The Problem of “Link Rot” in Bioinformatics

Have you ever searched for a particular tool or database that you urgently need to look for some analysis or information for your research and you go to Google search and look for the tool? It gives you some relevant information based on your search string. It usually returns the direct link to that tool or database, the paper published for that tool/database, or some bioinformatics resource directory and you click the link in excitement and your excitement turns into disappointment when you come to know that the link no longer works and you get a 404 error. This is known as Link Rot which is quite evident in Bioinformatics. Wikipedia defines link rot as following;

“Link rot (also called link death, link breaking, or reference rot) is the phenomenon of hyperlinks tending over time to cease to point to their originally targeted file, web page, or server due to that resource being relocated or becoming permanently unavailable. A link that no longer points to its target often called a broken or dead link, is a specific form of the dangling pointer.”

Most of you at any point in your academic or research carrier would have witnessed this while working on an individual project, your dissertation, your Ph.D. thesis, or while working on a research article. Link Rot is a very common problem generally on the World Wide Web and particularly in Bioinformatics.

Causes of Link Rot

Link rot can happen due to various reasons. There are several technical and non-technical reasons behind it. A medium feature by The Arweave Project has summarized the causes of Link rot in a comprehensive manner backed by some surprising numbers that suggest the ubiquity of this problem. The report referring to research published by Oguz and Koehler () points out that “98.4% of web links suffer from link rot during 20 years”.

Link Rot in Bioinformatics

While looking for the information on this topic, I came across hundreds of research and review papers published by leading publication firms like Science, Nature, Oxford academic, and PLoS, etc, talk about link rot in some way or the other.

In June 2019, Mongul et al. while working on the instability and archival stability of the omics tools analyzed 36,702 tools published from 2005 to 2017. They found that 28% of all the published tools were not accessible. For the 98 tools selected for the instability test, they found that 28% of the tools failed installation due to implementation errors.

In a similar study, Agnes Osz and colleagues analyzed 3649 web-based applications published during 1994 and 2017. They found that around 95% of all services were working during their first 2 years that dropped to 84% in the third year. And the numbers kept falling in the consecutive years. The concluded that around one-third of all the applications were out of services till the date.

The problem is not limited to Web servers and databases only. It is observed that journal articles also face the problem of link rot. According to a 2014 study published by Martin Klein and coworkers one out of five articles published in the domain of Science, Technology, and Medicine suffer from reference rot.

Though the problem of link rot or reference rot is not confined and has wide impacts on the scientific community, it is observed that it is generally not given due attention. Therefore, this is to give you a moment to think of new possibilities of solving this problem in general and in particular for the field of Bioinformatics.