DEBBIE: The Open Access Database of Experimental Scaffolds and Biomaterials Built Using an Automated Text Mining Pipeline

Abstract

AbstractBiomaterials research output has experienced an exponential increase over the last three decades. The majority of research is published in the form of scientific articles and is therefore available as unstructured text, making it a challenging input for computational processing. Computational tools are becoming essential to overcome this information overload. Among them, text mining systems present an attractive option for the automated extraction of information from text documents into structured datasets. This work presents the first automated system for biomaterial related information extraction from the National Library of Medicine's premier bibliographic database (MEDLINE) research abstracts into a searchable database. The system is a text mining pipeline that periodically retrieves abstracts from PubMed and identifies research and clinical studies of biomaterials. Thereafter, the pipeline identifies sixteen concept types of interest in the abstract using the Biomaterials Annotator, a tool for biomaterials Named Entity Recognition (NER). These concepts of interest, along with the abstract and relevant metadata are then deposited in DEBBIE, the Database of Experimental Biomaterials and their Biological Effect. DEBBIE is accessible through a web application that provides keyword searches and displays results in an intuitive and meaningful manner, aiming to facilitate an efficient mapping and organization of biomaterials information.