IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution

Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1—Quality control of curated sequences, 2—Call of variations, 3—Functional annotation, and 4—Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.

Holistic Analytics of Digital Artifacts

Investigation of every crime scene with digital evidence is predominantly required in identifying almost all atomic files behind the scenes that have been intentionally scrubbed out. Apart from the data generated across digital devices and the use of diverse technology that slows down the traditional digital forensic investigation strategies. Dynamically scrutinizing the concealed or sparse metadata matches from the less frequent archives of evidence spread across heterogeneous sources and finding their association with other artifacts across the collection is still a horrendous task for the investigators. The effort of this article via unique pockets (UP), unique groups (UG), and unique association (UA) model is to address the exclusive challenges mixed up in identifying incoherent associations that are buried well within the meager metadata field-value pairs. Both the existing similarity models and proposed unique mapping models are verified by the unique metadata association model.

From collection resources to intelligent data: Construction of intelligent digital humanities platform for local historical documents of Shanghai Jiao Tong University

Local historical documents originated from daily life of people belong to special collection resources that were not published publicly. They are valuable assets of universities and libraries. At present, most documents had only finished digitalization or partial datalization work. However, the requirements of deep knowledge mining in documents data, providing visual analysis, and effectively supporting the research of historic humanities scholars had not been fully met. Taking the local historical documents project of Shanghai Jiao Tong University as an example, using relevant techniques of digital humanities (DH), the in-depth analysis and utilization research of documents data were carried out. On the one hand, the core database of the documents was established based on standardizing metadata cataloguing and establishing metadata association. On the other hand, based on the core database, an intelligent DH system platform was constructed. The platform is to realize full-field retrieval and display of the documents, text analysis, association analysis, statistics, and visual presentation of knowledge. In addition, in the process of using the platform for research, humanities scholars can continuously expand the data dimensions and the relationships between data, achieve intelligent supplementation of documents data and platform self-learning. The concept of DH has led to a new direction of database construction and platform development. In the exploration and practice of DH, libraries should continue to widen thinking, improve service and innovation capabilities, and provide better research perspectives, research environments, research support, and research experience for humanities scholars.