Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Nature Biotechnology - Tập 26 Số 8 - Trang 889-896 - 2008
Chris Taylor1, Dawn Field2, Susanna‐Assunta Sansone1, Jan Aerts3, Rolf Apweiler1, Michael Ashburner4, Catherine A. Ball5, Pierre‐Alain Binz6, Molly A. Bogue7, Tim Booth2, Alvis Brāzma1, Ryan R. Brinkman8, Adam M. Clark9, Eric W. Deutsch10, Oliver Fiehn11, Jennifer Fostel12, Peter Ghazal13, F. Gibson14, Tanya Gray15, Graeme R. Grimes13, John M. Hancock16, Nigel Hardy17, Henning Hermjakob1, Randall K. Julian18, Matthew D. Kane19, Carsten Kettner20, Christopher R. Kinsinger21, Eugene Kolker22, Martin Kuiper23, Nicolas Le Novère1, Jim Leebens‐Mack24, Suzanna Lewis25, Phillip Lord14, Ann‐Marie Mallon16, Nishanth Marthandan26, Hiroshi Masuya27, Ruth McNally28, Alexander Mehrle29, Norman Morrison30, Sandra Orchard1, John Quackenbush31, James M. Reecy32, Donald G. Robertson33, Philippe Rocca‐Serra34, Henry Rodriguez21, Heiko Rosenfelder29, Javier Santoyo‐López13, Richard H. Scheuermann26, Daniel Schober1, Barry Smith35, Jason Snape36, Christian J. Stoeckert37, Keith F. Tipton38, Peter Sterk1, Andreas Untergasser39, Jo Vandesompele40, Stefan Wiemann29
1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridgeshire, UK
2Natural Environment Research Council Environmental Bioinformatics Centre, Mansfield Road, OX1 3SR, Oxford, UK
3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK
4Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
5Department of Biochemistry, Stanford Microarray Database, Stanford University School of Medicine, Stanford, 94305-5307, California, USA
6Swiss Institute of Bioinformatics, Michel-Servet 1, Geneva, 1211, Switzerland
7Jax Mouse Phenome Project, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, Maine, USA
8Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, V5Z 1L3, British Columbia, Canada
9The Lance Armstrong Foundation, PO Box 161150, Austin, 78716-1150, Texas, USA
10Institute for Systems Biology, 1441 N. 34th Street, Seattle, 98103, Washington, USA
11University of California Davis, Genome Center, 451 East Health Sciences Drive, Davis, 95616, California, USA
12National Institute of Environmental Health Sciences and Lockheed Martin Information Technology, Research Triangle Park, North Carolina, 27709-2233, USA
13Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4SB, UK
14School of Computing Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
15Molecular Evolution and Bioinformatics Group, Oxford Centre for Ecology and Hydrology, Mansfield Road, OX1 3SR, Oxford, UK
16Bioinformatics Group, Medical Research Council Mammalian Genetics Unit, Harwell, OX11 0RD, Oxfordshire, UK
17Department of Computer Science, Aberystwyth University, Penglais, SY23 3DB, Aberystwyth, UK
18Indigo BioSystems, Inc., 111 Congressional Boulevard, Suite 160, Carmel, 46032, Indiana, USA
19Division of Molecular and Cellular Biosciences, National Science Foundation, 4201 Wilson Boulevard, Arlington, 22230, Virginia, USA
20Beilstein-Institut zur Förderung der Chemischen Wissenschaften, Trakehner Strasse 7-9, Frankfurt am Main, D-60487, Germany
21Office of Technology and Industrial Relations, Office of the Director, National Cancer Institute, Bldg 31A, Rm 10A52, Bethesda, 20892, Maryland, USA
22Seattle Children's Hospital Research Institute, 1900 9th Avenue, Seattle, 98101, Washington, USA
23Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, Ghent, B-9052, Belgium
24Department of Plant Biology, University of Georgia, Athens, 30602-7271, Georgia, USA
25Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, 94729-3200, California, USA
26Department of Pathology, University of Texas Southwestern Medical Center, Dallas, 75390, Texas, USA
27RIKEN Genomic Sciences Center, 3-1-1 Koyadai, Tsukuba-shi, 305-0074, Ibaraki, Japan
28Economic and Social Research Council Centre for Economic and Social Aspects of Genomics (Cesagen), Lancaster University, Institute for Advanced Studies, IAS Building, County South, Lancaster, LA1 4YD, UK
29Division of Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany
30School of Computer Science, University of Manchester, Oxford Road, M13 9PL, Manchester, UK
31Department of Biostatistics and Computational Biology and Department of Cancer Biology, Department of Biostatistics, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, 02115, Massachusetts, USA
32Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, 50011-3150, Iowa, USA
33Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, 08543-4000, New Jersey, USA
34NuGO, The European Nutrigenomics Organisation,
35Department of Philosophy and Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, New York, 14260, USA
36AstraZeneca UK Ltd., Brixham, TQ5 8BA, Devon, UK
37Department of Genetics, Center for Bioinformatics, 423 Guardian Drive, Philadelphia, 19104-6021, Pennsylvania, USA
38School of Biochemistry and Immunology, Trinity College Dublin, College Green, Dublin 2, Ireland
39Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, The Netherlands
40Center for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium

Tóm tắt

Từ khóa


Tài liệu tham khảo

Quackenbush, J. Standardizing the standards. Mol. Syst. Biol. 2, 2006.0010 (2006).

Anonymous. Under the MIAME sun. Nat. Methods 3, 415 (2006).

Brazma, A. et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat. Genet. 29, 365–371 (2001).

Anonymous. Microarray standards at last. Nature 419, 323 (2002).

Ball, C.A. et al. A guide to microarray experiments—an open letter to the scientific journals. Lancet 360, 1019 (2002).

Ball, C.A. et al. Standards for microarray data. Science 298, 539 (2002).

Ball, C.A. et al. The underlying principles of scientific publication. Bioinformatics 18, 1409 (2002).

Taylor, C.F. et al. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 25, 887–893 (2007).

Le Novère, N. et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23, 1509–1515 (2005).

Altman, D.G., Simera, I., Hoey, J., Moher, D. & Schulz, K. EQUATOR: reporting guidelines for health research. Lancet 371, 1149–1150 (2008).

Field, D. & Sansone, S.-A. A special issue on data standards. OMICS 10, 84–93 (2006).

Morrison, N. et al. Concept of sample in OMICS technology. OMICS 10, 127–137 (2006).

Morrison, N. et al. Standard annotation of environmental OMICS data: application to the transcriptomics domain. OMICS 10, 172–178 (2006).

Jones, A.R. et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat. Biotechnol. 25, 1127–1133 (2007).

Sansone, S.-A. et al. A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS 10, 164–171 (2006).

Sansone, S.-A. et al. The first RSBI (ISA-TAB) workshop: “Can a simple format work for complex studies?” OMICS published online, doi:10.1089/omi.2008.0019 (2008).

Smith, B. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251–1255 (2007).

Taylor, C.F. et al. The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS 10, 145–151 (2006).

Fiehn, O. et al. Establishing reporting standards for metabolomic and metabonomic studies: a call for participation. OMICS 10, 158–163 (2006).

Field, D. et al. The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol. 26, 541–547 (2008).

Deutsch, E.W. et al. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat. Biotechnol. 26, 305–312 (2008).

Thông tin
Thông tin xuất bản

Nature Biotechnology

Tập 26 Số 8

889-896

Thông tin tác giả