Improving Publication Pipeline with Automated Biological Entity Detection and Validation Service

• Published in: Data and information management Vol. 3; no. 1; pp. 3 - 17
• Main Authors: Xu, Weijia, Gupta, Amit, Jaiswal, Pankaj, Taylor, Crispin, Lockhart, Patti, Regala, Jennifer
• Format: Journal Article
• Language: English
• Published: Warsaw Sciendo 01.03.2019; Elsevier Limited
• Subjects: Accessibility; Annotations; Applications programs; Automation; digital curation; digital library; entity extraction; Identification methods; machine learning; natural language processing; ontology; Periodicals; Pilot projects; Recall; text mining; Use statistics
• ISSN: 2543-9251; 2543-9251
• DOI: 10.2478/dim-2019-0003

With the increasing amount of digital journal submissions, there is a need to deploy new scalable computational methods to improve information accessibilities. One common task is to identify useful information and named entity from text documents such as journal article submission. However, there are many technical challenges to limit applicability of the general methods and lack of general tools. In this paper, we present domain informational vocabulary extraction (DIVE) project, which aims to enrich digital publications through detection of entity and key informational words and by adding additional annotations. In a first of its kind to our knowledge, our system engages authors of the peer-reviewed articles and the journal publishers by integrating DIVE implementation in the manuscript proofing and publication process. The system implements multiple strategies for biological entity detection, including using regular expression rules, ontology, and a keyword dictionary. These extracted entities are then stored in a database and made accessible through an interactive web application for curation and evaluation by authors. Through the web interface, the authors can make additional annotations and corrections to the current results. The updates can then be used to improve the entity detection in subsequent processed articles in the future. We describe our framework and deployment in details. In a pilot program, we have deployed the first phase of development as a service integrated with the journals Plant Physiology and The Plant cell published by the American Society of Plant Biologists (ASPB). We present usage statistics to date since its production on April 2018. We compare automated recognition results from DIVE with results from author curation and show the service achieved on average 80% recall and 70% precision per article. In contrast, an existing biological entity extraction tool, a biomedical named entity recognizer (ABNER), can only achieve 47% recall and return a much larger candidate set.