InteractOA: Showcasing the representation of knowledge from scientific literature in Wikidata

Abstract

Knowledge generated during the scientific process is still mostly stored in the form of scholarly articles. This lack of machine-readability hampers efforts to find, query, and reuse such findings efficiently and contributes to today’s information overload. While attempts have been made to semantify journal articles, widespread adoption of such approaches is still a long way off. One way to demonstrate the usefulness of such approaches to the scientific community is by showcasing the use of freely available, open-access knowledge graphs such as Wikidata as sustainable storage and representation solutions. Here we present an example from the life sciences in which knowledge items from scholarly literature are represented in Wikidata, linked to their exact position in open-access articles. In this way, they become part of a rich knowledge graph while maintaining clear ties to their origins. As example entities, we chose small regulatory RNAs (sRNAs) that play an important role in bacterial and archaeal gene regulation. These post-transcriptional regulators can influence the activities of multiple genes in various manners, forming complex interaction networks. We stored the information on sRNA molecule interaction taken from open-access articles in Wikidata and built an intuitive web interface called InteractOA, which makes it easy to visualize, edit, and query information. The tool also links information on small RNAs to their reference articles from PubMed Central on the statement level. InteractOA encourages researchers to contribute, save, and curate their own similar findings. InteractOA is hosted at https://interactoa.zbmed.de and its code is available under a permissive open source licence. In principle, the approach presented here can be applied to any other field of research.