- Email: [email protected]
Debunking minimum information myths: one hat need not fit all
New Biotechnology Volume 25, Number 4 April 2009
DISCUSSION
Debunking minimum information myths: one hat need not fit all Sandra Orchard, [email protected] and Chris F. Taylor
A recent meeting report published in this journal suggests that the work of the various bodies attempting to improve the quality of articles describing the results of biomedical experimental work has been misunderstood or, at best, misinterpreted. This response is an attempt to set the record straight and ensure that other groups are not discouraged from using these standards or from joining in their further development in either existing or novel areas of research. Minimum information (MI) guidelines have been written, and are being implemented, for many specialist areas in the biomedical sciences; for example, microarray-based transcriptomics (MIAME) [1], proteomics (MIAPE) [2] and the detection of molecular interactions (MIMIx) [3]. These documents exist to guide researchers as they prepare their work for submission as a journal article, and in an increasing number of cases, as a parallel deposition to a public domain repository. Their data can then (subject to intellectual property constraints) be accessed by the entire research community to be analysed in train with related bodies of information in a fully informed manner. Some MI guidelines will soon function as policy components for funders of biomedical science. Publishers also take a keen interest, for example as described in a recent editorial in Nature Cell Biology [4]. The express purpose of MI guidelines is to ensure that the data generated by an experiment are properly described. A report should meet the requirements of both sufficiency and practicability; that is, it should
contain sufficient data and metadata to ensure that the work can be understood (and in principle reproduced) while ensuring that the act of creating such a report is not disproportionately burdensome. Missing information is at the best frustrating, and at the worst may mislead by leaving the reader to fill gaps through inference. In this age of computational biology, we simply cannot ignore the potential value accruing to the regularisation of appropriately contextualised data sets. Where data sets fall short of such community-agreed prescriptions, the incomplete papers that result may be overlooked and the information contained within them may be lost. MI documents do not tell researchers how to work, but how to report the work they have done. It is the role of the journals, and their panels or reviewers, to determine whether an experimenter has properly designed the experiment and that adequate emphasis was placed on quality control. The MI community does not seek to ‘standardize control experiments’, nor will their products ‘be an
1871-6784/$ - see front matter ß 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.nbt.2008.12.001
impediment to research freedom’. The design and implementation of an experiment is a matter for individual research groups. MI guidelines simply ensure that key pieces of information are not omitted from manuscripts and database submissions (the latter frequently providing supplementary material for the former). Note also that the absence of guidance for a particular technique does not invalidate that technique – it is simply a gap in coverage (hopefully to be filled at a later date). The most prominent objection arising from the meeting reported by de Marco et al. was the perceived difficulty of covering diverse techniques in a single set of guidelines (one-hatfits-all). However, there is a simple answer: there is no limit on the numbers of ‘hats’ that can be deployed. Consider the example of proteomics, where there are established guidelines for several techniques (MIAPE [2]), but no attempt is made to cram that heterogeneous set of analytical approaches into one set of guidelines. Rather, they are presented as ‘modules’ to be used in various combinations as appropriate. The fact that diverse analytical approaches fall within one community’s scope should not hinder their development of MI guidelines. To be specific, there is no reason why MIPFE should not be taken forward in a similar manner to MIAPE – as a series of complementary modules, each applying to one or a set of techniques. In closing we would like to highlight the Minimum Information for Biological and Biomedical Investigations (MIBBI) project – a communal web-based resource for the users and developers of minimum information checklists [5]. MIBBI is coordinated by a group of community representatives from ongoing standardisation activities. It has two main components: the Portal, a ‘one-stop shop’ for
www.elsevier.com/locate/nbt
171
Features DISCUSSION
Features
DISCUSSION
those exploring the range of extant checklist projects and the Foundry, which fosters the collaborative development of an integrated set of checklists covering the whole of the biomedical sciences. Should potential authors be interested in accessing projects seeking to improve the quality of published data in their domain, they can visit the MIBBI site. A perusal of
Features DISCUSSION 172
www.elsevier.com/locate/nbt
New Biotechnology Volume 25, Number 4 April 2009
the documents collected there, will help much to dispel the myths apparently building up around these efforts.
References 1 Brazma, A. et al. (2001) Nat. Genet. 29, 365–371 2 Taylor, C.F. et al. (2007) Nat. Biotechnol. 25, 887–893 3 Orchard, S. (2007) Nat. Biotechnol. 25, 894–898
4 Nat. Cell Biol. 10 (2008) 1123–1124 http:// www.nature.com/ncb/journal/v10/n10/full/ncb10081123.html 5 Taylor, C.F. et al. (2008) Nat. Biotechnol. 26, 889–896
Sandra Orchard Chris F. Taylor EMBL – European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
DISCUSSION
Debunking minimum information myths: one hat need not fit all Sandra Orchard, [email protected] and Chris F. Taylor
A recent meeting report published in this journal suggests that the work of the various bodies attempting to improve the quality of articles describing the results of biomedical experimental work has been misunderstood or, at best, misinterpreted. This response is an attempt to set the record straight and ensure that other groups are not discouraged from using these standards or from joining in their further development in either existing or novel areas of research. Minimum information (MI) guidelines have been written, and are being implemented, for many specialist areas in the biomedical sciences; for example, microarray-based transcriptomics (MIAME) [1], proteomics (MIAPE) [2] and the detection of molecular interactions (MIMIx) [3]. These documents exist to guide researchers as they prepare their work for submission as a journal article, and in an increasing number of cases, as a parallel deposition to a public domain repository. Their data can then (subject to intellectual property constraints) be accessed by the entire research community to be analysed in train with related bodies of information in a fully informed manner. Some MI guidelines will soon function as policy components for funders of biomedical science. Publishers also take a keen interest, for example as described in a recent editorial in Nature Cell Biology [4]. The express purpose of MI guidelines is to ensure that the data generated by an experiment are properly described. A report should meet the requirements of both sufficiency and practicability; that is, it should
contain sufficient data and metadata to ensure that the work can be understood (and in principle reproduced) while ensuring that the act of creating such a report is not disproportionately burdensome. Missing information is at the best frustrating, and at the worst may mislead by leaving the reader to fill gaps through inference. In this age of computational biology, we simply cannot ignore the potential value accruing to the regularisation of appropriately contextualised data sets. Where data sets fall short of such community-agreed prescriptions, the incomplete papers that result may be overlooked and the information contained within them may be lost. MI documents do not tell researchers how to work, but how to report the work they have done. It is the role of the journals, and their panels or reviewers, to determine whether an experimenter has properly designed the experiment and that adequate emphasis was placed on quality control. The MI community does not seek to ‘standardize control experiments’, nor will their products ‘be an
1871-6784/$ - see front matter ß 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.nbt.2008.12.001
impediment to research freedom’. The design and implementation of an experiment is a matter for individual research groups. MI guidelines simply ensure that key pieces of information are not omitted from manuscripts and database submissions (the latter frequently providing supplementary material for the former). Note also that the absence of guidance for a particular technique does not invalidate that technique – it is simply a gap in coverage (hopefully to be filled at a later date). The most prominent objection arising from the meeting reported by de Marco et al. was the perceived difficulty of covering diverse techniques in a single set of guidelines (one-hatfits-all). However, there is a simple answer: there is no limit on the numbers of ‘hats’ that can be deployed. Consider the example of proteomics, where there are established guidelines for several techniques (MIAPE [2]), but no attempt is made to cram that heterogeneous set of analytical approaches into one set of guidelines. Rather, they are presented as ‘modules’ to be used in various combinations as appropriate. The fact that diverse analytical approaches fall within one community’s scope should not hinder their development of MI guidelines. To be specific, there is no reason why MIPFE should not be taken forward in a similar manner to MIAPE – as a series of complementary modules, each applying to one or a set of techniques. In closing we would like to highlight the Minimum Information for Biological and Biomedical Investigations (MIBBI) project – a communal web-based resource for the users and developers of minimum information checklists [5]. MIBBI is coordinated by a group of community representatives from ongoing standardisation activities. It has two main components: the Portal, a ‘one-stop shop’ for
www.elsevier.com/locate/nbt
171
Features DISCUSSION
Features
DISCUSSION
those exploring the range of extant checklist projects and the Foundry, which fosters the collaborative development of an integrated set of checklists covering the whole of the biomedical sciences. Should potential authors be interested in accessing projects seeking to improve the quality of published data in their domain, they can visit the MIBBI site. A perusal of
Features DISCUSSION 172
www.elsevier.com/locate/nbt
New Biotechnology Volume 25, Number 4 April 2009
the documents collected there, will help much to dispel the myths apparently building up around these efforts.
References 1 Brazma, A. et al. (2001) Nat. Genet. 29, 365–371 2 Taylor, C.F. et al. (2007) Nat. Biotechnol. 25, 887–893 3 Orchard, S. (2007) Nat. Biotechnol. 25, 894–898
4 Nat. Cell Biol. 10 (2008) 1123–1124 http:// www.nature.com/ncb/journal/v10/n10/full/ncb10081123.html 5 Taylor, C.F. et al. (2008) Nat. Biotechnol. 26, 889–896
Sandra Orchard Chris F. Taylor EMBL – European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK