Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project (original) (raw)

To fully understand the context, methods, data and conclusions that pertain to an experiment, one must have access to a range of background information. However, the current diversity of experimental designs and analytical techniques complicates the discovery and evaluation of experimental data; furthermore, the increasing rate of production of those data compounds the problem. Community opinion increasingly favors that a regularized set of the available metadata ('data about the data') pertaining to an experiment1,2 be associated with the results, making explicit both the biological and methodological contexts. Many journals and funding agencies now require that authors reporting microarray-based transcriptomics experiments comply with the Minimum Information about a Microarray Experiment (MIAME) checklist3 as a prerequisite for publication4,5,6,7. Similarly, minimum information guidelines for reporting proteomics experiments and describing systems biology models are gaining broader support in their respective database communities8,9; and progress is being made toward the standardization of the reporting of clinical trials in the medical literature10. Such minimum information checklists promote transparency in experimental reporting, enhance accessibility to data and support effective quality assessment, increasing the general value of a body of work (and the competitiveness of the originators).

Collaborative minimum information checklist development projects for diverse biologically and technologically delineated subject areas are ongoing. A special issue of the journal OMICS11 included invited pieces from eight communities supporting minimum information checklist development projects. However, until recently there were no mechanisms for such projects to coordinate their development. Consequently, the full range of checklists can be difficult to establish without intensive searching, and tracking their evolution is nontrivial. Furthermore, overlaps in scope and arbitrary decisions on wording and substructuring inhibit their use in combination. These issues present difficulties for checklist users, especially those who routinely combine information from several disciplines. Here we explore some of the issues arising from the development of checklists in relative isolation, discuss the potential benefits of greater coordination and describe the mechanisms we have put in place to facilitate such coordination. In summary, we present the MIBBI project (http://www.mibbi.org/), which maintains a web-based, freely accessible resource for checklist projects, providing straightforward access to extant checklists (and to complementary data formats, controlled vocabularies, tools and databases), thereby enhancing both transparency and accessibility, as discussed above. MIBBI is managed by representatives of its various participant communities and is fully open to comment from any interested party. Our goal is to facilitate the development of an integrated checklist resource site for the wider bioscience community.

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Acknowledgements

We. acknowledge funding from the UK Natural Environmental Research Council's Environmental Bioinformatics Centre and the UK Biotechnology and Biological Sciences Research Council (BB/E025080/1) to D.F. and S.-A.S. to support C.F.T. and MIBBI. Work on MIFlowCyt is supported by the US National Institutes of Health's National Institute of Biomedical Imaging and Bioengineering (EB005034-01) and by Bioinformatics Integration Support Contract A140076 from the US National Institute of Allergy and Infectious Diseases. R.R.B. is supported by the Michael Smith Foundation for Health Research, by the International Society for the Advancement of Cytology and by grant funding from the US National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health (R01EB005034). N.W.H. acknowledges the support of the European Union Framework VI project META-PHOR (Food-ST-2006-03622). F.G., P.L. and work on CARMEN are supported by the UK Engineering and Physical Sciences Research Council (EP/E002331/1). K.T. acknowledges support from Science Foundation Ireland. Work on MIAME/Tox and MIAME/Nutr by P.R-S. is supported by the NuGO (NoE 503630) and CarcinoGenomics (PL 037712) European Union projects. Work on MIARE is supported by the eDIKT project. Opinions, findings and conclusions or recommendations expressed in this paper are those of the authors and do not necessarily reflect the views of the US National Science Foundation or the US National Institutes of Health.

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Authors and Affiliations

1. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridgeshire, UK
   Chris F Taylor, Susanna-Assunta Sansone, Rolf Apweiler, Alvis Brazma, Henning Hermjakob, Nicolas Le Novère, Sandra Orchard, Philippe Rocca-Serra, Daniel Schober & Peter Sterk
2. Natural Environment Research Council Environmental Bioinformatics Centre, Mansfield Road, OX1 3SR, Oxford, UK
   Chris F Taylor, Dawn Field, Susanna-Assunta Sansone, Tim Booth, Tanya Gray & Norman Morrison
3. Molecular Evolution and Bioinformatics Group, Oxford Centre for Ecology and Hydrology, Mansfield Road, OX1 3SR, Oxford, UK
   Dawn Field & Tanya Gray
4. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK
   Jan Aerts
5. Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
   Michael Ashburner
6. Department of Biochemistry, Stanford Microarray Database, Stanford University School of Medicine, Stanford, 94305-5307, California, USA
   Catherine A Ball
7. Swiss Institute of Bioinformatics, Michel-Servet 1, Geneva, 1211, Switzerland
   Pierre-Alain Binz
8. Geneva Bioinformatics (GeneBio) SA, Avenue de Champel 25, Geneva, 1206, Switzerland
   Pierre-Alain Binz
9. Jax Mouse Phenome Project, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, Maine, USA
   Molly Bogue
10. Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, V5Z 1L3, British Columbia, Canada
    Ryan R Brinkman
11. The Lance Armstrong Foundation, PO Box 161150, Austin, 78716-1150, Texas, USA
    Adam Michael Clark
12. Institute for Systems Biology, 1441 N. 34th Street, Seattle, 98103, Washington, USA
    Eric W Deutsch
13. University of California Davis, Genome Center, 451 East Health Sciences Drive, Davis, 95616, California, USA
    Oliver Fiehn
14. National Institute of Environmental Health Sciences and Lockheed Martin Information Technology, Research Triangle Park, North Carolina, 27709-2233, USA
    Jennifer Fostel
15. Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4SB, UK
    Peter Ghazal, Graeme Grimes & Javier Santoyo-Lopez
16. School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
    Frank Gibson & Phillip Lord
17. Bioinformatics Group, Medical Research Council Mammalian Genetics Unit, Harwell, OX11 0RD, Oxfordshire, UK
    John M Hancock & Ann-Marie Mallon
18. Department of Computer Science, Aberystwyth University, Penglais, SY23 3DB, Aberystwyth, UK
    Nigel W Hardy
19. Indigo BioSystems, Inc., 111 Congressional Boulevard, Suite 160, Carmel, 46032, Indiana, USA
    Randall K Julian Jr
20. Division of Molecular and Cellular Biosciences, National Science Foundation, 4201 Wilson Boulevard, Arlington, 22230, Virginia, USA
    Matthew Kane
21. Beilstein-Institut zur Förderung der Chemischen Wissenschaften, Trakehner Strasse 7-9, Frankfurt am Main, D-60487, Germany
    Carsten Kettner
22. Office of Technology and Industrial Relations, Office of the Director, National Cancer Institute, Bldg 31A, Rm 10A52, Bethesda, 20892, Maryland, USA
    Christopher Kinsinger & Henry Rodriguez
23. Seattle Children's Hospital Research Institute, 1900 9th Avenue, Seattle, 98101, Washington, USA
    Eugene Kolker
24. Seattle Children's Hospital and Regional Medical Center, 4800 Sand Point Way NE, Seattle, 98105, Washington, USA
    Eugene Kolker
25. Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, Technologiepark 927, Ghent, B-9052, Belgium
    Martin Kuiper
26. Molecular Genetics, Ghent University, Ghent, B-9052, Belgium
    Martin Kuiper
27. Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
    Martin Kuiper
28. Department of Plant Biology, University of Georgia, Athens, 30602-7271, Georgia, USA
    Jim Leebens-Mack
29. Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, 94729-3200, California, USA
    Suzanna E Lewis
30. Department of Pathology, University of Texas Southwestern Medical Center, Dallas, 75390, Texas, USA
    Nishanth Marthandan & Richard H Scheuermann
31. RIKEN Genomic Sciences Center, 3-1-1 Koyadai, Tsukuba-shi, 305-0074, Ibaraki, Japan
    Hiroshi Masuya
32. Economic 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
    Ruth McNally
33. Division of Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany
    Alexander Mehrle, Heiko Rosenfelder & Stefan Wiemann
34. School of Computer Science, University of Manchester, Oxford Road, M13 9PL, Manchester, UK
    Norman Morrison
35. Department 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
    John Quackenbush
36. Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, 50011-3150, Iowa, USA
    James M Reecy
37. Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, 08543-4000, New Jersey, USA
    Donald G Robertson
38. NuGO, The European Nutrigenomics Organisation,
    Philippe Rocca-Serra
39. Department of Philosophy and Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, New York, 14260, USA
    Barry Smith
40. AstraZeneca UK Ltd., Brixham, TQ5 8BA, Devon, UK
    Jason Snape
41. Department of Genetics, Center for Bioinformatics, 423 Guardian Drive, Philadelphia, 19104-6021, Pennsylvania, USA
    Christian J Stoeckert Jr
42. School of Biochemistry and Immunology, Trinity College Dublin, College Green, Dublin, 2, Ireland
    Keith Tipton
43. Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, The Netherlands
    Andreas Untergasser
44. Center for Medical Genetics, Ghent University Hospital, Ghent, 9000, Belgium
    Jo Vandesompele

Authors

1. Chris F Taylor
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2. Dawn Field
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3. Susanna-Assunta Sansone
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4. Jan Aerts
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5. Rolf Apweiler
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6. Michael Ashburner
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7. Catherine A Ball
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8. Pierre-Alain Binz
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9. Molly Bogue
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10. Tim Booth
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11. Alvis Brazma
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12. Ryan R Brinkman
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13. Adam Michael Clark
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14. Eric W Deutsch
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15. Oliver Fiehn
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16. Jennifer Fostel
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17. Peter Ghazal
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18. Frank Gibson
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19. Tanya Gray
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20. Graeme Grimes
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21. John M Hancock
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22. Nigel W Hardy
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23. Henning Hermjakob
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24. Randall K Julian Jr
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25. Matthew Kane
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26. Carsten Kettner
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27. Christopher Kinsinger
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28. Eugene Kolker
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29. Martin Kuiper
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30. Nicolas Le Novère
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31. Jim Leebens-Mack
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32. Suzanna E Lewis
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33. Phillip Lord
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34. Ann-Marie Mallon
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35. Nishanth Marthandan
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36. Hiroshi Masuya
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37. Ruth McNally
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38. Alexander Mehrle
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39. Norman Morrison
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40. Sandra Orchard
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41. John Quackenbush
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42. James M Reecy
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43. Donald G Robertson
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44. Philippe Rocca-Serra
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45. Henry Rodriguez
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46. Heiko Rosenfelder
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47. Javier Santoyo-Lopez
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48. Richard H Scheuermann
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49. Daniel Schober
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50. Barry Smith
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51. Jason Snape
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52. Christian J Stoeckert Jr
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53. Keith Tipton
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54. Peter Sterk
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55. Andreas Untergasser
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56. Jo Vandesompele
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57. Stefan Wiemann
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Corresponding authors

Correspondence toChris F Taylor, Dawn Field or Susanna-Assunta Sansone.

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Competing interests

D.F., S.-A.S. and C.F.T. conceived and designed the concept of MIBBI as synergistic project; D.F. and S.-A.S. raised the funds to support MIBBI activities, and C.F.T. performed the analysis presented in this paper; all authors discussed the results and implications and commented on the manuscript.

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Taylor, C., Field, D., Sansone, SA. et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.Nat Biotechnol 26, 889–896 (2008). https://doi.org/10.1038/nbt.1411

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• Issue Date: August 2008
• DOI: https://doi.org/10.1038/nbt.1411