Towards BioDBcore: a community-defined information specification for biological databases

被引：23

作者：

Gaudet, Pascale ^{[1
,2
]}

Bairoch, Amos ^{[1
]}

Field, Dawn ^{[3
]}

Sansone, Susanna-Assunta ^{[4
]}

Taylor, Chris ^{[5
]}

Attwood, Teresa K. ^{[6
,7
]}

Bateman, Alex ^{[8
]}

Blake, Judith A. ^{[9
]}

Bult, Carol J. ^{[9
]}

Cherry, J. Michael ^{[10
]}

Chisholm, Rex L. ^{[2
]}

Cochrane, Guy ^{[5
]}

Cook, Charles E. ^{[4
]}

Eppig, Janan T. ^{[9
]}

Galperin, Michael Y. ^{[11
]}

Gentleman, Robert ^{[12
,13
]}

Goble, Carole A. ^{[7
]}

Gojobori, Takashi ^{[14
,15
,16
]}

Hancock, John M. ^{[17
]}

Howe, Douglas G. ^{[18
]}

Imanishi, Tadashi ^{[14
]}

Kelso, Janet ^{[13
,19
]}

Landsman, David ^{[13
]}

Lewis, Suzanna E. ^{[20
]}

Karsch-Mizrachi, Ilene ^{[11
]}

Orchard, Sandra ^{[5
]}

Ouellette, B. F. Francis ^{[13
,21
]}

Ranganathan, Shoba ^{[22
,23
]}

Richardson, Lorna ^{[24
]}

Rocca-Serra, Philippe ^{[4
]}

Schofield, Paul N. ^{[25
]}

Smedley, Damian ^{[5
]}

Southan, Christopher ^{[26
]}

Tan, Tin Wee ^{[23
]}

Tatusova, Tatiana ^{[11
]}

Whetzel, Patricia L. ^{[27
]}

White, Owen ^{[28
]}

Yamasaki, Chisato ^{[14
]}

机构：

[1] CMU, Swiss Inst Bioinformat, CH-1211 Geneva 4, Switzerland

[2] Northwestern Univ, Feinberg Sch Med, Chicago, IL 60611 USA

[3] NERC, Ctr Ecol & Hydrol, Oxford OX1 3SR, England

[4] Univ Oxford, Oxford E Res Ctr, Oxford OX1 3QG, England

[5] European Bioinformat Inst, European Mol Biol Lab EMBL Outstn, Cambridge CB10 1SD, England

[6] Univ Manchester, Fac Life Sci, Manchester M13 9PT, Lancs, England

[7] Univ Manchester, Sch Comp Sci, Manchester M13 9PT, Lancs, England

[8] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[9] Jackson Lab, Bar Harbor, ME 04609 USA

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

[11] Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA

[12] Genentech Inc, San Francisco, CA 94080 USA

[13] Oxford Univ Press, DATABASE, Journal Biol Databases & Curat, Oxford OX2 6DP, England

[14] Natl Inst Adv Ind Sci & Technol, Biomed Informat Res Ctr, Koto Ku, Tokyo 1350064, Japan

[15] Natl Inst Genet, Ctr Informat Biol, Mishima, Shizuoka 4118540, Japan

[16] Natl Inst Genet, DNA Data Bank Japan, Mishima, Shizuoka 4118540, Japan

[17] MRC Harwell, Mammalian Genet Unit, Didcot OX11 0RD, Oxon, England

[18] 5291 Univ Oregon, Zebrafish Model Organism Database, Eugene, OR 97401 USA

[19] Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany

[20] Univ Calif Berkeley, Lawrence Berkeley Lab, Genom Div, Berkeley, CA 94720 USA

[21] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada

[22] Macquarie Univ, Dept Chem & Biomol Sci, Sydney, NSW 2109, Australia

[23] Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117548, Singapore

[24] Western Gen Hosp, MRC Human Genet Unit, Inst Genet & Mol Med, Edinburgh EH4 2XU, Midlothian, Scotland

[25] Univ Cambridge, Dept Physiol Dev & Neurosci, Cambridge CB2 3EG, England

[26] ChrisDS Consulting, Gothenburg, Sweden

[27] Stanford Univ, Stanford Ctr Biomed Informat Res, Natl Ctr Biomed Ontol, Stanford, CA 94305 USA

[28] Univ Maryland, Inst Genome Sci, Sch Med, Baltimore, MD 21201 USA

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

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：

BIOINFORMATICS; RESOURCES;

D O I：

10.1093/nar/gkq1173

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.

引用

页码：D7 / D10

页数：4

共 12 条

[11] Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi) [J].

Tan, Tin Wee ;

Tong, Joo Chuan ;

Khan, Asif M. ;

de Silva, Mark ;

Lim, Kuan Siong ;

Ranganathan, Shoba .

BMC GENOMICS, 2010, 11

[12] Promoting coherent minimum reporting guidelines for biological and biomedical investigations:: the MIBBI project [J].

Taylor, Chris F. ;

Field, Dawn ;

Sansone, Susanna-Assunta ;

Aerts, Jan ;

Apweiler, Rolf ;

Ashburner, Michael ;

Ball, Catherine A. ;

Binz, Pierre-Alain ;

Bogue, Molly ;

Booth, Tim ;

Brazma, Alvis ;

Brinkman, Ryan R. ;

Clark, Adam Michael ;

Deutsch, Eric W. ;

Fiehn, Oliver ;

Fostel, Jennifer ;

Ghazal, Peter ;

Gibson, Frank ;

Gray, Tanya ;

Grimes, Graeme ;

Hancock, John M. ;

Hardy, Nigel W. ;

Hermjakob, Henning ;

Julian, Randall K., Jr. ;

Kane, Matthew ;

Kettner, Carsten ;

Kinsinger, Christopher ;

Kolker, Eugene ;

Kuiper, Martin ;

Le Novere, Nicolas ;

Leebens-Mack, Jim ;

Lewis, Suzanna E. ;

Lord, Phillip ;

Mallon, Ann-Marie ;

Marthandan, Nishanth ;

Masuya, Hiroshi ;

McNally, Ruth ;

Mehrle, Alexander ;

Morrison, Norman ;

Orchard, Sandra ;

Quackenbush, John ;

Reecy, James M. ;

Robertson, Donald G. ;

Rocca-Serra, Philippe ;

Rodriguez, Henry ;

Rosenfelder, Heiko ;

Santoyo-Lopez, Javier ;

Scheuermann, Richard H. ;

Schober, Daniel ;

Smith, Barry .

NATURE BIOTECHNOLOGY, 2008, 26 (08) :889-896

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