Toward interoperable bioscience data

被引：257

作者：

Sansone, Susanna-Assunta ^{[1
]}

Rocca-Serra, Philippe ^{[1
]}

Field, Dawn ^{[2
]}

Maguire, Eamonn ^{[1
]}

Taylor, Chris ^{[2
,3
]}

Hofmann, Oliver ^{[4
]}

Fang, Hong ^{[5
]}

Neumann, Steffen ^{[6
]}

Tong, Weida ^{[7
]}

Amaral-Zettler, Linda ^{[8
]}

Begley, Kimberly ^{[4
,9
]}

Booth, Tim ^{[2
]}

Bougueleret, Lydie ^{[10
]}

Burns, Gully ^{[11
]}

Chapman, Brad ^{[4
]}

Clark, Tim ^{[12
,13
]}

Coleman, Lee-Ann ^{[14
]}

Copeland, Jay ^{[15
]}

Das, Sudeshna ^{[12
,13
]}

de Daruvar, Antoine ^{[16
,17
]}

de Matos, Paula ^{[3
]}

Dix, Ian ^{[18
]}

Edmunds, Scott ^{[19
]}

Evelo, Chris T. ^{[20
,21
]}

Forster, Mark J. ^{[22
]}

Gaudet, Pascale ^{[23
,24
]}

Gilbert, Jack ^{[25
]}

Goble, Carole ^{[26
]}

Griffin, Julian L. ^{[27
,28
,29
]}

Jacob, Daniel ^{[17
,30
]}

Kleinjans, Jos ^{[31
]}

Harland, Lee ^{[32
]}

Haug, Kenneth ^{[3
]}

Hermjakob, Henning ^{[3
]}

Sui, Shannan J. Ho ^{[4
]}

Laederach, Alain ^{[33
]}

Liang, Shaoguang ^{[19
]}

Marshall, Stephen ^{[34
]}

McGrath, Annette ^{[35
]}

Merrill, Emily ^{[13
]}

Reilly, Dorothy ^{[34
]}

Roux, Magali ^{[36
,37
]}

Shamu, Caroline E. ^{[15
]}

Shang, Catherine A. ^{[38
]}

Steinbeck, Christoph ^{[3
]}

Trefethen, Anne ^{[1
]}

Williams-Jones, Bryn ^{[32
]}

Wolstencroft, Katherine ^{[26
]}

Xenarios, Ioannis ^{[10
,39
]}

Hide, Winston ^{[4
]}

机构：

[1] Univ Oxford, Oxford E Res Ctr, Oxford, England

[2] Wallingford Ctr Ecol & Hydrol CEH, Environm Bioinformat Ctr, Nat Environm Res Council, Oxford, England

[3] European Bioinformat Inst, European Mol Biol Lab EMBL Outstn, Cambridge, England

[4] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[5] US FDA, ICF Int, Natl Ctr Toxicol Res, Jefferson, AR USA

[6] Leibniz Inst Plant Biochem, Dept Stress & Dev Biol, Halle, Germany

[7] US FDA, Ctr Bioinformat, Natl Ctr Toxicol Res, Jefferson, AR USA

[8] Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA

[9] Ontario Inst Canc Res Informat & Biocomp, Toronto, ON, Canada

[10] Swiss Prot Grp, Swiss Inst Bioinformat, Geneva, Switzerland

[11] Univ So Calif, Inst Informat Sci, Marina Del Rey, CA 90292 USA

[12] Harvard Univ, Sch Med, Dept Neurol, Boston, MA 02115 USA

[13] Massachusetts Gen Hosp, Dept Neurol, Boston, MA 02114 USA

[14] British Lib, London, England

[15] Harvard Univ, Sch Med, Dept Syst Biol, Boston, MA USA

[16] Univ Bordeaux, Lab Bordelais Rech lnformat LaBRI, CNRS, UMR 5800, Talence, France

[17] Univ Bordeaux, Ctr Bioinformat Bordeaux CBiB, Bordeaux, France

[18] AstraZeneca Plc, Knowledge Engn & Informat Sci, Discovery Informat, Macclesfield, Cheshire, England

[19] BGI Shenzhen, Yantian, Peoples R China

[20] Maastricht Univ, Dept Bioinformat BiGCaT, Maastricht, Netherlands

[21] Netherlands Bioinformat Ctr, NBIC Fac, Nijmegen, Netherlands

[22] Syngenta RDIS, Bracknell, Berks, England

[23] Northwestern Univ, Ctr Genet Med, Chicago, IL 60611 USA

[24] Swiss Inst Bioinformat Computat Anal & Lab Invest, Geneva, Switzerland

[25] Argonne Natl Lab, Argonne, IL 60439 USA

[26] Univ Manchester, Sch Comp Sci, Manchester, Lancs, England

[27] Univ Cambridge, Dept Biochem, Cambridge CB2 1QW, England

[28] Univ Cambridge, Cambridge Syst Biol Ctr, Cambridge, England

[29] Med Res Council MRC Human Nutr Res, Elsie Widdowson Lab, Cambridge, England

[30] INRA, Fruit Biol & Pathol Ctr, UMR 1332, Villenave Dornon, France

[31] PA Maastricht Univ, Dept Toxicogenom, Netherlands Toxicogenom Ctr, Maastricht, Netherlands

[32] ConnectedDiscovery, London, England

[33] Univ N Carolina, Dept Biol, Chapel Hill, NC USA

[34] Novartis Inst BioMed Res, Quantitat Biol Unit, Cambridge, MA USA

[35] CSIRO Math Informat & Stat, Canberra, ACT, Australia

[36] CNRS UPS76, Inst Sci & Technol Informat, Vandoeuvre Les Nancy, France

[37] Univ Paris 06, CNRS UMR 7606, Paris, France

[38] Macquarie Univ, Sydney, NSW 2109, Australia

[39] Vital IT, Swiss Inst Bioinformat, Lausanne, Switzerland

来源：

NATURE GENETICS | 2012年 / 44卷 / 02期

基金：

英国生物技术与生命科学研究理事会; 英国医学研究理事会;

关键词：

D O I：

10.1038/ng.1054

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

引用

页码：121 / 126

页数：6

共 29 条

[1] Standard cooperating procedures [J].

不详 .

NATURE GENETICS, 2011, 43 (06) :501-501

[2] Data's shameful neglect [J].

不详 .

NATURE, 2009, 461 (7261) :145-145

[3]

[Anonymous], 2011, GENOME BIOL, V12, P402

[4]

[Anonymous], 2010, NAT GENET, V42, P1

[5] OPINION Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery [J].

Barnes, Michael R. ;

Harland, Lee ;

Foord, Steven M. ;

Hall, Matthew D. ;

Dix, Ian ;

Thomas, Scott ;

Williams-Jones, Bryn I. ;

Brouwer, Cory R. .

NATURE REVIEWS DRUG DISCOVERY, 2009, 8 (09) :701-708

[6] NCBI GEO: archive for high-throughput functional genomic data [J].

Barrett, Tanya ;

Troup, Dennis B. ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Rudnev, Dmitry ;

Evangelista, Carlos ;

Kim, Irene F. ;

Soboleva, Alexandra ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Muertter, Rolf N. ;

Edgar, Ron .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D885-D890

[7]

BIRNEY E, 2009, NATURE, V461, P168, DOI DOI 10.1038/461168A

[8] Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data [J].

Chen, Bin ;

Dong, Xiao ;

Jiao, Dazhi ;

Wang, Huijun ;

Zhu, Qian ;

Ding, Ying ;

Wild, David J. .

BMC BIOINFORMATICS, 2010, 11

[9] Editorial [J].

Christie, Alastair ;

Campbell, Jim .

SOCIAL WORK EDUCATION, 2009, 28 (06) :579-582

[10] The BioPAX community standard for pathway data sharing [J].

Demir, Emek ;

Cary, Michael P. ;

Paley, Suzanne ;

Fukuda, Ken ;

Lemer, Christian ;

Vastrik, Imre ;

Wu, Guanming ;

D'Eustachio, Peter ;

Schaefer, Carl ;

Luciano, Joanne ;

Schacherer, Frank ;

Martinez-Flores, Irma ;

Hu, Zhenjun ;

Jimenez-Jacinto, Veronica ;

Joshi-Tope, Geeta ;

Kandasamy, Kumaran ;

Lopez-Fuentes, Alejandra C. ;

Mi, Huaiyu ;

Pichler, Elgar ;

Rodchenkov, Igor ;

Splendiani, Andrea ;

Tkachev, Sasha ;

Zucker, Jeremy ;

Gopinath, Gopal ;

Rajasimha, Harsha ;

Ramakrishnan, Ranjani ;

Shah, Imran ;

Syed, Mustafa ;

Anwar, Nadia ;

Babur, Oezguen ;

Blinov, Michael ;

Brauner, Erik ;

Corwin, Dan ;

Donaldson, Sylva ;

Gibbons, Frank ;

Goldberg, Robert ;

Hornbeck, Peter ;

Luna, Augustin ;

Murray-Rust, Peter ;

Neumann, Eric ;

Reubenacker, Oliver ;

Samwald, Matthias ;

van Iersel, Martijn ;

Wimalaratne, Sarala ;

Allen, Keith ;

Braun, Burk ;

Whirl-Carrillo, Michelle ;

Cheung, Kei-Hoi ;

Dahlquist, Kam ;

Finney, Andrew .

NATURE BIOTECHNOLOGY, 2010, 28 (09) :935-942

← 1 2 3 →