Files and code for English dictionaries, gold and silver standard corpora for biomedical natural language processing related to SARS-CoV-2 and COVID-19

BACKGROUND

Automated information extraction with natural language processing (NLP) tools is required to gain systematic insights from the large number of COVID-19 publications, reports and social media posts, which far exceed human processing capabilities. A key challenge for NLP is the extensive variation in terminology used to describe medical entities, which was especially pronounced for this newly emergent disease.

FINDINGS

Here we present an NLP toolbox comprising very large English dictionaries of synonyms for SARS-CoV-2 (including variant names) and COVID-19, which can be used with dictionary-based NLP tools. We also present a silver standard corpus generated with the dictionaries, and a gold standard corpus, consisting of PubMed abstracts manually annotated for disease, virus, symptom, protein/gene, cell type, chemical and species terms, which can be used to train and evaluate COVID-19-related NLP tools. Code for annotation, which can be used to expand the silver standard corpus or for text mining is also included. This toolbox is freely available on Github (on https://github.com/Aitslab/corona) and here.

CONCLUSIONS

The toolbox can be used for a variety of text analytics tasks related to the COVID-19 crisis and has already been used to create a COVID-19 knowledge graph, study the variability and evolution of COVID-19-related terminology and develop and benchmark text mining tools.