Using a Secure, Continually Updating, Web Source Processing Pipeline to Support the Real-Time Data Synthesis and Analysis of Scientific Literature: Development and Validation Study
Authors: Vaghela Uddhav , Rabinowicz Simon , Bratsos Paris , Martin Guy , Fritzilas Epameinondas , Markar Sheraz , Purkayastha Sanjay , Stringer Karl , Singh Harshdeep , Llewellyn Charlie , Dutta Debabrata , Clarke Jonathan M , Howard Matthew ,   PanSurg REDASA Curators, Serban Ovidiu , Kinross James 
Published: April 2021

Background

The scale and quality of the global scientific response to the COVID-19 pandemic have unquestionably saved lives. However, the COVID-19 pandemic has also triggered an unprecedented “infodemic”; the velocity and volume of data production have overwhelmed many key stakeholders such as clinicians and policy makers, as they have been unable to process structured and unstructured data for evidence-based decision making. Solutions that aim to alleviate this data synthesis–related challenge are unable to capture heterogeneous web data in real time for the production of concomitant answers and are not based on the high-quality information in responses to a free-text query.

Objective

The main objective of this project is to build a generic, real-time, continuously updating curation platform that can support the data synthesis and analysis of a scientific literature framework. Our secondary objective is to validate this platform and the curation methodology for COVID-19–related medical literature by expanding the COVID-19 Open Research Dataset via the addition of new, unstructured data.

Methods

To create an infrastructure that addresses our objectives, the PanSurg Collaborative at Imperial College London has developed a unique data pipeline based on a web crawler extraction methodology. This data pipeline uses a novel curation methodology that adopts a human-in-the-loop approach for the characterization of quality, relevance, and key evidence across a range of scientific literature sources.

Results

REDASA (Realtime Data Synthesis and Analysis) is now one of the world’s largest and most up-to-date sources of COVID-19–related evidence; it consists of 104,000 documents. By capturing curators’ critical appraisal methodologies through the discrete labeling and rating of information, REDASA rapidly developed a foundational, pooled, data science data set of over 1400 articles in under 2 weeks. These articles provide COVID-19–related information and represent around 10% of all papers about COVID-19.

Conclusions

This data set can act as ground truth for the future implementation of a live, automated systematic review. The three benefits of REDASA’s design are as follows: (1) it adopts a user-friendly, human-in-the-loop methodology by embedding an efficient, user-friendly curation platform into a natural language processing search engine; (2) it provides a curated data set in the JavaScript Object Notation format for experienced academic reviewers’ critical appraisal choices and decision-making methodologies; and (3) due to the wide scope and depth of its web crawling method, REDASA has already captured one of the world’s largest COVID-19–related data corpora for searches and curation.