The BioPAX community standard for pathway data sharing

被引：454

作者：

Demir, Emek ^{[2
,3
,4
]}

Cary, Michael P. ^{[2
]}

Paley, Suzanne

Fukuda, Ken ^{[66
]}

Lemer, Christian ^{[6
]}

Vastrik, Imre ^{[7
]}

Wu, Guanming ^{[8
]}

D'Eustachio, Peter ^{[9
]}

Schaefer, Carl ^{[10
]}

Luciano, Joanne ^{[11
]}

Schacherer, Frank ^{[12
]}

Martinez-Flores, Irma ^{[13
]}

Hu, Zhenjun ^{[14
]}

Jimenez-Jacinto, Veronica ^{[13
]}

Joshi-Tope, Geeta ^{[15
]}

Kandasamy, Kumaran ^{[16
,17
,18
,19
]}

Lopez-Fuentes, Alejandra C.

Mi, Huaiyu ^{[5
]}

Pichler, Elgar

Rodchenkov, Igor ^{[1
]}

Splendiani, Andrea ^{[20
,21
]}

Tkachev, Sasha ^{[22
]}

Zucker, Jeremy ^{[23
]}

Gopinath, Gopal ^{[24
]}

Rajasimha, Harsha ^{[25
,26
]}

Ramakrishnan, Ranjani ^{[27
]}

Shah, Imran ^{[28
]}

Syed, Mustafa ^{[29
]}

Anwar, Nadia ^{[2
]}

Babur, Oezguen ^{[2
,3
,4
]}

Blinov, Michael ^{[30
]}

Brauner, Erik ^{[31
]}

Corwin, Dan ^{[32
]}

Donaldson, Sylva ^{[1
]}

Gibbons, Frank ^{[31
]}

Goldberg, Robert ^{[33
]}

Hornbeck, Peter ^{[22
]}

Luna, Augustin ^{[34
]}

Murray-Rust, Peter ^{[35
]}

Neumann, Eric ^{[36
]}

Reubenacker, Oliver ^{[37
]}

Samwald, Matthias ^{[38
,39
]}

van Iersel, Martijn ^{[40
]}

Wimalaratne, Sarala ^{[41
]}

Allen, Keith ^{[42
]}

Braun, Burk ^{[12
]}

Whirl-Carrillo, Michelle ^{[43
]}

Cheung, Kei-Hoi ^{[44
]}

Dahlquist, Kam ^{[45
]}

Finney, Andrew ^{[46
]}

机构：

[1] Univ Toronto, Banting & Best Dept Med Res, Donnelly Ctr Cellular & Biomol Res, Toronto, ON, Canada

[2] Mem Sloan Kettering Canc Ctr, New York, NY 10021 USA

[3] Bilkent Univ, Ctr Bioinformat, Ankara, Turkey

[4] Bilkent Univ, Dept Comp Engn, Ankara, Turkey

[5] SRI Int, Ctr Artificial Intelligence, Menlo Pk, CA 94025 USA

[6] Univ Libre Bruxelles, Brussels, Belgium

[7] European Bioinformat Inst, Cambridge, England

[8] Ontario Inst Canc Res, Toronto, ON, Canada

[9] NYU, Sch Med, New York, NY USA

[10] NCI, Ctr Biomed Informat & Informat Technol, Rockville, MD USA

[11] Predict Med, Belmont, MA USA

[12] BIOBASE Corp, Beverly, MA USA

[13] Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Cuernavaca 62191, Morelos, Mexico

[14] Boston Univ, Biomol Syst Lab, Boston, MA 02215 USA

[15] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[16] Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD USA

[17] Johns Hopkins Univ, Dept Biol Chem, Baltimore, MD USA

[18] Johns Hopkins Univ, Dept Pathol, Baltimore, MD USA

[19] Johns Hopkins Univ, Dept Oncol, Baltimore, MD USA

[20] Univ Rennes 1, Fac Med, Rennes, France

[21] Rothamsted Res, Harpenden, Herts, England

[22] Cell Signaling Technol Inc, Danvers, MA USA

[23] Broad Inst, Cambridge, MA USA

[24] US FDA, Ctr Food Safety & Appl Nutr, Laurel, MD USA

[25] Virginia Polytech Inst & State Univ, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA

[26] NEI, Neurobiol Neurodegenerat & Repair Lab, NIH, Bethesda, MD 20892 USA

[27] Oregon Hlth & Sci Univ, Dept Behav Neurosci, Portland, OR 97201 USA

[28] US Environm Protect Agcy Durham, Durham, NC USA

[29] Argonne Natl Lab, Math & Comp Sci Div, Argonne, IL 60439 USA

[30] Univ Connecticut, Ctr Hlth, Farmington, CT USA

[31] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA

[32] Lexikos Corp, Boston, MA USA

[33] Natl Inst Stand & Technol, Div Biotechnol, Gaithersburg, MD 20899 USA

[34] NCI, Ctr Canc Res, NIH, Bethesda, MD 20892 USA

[35] Univ Cambridge, Dept Chem, Unilever Ctr Mol Sci Informat, Cambridge CB2 1EW, England

[36] Clin Semant Grp, Lexington, MA USA

[37] Univ Connecticut, Ctr Hlth, Ctr Cell Anal & Modeling, Storrs, CT USA

[38] Natl Univ Ireland, Digital Enterprise Res Inst, Galway, Ireland

[39] Konrad Lorenz Inst Evolut & Cognit Res, Altenberg, Austria

[40] Maastricht Univ, Dept Bioinformat, Maastricht, Netherlands

[41] Univ Auckland, Auckland 1, New Zealand

[42] Syngenta Biotech Inc, Res Triangle Pk, NC USA

[43] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[44] Yale Univ, Yale Ctr Med Informat, New Haven, CT USA

[45] Loyola Marymount Univ, Los Angeles, CA 90045 USA

[46] Physiomics PLC, Magdalen Ctr, Oxford, England

[47] St Johns Univ, Jamaica, NY 11439 USA

[48] Columbia Univ, New York, NY USA

[49] SRA Int, Fairfax, VA USA

[50] Novartis Knowledge Ctr, Cambridge, MA USA

来源：

NATURE BIOTECHNOLOGY | 2010年 / 28卷 / 09期

基金：

美国国家卫生研究院; 英国生物技术与生命科学研究理事会;

关键词：

COLLABORATIVE CONSTRUCTION; INTERACTION NETWORK; REPRESENTATION; ONTOLOGY; SOFTWARE; KNOWLEDGEBASE; INFORMATION; UNIFICATION; ENVIRONMENT; EVOLUTION;

D O I：

10.1038/nbt.1666

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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. (C) 2010 Nature America, Inc. All rights reserved.

引用

页码：935 / 942

页数：8

共 65 条

[1] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[2] Pathguide: a Pathway Resource List [J].

Bader, Gary D. ;

Cary, Michael P. ;

Sander, Chris .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D504-D506

[3] BIND - a data specification for storing and describing biomolecular interactions, molecular complexes and pathways [J].

Bader, GD ;

Hogue, CWV .

BIOINFORMATICS, 2000, 16 (05) :465-477

[4]

Bader GD, 2003, NUCLEIC ACIDS RES, V31, P248, DOI 10.1093/nar/gkg056

[5] Publishing on the semantic web - The coming Internet revolution will profoundly affect scientific information. [J].

Berners-Lee, T ;

Hendler, J .

NATURE, 2001, 410 (6832) :1023-1024

[6] Pathway information for systems biology [J].

Cary, MP ;

Bader, GD ;

Sander, C .

FEBS LETTERS, 2005, 579 (08) :1815-1820

[7] The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases [J].

Caspi, Ron ;

Altman, Tomer ;

Dale, Joseph M. ;

Dreher, Kate ;

Fulcher, Carol A. ;

Gilham, Fred ;

Kaipa, Pallavi ;

Karthikeyan, Athikkattuvalasu S. ;

Kothari, Anamika ;

Krummenacker, Markus ;

Latendresse, Mario ;

Mueller, Lukas A. ;

Paley, Suzanne ;

Popescu, Liviu ;

Pujar, Anuradha ;

Shearer, Alexander G. ;

Zhang, Peifen ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D473-D479

[8] cPath: open source software for collecting, storing, and querying biological pathways [J].

Cerami, Ethan G. ;

Bader, Gary D. ;

Gross, Benjamin E. ;

Sander, Chris .

BMC BIOINFORMATICS, 2006, 7 (1)

[9] MINT: the molecular INTeraction database [J].

Chatr-aryamontri, Andrew ;

Ceol, Arnaud ;

Palazzi, Luisa Montecchi ;

Nardelli, Giuliano ;

Schneider, Maria Victoria ;

Castagnoli, Luisa ;

Cesareni, Gianni .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D572-D574

[10] Comprehensive genomic characterization defines human glioblastoma genes and core pathways [J].

Chin, L. ;

Meyerson, M. ;

Aldape, K. ;

Bigner, D. ;

Mikkelsen, T. ;

VandenBerg, S. ;

Kahn, A. ;

Penny, R. ;

Ferguson, M. L. ;

Gerhard, D. S. ;

Getz, G. ;

Brennan, C. ;

Taylor, B. S. ;

Winckler, W. ;

Park, P. ;

Ladanyi, M. ;

Hoadley, K. A. ;

Verhaak, R. G. W. ;

Hayes, D. N. ;

Spellman, Paul T. ;

Absher, D. ;

Weir, B. A. ;

Ding, L. ;

Wheeler, D. ;

Lawrence, M. S. ;

Cibulskis, K. ;

Mardis, E. ;

Zhang, Jinghui ;

Wilson, R. K. ;

Donehower, L. ;

Wheeler, D. A. ;

Purdom, E. ;

Wallis, J. ;

Laird, P. W. ;

Herman, J. G. ;

Schuebel, K. E. ;

Weisenberger, D. J. ;

Baylin, S. B. ;

Schultz, N. ;

Yao, Jun ;

Wiedemeyer, R. ;

Weinstein, J. ;

Sander, C. ;

Gibbs, R. A. ;

Gray, J. ;

Kucherlapati, R. ;

Lander, E. S. ;

Myers, R. M. ;

Perou, C. M. ;

McLendon, Roger .

NATURE, 2008, 455 (7216) :1061-1068

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