The BioPAX community standard for pathway data sharing

Emek Demir; Michael P. Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C. Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Özgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Reubenacker; Matthias Samwald; Martijn Van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H. Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S. Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D. Karp; Chris Sander; Gary D. Bader

doi:10.1038/nbt.1666

The BioPAX community standard for pathway data sharing

Emek Demir
, Michael P. Cary
, Suzanne Paley
, Ken Fukuda
, Christian Lemer
, Imre Vastrik
, Guanming Wu
, Peter D'Eustachio
, Carl Schaefer
, Joanne Luciano
, Frank Schacherer
, Irma Martinez-Flores
, Zhenjun Hu
, Veronica Jimenez-Jacinto
, Geeta Joshi-Tope
, Kumaran Kandasamy
, Alejandra C. Lopez-Fuentes
, Huaiyu Mi
, Elgar Pichler
, Igor Rodchenkov

Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Özgün Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Reubenacker, Matthias Samwald, Martijn Van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei Hoi Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H. Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S. Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D. Karp, Chris Sander, Gary D. Bader

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

575 Scopus citations

Abstract

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

Original language	English (US)
Pages (from-to)	935-942
Number of pages	8
Journal	Nature Biotechnology
Volume	28
Issue number	9
DOIs	https://doi.org/10.1038/nbt.1666
State	Published - Sep 1 2010

Funding

Funded by the US Department of Energy workshop grant DE-FG02-04ER63931, the caBIG program, the US National Institute of General Medical Sciences workshop grant 1R13GM076939, grant P41HG004118 from the US National Human Genome Research Institute and Genome Canada through the Ontario Genomics Institute (2007-OGI-TD-05) and US National Institutes of Health grant R01GM071962-07. Thanks to many people who contributed to discussions on BioPAX mailing lists, at conferences and at BioPAX workshops, especially A. Ruttenberg and J. Rees.

Funders	Funder number
US Department of Energy	DE-FG02-04ER63931
Author National Institutes of Health National Institutes of Health National Institutes of Health National Institutes of Health The Bev Hartig Huntington's Disease Foundation National Institutes of Health	R01GM071962-07
National Human Genome Research Institute
National Institute of General Medical Sciences	P41HG004118, R13GM076939
Genome Canada/Genome British Columbia
Ontario Genomics Institute	2007-OGI-TD-05

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Biomedical Engineering
Molecular Medicine

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10.1038/nbt.1666

Cite this

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., ... Bader, G. D. (2010). The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28(9), 935-942. https://doi.org/10.1038/nbt.1666

Demir, E, Cary, MP, Paley, S, Fukuda, K, Lemer, C, Vastrik, I, Wu, G, D'Eustachio, P, Schaefer, C, Luciano, J, Schacherer, F, Martinez-Flores, I, Hu, Z, Jimenez-Jacinto, V, Joshi-Tope, G, Kandasamy, K, Lopez-Fuentes, AC, Mi, H, Pichler, E, Rodchenkov, I, Splendiani, A, Tkachev, S, Zucker, J, Gopinath, G, Rajasimha, H, Ramakrishnan, R, Shah, I, Syed, M, Anwar, N, Babur, Ö, Blinov, M, Brauner, E, Corwin, D, Donaldson, S, Gibbons, F, Goldberg, R, Hornbeck, P, Luna, A, Murray-Rust, P, Neumann, E, Reubenacker, O, Samwald, M, Van Iersel, M, Wimalaratne, S, Allen, K, Braun, B, Whirl-Carrillo, M, Cheung, KH, Dahlquist, K, Finney, A, Gillespie, M, Glass, E, Gong, L, Haw, R, Honig, M, Hubaut, O, Kane, D, Krupa, S, Kutmon, M, Leonard, J, Marks, D, Merberg, D, Petri, V, Pico, A, Ravenscroft, D, Ren, L, Shah, N, Sunshine, M, Tang, R, Whaley, R, Letovksy, S, Buetow, KH, Rzhetsky, A, Schachter, V, Sobral, BS, Dogrusoz, U, McWeeney, S, Aladjem, M, Birney, E, Collado-Vides, J, Goto, S, Hucka, M, Novère, NL, Maltsev, N, Pandey, A, Thomas, P, Wingender, E, Karp, PD, Sander, C & Bader, GD 2010, 'The BioPAX community standard for pathway data sharing', Nature Biotechnology, vol. 28, no. 9, pp. 935-942. https://doi.org/10.1038/nbt.1666

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title = "The BioPAX community standard for pathway data sharing",

abstract = "Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.",

author = "Emek Demir and Cary, \{Michael P.\} and Suzanne Paley and Ken Fukuda and Christian Lemer and Imre Vastrik and Guanming Wu and Peter D'Eustachio and Carl Schaefer and Joanne Luciano and Frank Schacherer and Irma Martinez-Flores and Zhenjun Hu and Veronica Jimenez-Jacinto and Geeta Joshi-Tope and Kumaran Kandasamy and Lopez-Fuentes, \{Alejandra C.\} and Huaiyu Mi and Elgar Pichler and Igor Rodchenkov and Andrea Splendiani and Sasha Tkachev and Jeremy Zucker and Gopal Gopinath and Harsha Rajasimha and Ranjani Ramakrishnan and Imran Shah and Mustafa Syed and Nadia Anwar and {\"O}zg{\"u}n Babur and Michael Blinov and Erik Brauner and Dan Corwin and Sylva Donaldson and Frank Gibbons and Robert Goldberg and Peter Hornbeck and Augustin Luna and Peter Murray-Rust and Eric Neumann and Oliver Reubenacker and Matthias Samwald and \{Van Iersel\}, Martijn and Sarala Wimalaratne and Keith Allen and Burk Braun and Michelle Whirl-Carrillo and Cheung, \{Kei Hoi\} and Kam Dahlquist and Andrew Finney and Marc Gillespie and Elizabeth Glass and Li Gong and Robin Haw and Michael Honig and Olivier Hubaut and David Kane and Shiva Krupa and Martina Kutmon and Julie Leonard and Debbie Marks and David Merberg and Victoria Petri and Alex Pico and Dean Ravenscroft and Liya Ren and Nigam Shah and Margot Sunshine and Rebecca Tang and Ryan Whaley and Stan Letovksy and Buetow, \{Kenneth H.\} and Andrey Rzhetsky and Vincent Schachter and Sobral, \{Bruno S.\} and Ugur Dogrusoz and Shannon McWeeney and Mirit Aladjem and Ewan Birney and Julio Collado-Vides and Susumu Goto and Michael Hucka and Nov{\`e}re, \{Nicolas Le\} and Natalia Maltsev and Akhilesh Pandey and Paul Thomas and Edgar Wingender and Karp, \{Peter D.\} and Chris Sander and Bader, \{Gary D.\}",

note = "Funding Information: Funded by the US Department of Energy workshop grant DE-FG02-04ER63931, the caBIG program, the US National Institute of General Medical Sciences workshop grant 1R13GM076939, grant P41HG004118 from the US National Human Genome Research Institute and Genome Canada through the Ontario Genomics Institute (2007-OGI-TD-05) and US National Institutes of Health grant R01GM071962-07. Thanks to many people who contributed to discussions on BioPAX mailing lists, at conferences and at BioPAX workshops, especially A. Ruttenberg and J. Rees.",

year = "2010",

month = sep,

day = "1",

doi = "10.1038/nbt.1666",

language = "English (US)",

volume = "28",

pages = "935--942",

journal = "Nature Biotechnology",

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T1 - The BioPAX community standard for pathway data sharing

AU - Demir, Emek

AU - Cary, Michael P.

AU - Paley, Suzanne

AU - Fukuda, Ken

AU - Lemer, Christian

AU - Vastrik, Imre

AU - Wu, Guanming

AU - D'Eustachio, Peter

AU - Schaefer, Carl

AU - Luciano, Joanne

AU - Schacherer, Frank

AU - Martinez-Flores, Irma

AU - Hu, Zhenjun

AU - Jimenez-Jacinto, Veronica

AU - Joshi-Tope, Geeta

AU - Kandasamy, Kumaran

AU - Lopez-Fuentes, Alejandra C.

AU - Mi, Huaiyu

AU - Pichler, Elgar

AU - Rodchenkov, Igor

AU - Splendiani, Andrea

AU - Tkachev, Sasha

AU - Zucker, Jeremy

AU - Gopinath, Gopal

AU - Rajasimha, Harsha

AU - Ramakrishnan, Ranjani

AU - Shah, Imran

AU - Syed, Mustafa

AU - Anwar, Nadia

AU - Babur, Özgün

AU - Blinov, Michael

AU - Brauner, Erik

AU - Corwin, Dan

AU - Donaldson, Sylva

AU - Gibbons, Frank

AU - Goldberg, Robert

AU - Hornbeck, Peter

AU - Luna, Augustin

AU - Murray-Rust, Peter

AU - Neumann, Eric

AU - Reubenacker, Oliver

AU - Samwald, Matthias

AU - Van Iersel, Martijn

AU - Wimalaratne, Sarala

AU - Allen, Keith

AU - Braun, Burk

AU - Whirl-Carrillo, Michelle

AU - Cheung, Kei Hoi

AU - Dahlquist, Kam

AU - Finney, Andrew

AU - Gillespie, Marc

AU - Glass, Elizabeth

AU - Gong, Li

AU - Haw, Robin

AU - Honig, Michael

AU - Hubaut, Olivier

AU - Kane, David

AU - Krupa, Shiva

AU - Kutmon, Martina

AU - Leonard, Julie

AU - Marks, Debbie

AU - Merberg, David

AU - Petri, Victoria

AU - Pico, Alex

AU - Ravenscroft, Dean

AU - Ren, Liya

AU - Shah, Nigam

AU - Sunshine, Margot

AU - Tang, Rebecca

AU - Whaley, Ryan

AU - Letovksy, Stan

AU - Buetow, Kenneth H.

AU - Rzhetsky, Andrey

AU - Schachter, Vincent

AU - Sobral, Bruno S.

AU - Dogrusoz, Ugur

AU - McWeeney, Shannon

AU - Aladjem, Mirit

AU - Birney, Ewan

AU - Collado-Vides, Julio

AU - Goto, Susumu

AU - Hucka, Michael

AU - Novère, Nicolas Le

AU - Maltsev, Natalia

AU - Pandey, Akhilesh

AU - Thomas, Paul

AU - Wingender, Edgar

AU - Karp, Peter D.

AU - Sander, Chris

AU - Bader, Gary D.

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PY - 2010/9/1

Y1 - 2010/9/1

N2 - Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

AB - Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

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U2 - 10.1038/nbt.1666

DO - 10.1038/nbt.1666

M3 - Review article

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AN - SCOPUS:77956664073

SN - 1087-0156

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SP - 935

EP - 942

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 9

ER -

The BioPAX community standard for pathway data sharing

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