Mining impactful discoveries from the biomedical literature

Abstract

Abstract Background Literature-based discovery (LBD) aims to help researchers to identify relations between concepts which are worthy of further investigation by text-mining the biomedical literature. While the LBD literature is rich and the field is considered mature, standard practice in the evaluation of LBD methods is methodologically poor and has not progressed on par with the domain. The lack of properly designed and decent-sized benchmark dataset hinders the progress of the field and its development into applications usable by biomedical experts. Results This work presents a method for mining past discoveries from the biomedical literature. It leverages the impact made by a discovery, using descriptive statistics to detect surges in the prevalence of a relation across time. The validity of the method is tested against a baseline representing the state-of-the-art “time-sliced” method. Conclusions This method allows the collection of a large amount of time-stamped discoveries. These can be used for LBD evaluation, alleviating the long-standing issue of inadequate evaluation. It might also pave the way for more fine-grained LBD methods, which could exploit the diversity of these past discoveries to train supervised models. Finally the dataset (or some future version of it inspired by our method) could be used as a methodological tool for systematic reviews. We provide an online exploration tool in this perspective, available at https://brainmend.adaptcentre.ie/ .

Keywords

• Literature-based discovery
• Evaluation
• Benchmark dataset
• Time-sliced method