biology articles code

Living Bibliography

Living Bibliography was born when, a few weeks ago, on a Saturday morning, I bumped into the Hack4Knowledge, a meeting to build apps, tools, and remixes with existing databases to innovate and enrich the creation and dissemination of knowledge.

I was already playing with the Mendeley API and took the opportunity to put an idea into practice: aggregate bibliographic references related to a taxon. It is not a particularly new idea, and it also does not differ much from searching a taxon name on Google or Scopus. But since the Mendeley database is based on its users’ collections, it is possible to extract some interesting information. For example, find out which articles are more popular or create trending topics with popular taxa based on the number of readers and related publications.

Living Bibliography homepage
Living Bibliography homepage

Regardless of the source, article data also allows extracting useful information such as the most active authors on a certain taxon, network of collaborators, annual variation in the number of related articles, popular research topics for each group, etc. Integrating the data and using visualization tools, it would be possible to “see” holes in the knowledge or follow the history of one’s research.

Imagine if every article was freely available with contained information (metadata) about the studied organisms with taxonomic classification, occurrence data, collection sites, DNA sequences, citations with semantic markup, research topics, hypotheses to test, methods, raw data, etc. Anyone would be able to have a summary of the current knowledge about an organism. Especially interesting to set research guidelines and avoid spending money on the same mistakes; optimization of science. And do not forget about the possibility to attach observations, annotations, discussions, unsolved questions, and other collaborative activities.

Well, after creating a prototype of the idea, I have just put the basic functions of the aggregator to work. Nothing I wrote above is included, just a search interface where you can use a scientific or common name and a page for each taxon with a list of related references and some sorting options. If a taxon is not in the database, it searches in real time; therefore, it is necessary to wait for a little while and reload the page (at least until I automate this).

Taxon page in Living Bibliography
Taxon page in Living Bibliography

If you are interested, you can test the Living Bibliography at Just remember it is completely experimental, I do not guarantee that your favorite articles will appear or that the information will be accurate. There are many duplicated articles, wrong author names, badly formatted titles, swapped journal names, and so on at Mendeley. I don’t know how much I’ll be able to work on it, but the source code is open, and I would love to hear ideas and suggestions :)

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