The BioPAX community standard for pathway data sharing

E. Demir, M. P. Cary, S. Paley, K. Fukuda, C. Lemer, I. Vastrik, G. Wu, P. D'Eustachio, C. Schaefer, J. Luciano, F. Schacherer, I. Martinez Flores, Z. Hu, V. Jimenez Jacinto, G. Joshi Tope, K. Kandasamy, A. C. Lopez Fuentes, H. Mi, E. Pichler, I. RodchenkovA. Splendiani, S. Tkachev, J. Zucker, G. Gopinath, H. Rajasimha, R. Ramakrishnan, I. Shah, M. Syed, N. Anwar, O. Babur, M. Blinov, E. Brauner, D. Corwin, S. Donaldson, F. Gibbons, R. Goldberg, P. Hornbeck, A. Luna, P. Murray Rust, E. Neumann, O. Reubenacker, M. Samwald, M.P. van Iersel, S. Wimalaratne, K. Allen, B. Braun, M. Whirl Carrillo, K. H. Cheung, K. Dahlquist, A. Finney, M. Gillespie, E. Glass, L. Gong, R. Haw, M. Honig, O. Hubaut, D. Kane, S. Krupa, M. Kutmon, J. Leonard, D. Marks, D. Merberg, V. Petri, A. Pico, D. Ravenscroft, L. Ren, N. Shah, M. Sunshine, R. Tang, R. Whaley, S. Letovksy, K. H. Buetow, A. Rzhetsky, V. Schachter, B. S. Sobral, U. Dogrusoz, S. McWeeney, M. Aladjem, E. Birney, J. Collado Vides, S. Goto, M. Hucka, N. Le Novere, N. Maltsev, A. Pandey, P. Thomas, E. Wingender, P. D. Karp, C. Sander, G.D. Bader

Research output: Contribution to journalArticleAcademicpeer-review

299 Citations (Scopus)

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 languageEnglish
Pages (from-to)935-42
JournalNature Biotechnology
Volume28
Issue number9
DOIs
Publication statusPublished - 1 Jan 2010

Cite this

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., ... Bader, G. D. (2010). The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28(9), 935-42. https://doi.org/10.1038/nbt.1666
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. ; Rodchenkov, I. ; Splendiani, A. ; Tkachev, S. ; Zucker, J. ; Gopinath, G. ; Rajasimha, H. ; Ramakrishnan, R. ; Shah, I. ; Syed, M. ; Anwar, N. ; Babur, O. ; 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.P. ; Wimalaratne, S. ; Allen, K. ; Braun, B. ; Whirl Carrillo, M. ; Cheung, K. H. ; 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, K. H. ; Rzhetsky, A. ; Schachter, V. ; Sobral, B. S. ; Dogrusoz, U. ; McWeeney, S. ; Aladjem, M. ; Birney, E. ; Collado Vides, J. ; Goto, S. ; Hucka, M. ; Le Novere, N. ; Maltsev, N. ; Pandey, A. ; Thomas, P. ; Wingender, E. ; Karp, P. D. ; Sander, C. ; Bader, G.D. / The BioPAX community standard for pathway data sharing. In: Nature Biotechnology. 2010 ; Vol. 28, No. 9. pp. 935-42.
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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 = "E. Demir and Cary, {M. P.} and S. Paley and K. Fukuda and C. Lemer and I. Vastrik and G. Wu and P. D'Eustachio and C. Schaefer and J. Luciano and F. Schacherer and {Martinez Flores}, I. and Z. Hu and {Jimenez Jacinto}, V. and {Joshi Tope}, G. and K. Kandasamy and {Lopez Fuentes}, {A. C.} and H. Mi and E. Pichler and I. Rodchenkov and A. Splendiani and S. Tkachev and J. Zucker and G. Gopinath and H. Rajasimha and R. Ramakrishnan and I. Shah and M. Syed and N. Anwar and O. Babur and M. Blinov and E. Brauner and D. Corwin and S. Donaldson and F. Gibbons and R. Goldberg and P. Hornbeck and A. Luna and {Murray Rust}, P. and E. Neumann and O. Reubenacker and M. Samwald and {van Iersel}, M.P. and S. Wimalaratne and K. Allen and B. Braun and {Whirl Carrillo}, M. and Cheung, {K. H.} and K. Dahlquist and A. Finney and M. Gillespie and E. Glass and L. Gong and R. Haw and M. Honig and O. Hubaut and D. Kane and S. Krupa and M. Kutmon and J. Leonard and D. Marks and D. Merberg and V. Petri and A. Pico and D. Ravenscroft and L. Ren and N. Shah and M. Sunshine and R. Tang and R. Whaley and S. Letovksy and Buetow, {K. H.} and A. Rzhetsky and V. Schachter and Sobral, {B. S.} and U. Dogrusoz and S. McWeeney and M. Aladjem and E. Birney and {Collado Vides}, J. and S. Goto and M. Hucka and {Le Novere}, N. and N. Maltsev and A. Pandey and P. Thomas and E. Wingender and Karp, {P. D.} and C. Sander and G.D. Bader",
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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, O, 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, MP, 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, Le Novere, N, 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. 935-42. https://doi.org/10.1038/nbt.1666

The BioPAX community standard for pathway data sharing. / 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.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, O.; 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.P.; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl Carrillo, M.; Cheung, K. H.; 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, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Dogrusoz, U.; McWeeney, S.; Aladjem, M.; Birney, E.; Collado Vides, J.; Goto, S.; Hucka, M.; Le Novere, N.; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G.D.

In: Nature Biotechnology, Vol. 28, No. 9, 01.01.2010, p. 935-42.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - The BioPAX community standard for pathway data sharing

AU - Demir, E.

AU - Cary, M. P.

AU - Paley, S.

AU - Fukuda, K.

AU - Lemer, C.

AU - Vastrik, I.

AU - Wu, G.

AU - D'Eustachio, P.

AU - Schaefer, C.

AU - Luciano, J.

AU - Schacherer, F.

AU - Martinez Flores, I.

AU - Hu, Z.

AU - Jimenez Jacinto, V.

AU - Joshi Tope, G.

AU - Kandasamy, K.

AU - Lopez Fuentes, A. C.

AU - Mi, H.

AU - Pichler, E.

AU - Rodchenkov, I.

AU - Splendiani, A.

AU - Tkachev, S.

AU - Zucker, J.

AU - Gopinath, G.

AU - Rajasimha, H.

AU - Ramakrishnan, R.

AU - Shah, I.

AU - Syed, M.

AU - Anwar, N.

AU - Babur, O.

AU - Blinov, M.

AU - Brauner, E.

AU - Corwin, D.

AU - Donaldson, S.

AU - Gibbons, F.

AU - Goldberg, R.

AU - Hornbeck, P.

AU - Luna, A.

AU - Murray Rust, P.

AU - Neumann, E.

AU - Reubenacker, O.

AU - Samwald, M.

AU - van Iersel, M.P.

AU - Wimalaratne, S.

AU - Allen, K.

AU - Braun, B.

AU - Whirl Carrillo, M.

AU - Cheung, K. H.

AU - Dahlquist, K.

AU - Finney, A.

AU - Gillespie, M.

AU - Glass, E.

AU - Gong, L.

AU - Haw, R.

AU - Honig, M.

AU - Hubaut, O.

AU - Kane, D.

AU - Krupa, S.

AU - Kutmon, M.

AU - Leonard, J.

AU - Marks, D.

AU - Merberg, D.

AU - Petri, V.

AU - Pico, A.

AU - Ravenscroft, D.

AU - Ren, L.

AU - Shah, N.

AU - Sunshine, M.

AU - Tang, R.

AU - Whaley, R.

AU - Letovksy, S.

AU - Buetow, K. H.

AU - Rzhetsky, A.

AU - Schachter, V.

AU - Sobral, B. S.

AU - Dogrusoz, U.

AU - McWeeney, S.

AU - Aladjem, M.

AU - Birney, E.

AU - Collado Vides, J.

AU - Goto, S.

AU - Hucka, M.

AU - Le Novere, N.

AU - Maltsev, N.

AU - Pandey, A.

AU - Thomas, P.

AU - Wingender, E.

AU - Karp, P. D.

AU - Sander, C.

AU - Bader, G.D.

PY - 2010/1/1

Y1 - 2010/1/1

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.

U2 - 10.1038/nbt.1666

DO - 10.1038/nbt.1666

M3 - Article

VL - 28

SP - 935

EP - 942

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 9

ER -

Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I et al. The BioPAX community standard for pathway data sharing. Nature Biotechnology. 2010 Jan 1;28(9):935-42. https://doi.org/10.1038/nbt.1666