tan, SZK, Thompson, CL, Tickle, T, Tilgner, H, Varghese, M, Wester, B, White, O, Zeng, H, Aevermann, B, Allemang, D, Ament, S, Athey, TL, Baker, C, Baker, KS, Baker, PM, Bandrowski, A, Banerjee, S, Bishwakarma, P, Carr, A, Chen, M, Choudhury, R, Cool, J, Creasy, H, D'Orazi, F, Degatano, K, Dichter, B, Ding, SL, Dolbeare, T, Ecker, JR, Fang, R, Fillion-Robin, JC, Fliss, TP, Gee, J, Gillespie, T, Gouwens, N, Zhang, GQ, Halchenko, YO, Harris, NL, Herb, BR, Hintiryan, H, Hood, G, Horvath, S, Huo, B, Jarecka, D, Jiang, S, Khajouei, F, Kiernan, EA, Kir, H, Kruse, L, Lee, C, Lelieveldt, B, Li, Y, Liu, H, Liu, L, Markuhar, A, Mathews, J, Mathews, KL, Mezias, C, Miller, MI, Mollenkopf, T, Mufti, S, Mungall, CJ, Orvis, J, Puchades, MA, Qu, L, Receveur, JP, Ren, B, Sjoquist, N, Staats, Tward, D, van Velthoven, CTJ, Wang, Q, Xie, F, Xu, H, Yao, Z, Yun, Z, Zhang, YR, Zheng, WJ & Zingg, B 2023, 'A guide to the BRAIN Initiative Cell Census Network data ecosystem', PLoS Biology, vol. 21, no. 6 June, e3002133. https://doi.org/10.1371/journal.pbio.3002133

TY - JOUR

T1 - A guide to the BRAIN Initiative Cell Census Network data ecosystem

AU - Hawrylycz, Michael

AU - Martone, Maryann E.

AU - Ascoli, Giorgio A.

AU - Bjaalie, Jan G.

AU - Dong, Hong Wei

AU - Ghosh, Satrajit S.

AU - Gillis, Jesse

AU - Hertzano, Ronna

AU - Haynor, David R.

AU - Hof, Patrick R.

AU - Kim, Yongsoo

AU - Lein, Ed

AU - Liu, Yufeng

AU - Miller, Jeremy A.

AU - Mitra, Partha P.

AU - Mukamel, Eran

AU - Ng, Lydia

AU - Osumi-Sutherland, David

AU - Peng, Hanchuan

AU - Ray, Patrick L.

AU - Sanchez, Raymond

AU - Regev, Aviv

AU - Ropelewski, Alex

AU - Scheuermann, Richard H.

AU - Tan, Shawn Zheng Kai

AU - Thompson, Carol L.

AU - Tickle, Timothy

AU - Tilgner, Hagen

AU - Varghese, Merina

AU - Wester, Brock

AU - White, Owen

AU - Zeng, Hongkui

AU - Aevermann, Brian

AU - Allemang, David

AU - Ament, Seth

AU - Athey, Thomas L.

AU - Baker, Cody

AU - Baker, Katherine S.

AU - Baker, Pamela M.

AU - Bandrowski, Anita

AU - Banerjee, Samik

AU - Bishwakarma, Prajal

AU - Carr, Ambrose

AU - Chen, Min

AU - Choudhury, Roni

AU - Cool, Jonah

AU - Creasy, Heather

AU - D'Orazi, Florence

AU - Degatano, Kylee

AU - Dichter, Benjamin

AU - Ding, Song Lin

AU - Dolbeare, Tim

AU - Ecker, Joseph R.

AU - Fang, Rongxin

AU - Fillion-Robin, Jean Christophe

AU - Fliss, Timothy P.

AU - Gee, James

AU - Gillespie, Tom

AU - Gouwens, Nathan

AU - Zhang, Guo Qiang

AU - Halchenko, Yaroslav O.

AU - Harris, Nomi L.

AU - Herb, Brian R.

AU - Hintiryan, Houri

AU - Hood, Gregory

AU - Horvath, Sam

AU - Huo, Bingxing

AU - Jarecka, Dorota

AU - Jiang, Shengdian

AU - Khajouei, Farzaneh

AU - Kiernan, Elizabeth A.

AU - Kir, Huseyin

AU - Kruse, Lauren

AU - Lee, Changkyu

AU - Lelieveldt, Boudewijn

AU - Li, Yang

AU - Liu, Hanqing

AU - Liu, Lijuan

AU - Markuhar, Anup

AU - Mathews, James

AU - Mathews, Kaylee L.

AU - Mezias, Chris

AU - Miller, Michael I.

AU - Mollenkopf, Tyler

AU - Mufti, Shoaib

AU - Mungall, Christopher J.

AU - Orvis, Joshua

AU - Puchades, Maja A.

AU - Qu, Lei

AU - Receveur, Joseph P.

AU - Ren, Bing

AU - Sjoquist, Nathan

AU - Staats,

AU - Tward, Daniel

AU - van Velthoven, Cindy T.J.

AU - Wang, Quanxin

AU - Xie, Fangming

AU - Xu, Hua

AU - Yao, Zizhen

AU - Yun, Zhixi

AU - Zhang, Yun Renee

AU - Zheng, W. Jim

AU - Zingg, Brian

N1 - Publisher Copyright: Copyright: © 2023 Hawrylycz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2023/6

Y1 - 2023/6

N2 - Characterizing cellular diversity at different levels of biological organization and across AU data: Ple modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

AB - Characterizing cellular diversity at different levels of biological organization and across AU data: Ple modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

UR - http://www.scopus.com/inward/record.url?scp=85164233059&partnerID=8YFLogxK

U2 - 10.1371/journal.pbio.3002133

DO - 10.1371/journal.pbio.3002133

M3 - Article

C2 - 37390046

AN - SCOPUS:85164233059

SN - 1544-9173

VL - 21

JO - PLoS Biology

JF - PLoS Biology

IS - 6 June

M1 - e3002133

ER -

A guide to the BRAIN Initiative Cell Census Network data ecosystem

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