Correspondence | Published:

Bioinformatics code must enforce citation

Naturevolume 417page588 (2002) | Download Citation

Subjects

Sir

Despite repeated calls for the development of open, interoperable databases and software systems in bioinformatics (for example refs 13), Lincoln Stein in his Commentary “Creating a bioinformatics nation”, with some justification compares the state of bioinformatics to the mediaeval city-states of Italy, and proposes a unifying code of conduct4. In considering his proposal, we must ask why such a chaotic situation arose, and why it has been so persistent.

There are many reasons for the existing chaos. Bioinformatics is a rapidly evolving field. Stable interfaces take time to design, implement and maintain. Algorithms and tools evolve and incorporate feedback from users, and the interfaces must necessarily evolve as well. But standards have been developed and widely accepted in other fields undergoing rapid technological change, such as the Internet.

The difference is that academic scientists are responsible for most of the software and data in bioinformatics. Academic careers are advanced by publications that establish priority and citations that validate the impact of the work. Being the first to develop a new approach forms the basis for a peer-reviewed publication, which is not the case for developing and maintaining a standard interface to an old tool or data set. Academic scientists cannot be expected to sacrifice their careers in the interest of community standards. Significant responsibility for standards development and implementation must fall to service organizations such as database providers. These organizations need the support of the academic community in standards development, whereas academic scientists need to benefit from the time and effort they contribute to the process.

Modern bioinformatics software systems are complex. A genome-annotation system, for example, draws on dozens of software components, involving teams of dozens or even hundreds of developers. We need ways to recognize the often-critical contributions of these individuals to the overall result. Stein's code of conduct would facilitate the development of seamlessly interoperable systems in a way that hides the underlying complexity of a calculation from the user. From an academic scientist's perspective, this goal is in direct conflict with the need for recognition and citation and will do nothing for the career of the developer. An academic scientist, therefore, has a strong career imperative to force users to deal directly with their tool or website, and little incentive to make the technology accessible through interoperable systems.

BLAST5 and FASTA6 are “citation classics”, but they are also at the top of the list of “failure to be cited classics”. Projects like NCBI7 and Ensembl8 have made useful software tools and large volumes of data widely available, but do not give users the information necessary to cite appropriately the algorithms and software needed to access the system. Ensembl, for example, provides users with alignments performed by BLAST and SSAHA9 using EST sequences10,11 aligned to the human genome sequence12 and gene models created by GenScan13. And yet Ensembl lists a citation only to itself on its home page, and the NCBI genome resources pages provide no citation information for the underlying bioinformatics.

If bioinformatics is to emerge as a strong “nation state”, Stein's code of conduct needs to address the career imperatives of computational biologists. First and foremost, it must require people to cite their sources. Interfaces and data sets should include explicit citation information, so that systems assembled from components can recursively retrieve citation data from their components and present the user with information for all the modules used in a task.

Graphical user interfaces provide ready mechanisms to display the properties of an object. A user clicking on a gene model should be able to retrieve citation information quickly and automatically for the software and data used to assemble that model. This object- and task-specific citation approach would also provide a mechanism for recognizing the specific contributions of developers in large teams. The use of algorithms, software or data without attribution is plagiarism. Manuscripts that fail to cite bioinformatics sources properly are not acceptable for publication in peer-reviewed journals, and software systems that fail to cite their component sources are not appropriate for use by the scientific community.

References

  1. 1

    Boguski, M. S. Curr. Opin. Genet. Dev. 4, 383–388 (1994).

  2. 2

    Fasman, K. H. J. Comput. Biol. 1, 165–171 (1994).

  3. 3

    Karp, P. D. Trends Biotechnol. 14, 273–279 (1996).

  4. 4

    Stein, L. Nature 417, 119–120 (2002).

  5. 5

    Altschul, S. F. et al. J. Mol. Biol. 215, 403–410 (1990).

  6. 6

    Pearson, W. R. & Lipman, D. J. Proc. Natl Acad. Sci. USA 85, 2444–2448 (1988).

  7. 7

    Wheeler, D. L. et al. Nucleic Acids Res. 30, 13–16 (2002).

  8. 8

    Hubbard, T. et al. Nucleic Acids Res. 30, 38–41 (2002).

  9. 9

    Ning, Z., Cox, A. J. & Mullikin, J. C. Genome Res. 11, 1725–1729 (2001).

  10. 10

    Hillier, L. D. et al. Genome Res. 6, 807–828 (1996).

  11. 11

    Adams, M. D. et al. Nature Genet. 4, 373–380 (1993).

  12. 12

    International Human Genome Sequencing Consortium. Nature 409, 860–921 (2001).

  13. 13

    Burge, C. & Karlin, S. J. Mol. Biol. 268, 78–94 (1997).

Download references

Author information

Affiliations

  1. University of Michigan School of Medicine, Ann Arbor, 48109, Michigan, USA

    • David J. States

Authors

  1. Search for David J. States in:

About this article

Publication history

Issue Date

DOI

https://doi.org/10.1038/417588b

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Newsletter Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing