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A note on Versions and Citation

In this article, we emphasise the correct way in which to cite the work of others in bioinformatics.

Just as it is important to record citations for the literature we consult, it is equally important to cite the websites from which we gather information. When citing databases, it is common to acknowledge the authors and researchers that created the database with a link to the appropriate website; however this is not always the most appropriate way to cite their work or research.

Databases are the result of scientific and informatics research open to other researchers and or the public and in most cases, the authors would have produced a peer-reviewed article describing the methods they used alongside the online implementation. These are the citations that we need to use to reference their work appropriately.

For example, the Pfam server http://pfam.xfam.org/ shows the following citation suggestion at the bottom of its page:

Citing Pfam

‘If you find Pfam useful, please consider citing the reference that describes this work: The Pfam protein families database: towards a more sustainable future: R.D. Finn, P. Coggill, R.Y. Eberhardt, S.R. Eddy, J. Mistry, A.L. Mitchell, S.C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G.A. Salazar, J. Tate, A. Bateman. Nucleic Acids Research (2016) Database Issue 44:D279-D285’

It is equally important to record the version or release of the database or software. In the case of a database, the date of access should also be recorded. This is the equivalent of citing the correct edition of a book. In databases, new versions or releases will have significant modifications in the same way as new editions of a book can have important updates on certain topics. In the case of Pfam, their version or database release is shown in the home page. If this or the citation information is missing from a database or server one can use the URL and data of access but you should also feel free to contact the authors, they will gladly assist you in giving the correct citation for their work.

As an exercise, go to the Uniprot database and look for their suggested citation. Can you find it? What about the database version or release?

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This article is from the free online course:

Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

Wellcome Genome Campus Advanced Courses and Scientific Conferences