URIs for scientific software (maybe using figshare)

Posted October 22nd, 2013 by konrad

Update: Mark Hahnel just pointed out that there should be no such test entities made public (so you don’t need to test it – I can tell you that it works) and that there will be a sandbox fur such purposes soon. But in general the approach could be used. Figshare is considering code submission for a while but wants to make sure to make things right and do this without inventing the wheel. He also pointed me to a recent tweet linking to an even better solution (which is so far a proof of concept) than the one presented below.

detourI am planning to submit a paper which is covering a bioinformatical software tool. As usually I would like to provide a link to a web page where the software can be downloaded and which contains a reference to the software repository. So far I am not sure if this page will be hosted on the institute sever, github or another location. Here a problem arises that many scientist face if they want to add an URL to a scientific publication. As long as an articles is a static piece of text and is not easily editable it is nearly impossible for the author to inform the reader about changes of an URL. Maybe I am missing something but there seems to be no common recommendation by publishers about how tackle this issue. The general solution would be to create a stable Uniform Resource Identifier (URI) for the content one would like to share. The URI can be an Uniform Resource Locator (URL) e.g. a web address – so in our case the trouble maker which might change – or a Uniform resource name (URN). Well known examples of URN systems are the ISBN system or the DOI system. The later one works pretty well for scientific journal publications. Using this for smaller pieces of research like images, software and data was not very practical as you have to be a paying member to get a name space and to generate DOIs. As far as I see, figshare was a game changer as it is the first platform which offers the creation of DOIs for each item (image, data set, poster, etc.) that is shared on it. Back to the initially described problem – how can I generate a resilient URN for my software?

File types offered by figshare

File types offered by figshare

A test entry

A test entry

Unfortunately figshare does not offer a data type for this purpose – software or URL. But one can create a “data sets” base on a plain text and simply write the current URL of the software into that file. This is definitely not very clean and just a small hack but it seems to work. It would be great if figshare sees the need for such a redirection to software sources and offers a new entity type for this. But maybe I am on a wrong track anyway and there are better solution for my problem. I would be very happy if anybody could refer me to one.

[1] Wren JD. URL decay in MEDLINE–a 4-year follow-up study. Bioinformatics. 2008 Jun 1;24(11):1381-5. doi:10.1093/bioinformatics/btn127. Epub 2008 Apr 15. PubMed PMID: 18413326

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