Related papers: SBtab - Conventions for structured data tables in …
In the SysLab project we develop a software engineering method based on a mathematical foundation. The SysLab system model serves as an abstract mathematical model for information systems and their components. It is used to formalize the…
Cancer Biotherapy (CB), as opposed to cancer chemotherapy, is the use of macromolecular, biological agents instead of organic chemicals or drugs to treat cancer. Biological agents usually have higher selectivity and have less toxic side…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with…
While data sharing is crucial for knowledge development, privacy concerns and strict regulation (e.g., European General Data Protection Regulation (GDPR)) unfortunately limit its full effectiveness. Synthetic tabular data emerges as an…
Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases…
Nowadays, information management systems deal with data originating from different sources including relational databases, NoSQL data stores, and Web data formats, varying not only in terms of data formats, but also in the underlying data…
Refactoring is a change made to the internal structure of software to make it easier to understand and cheaper to modify without changing its observable behaviour. A database refactoring is a small change to the database schema which…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
This is a thought piece on data-intensive science requirements for databases and science centers. It argues that peta-scale datasets will be housed by science centers that provide substantial storage and processing for scientists who access…
Synthetic data generation using large language models (LLMs) demonstrates substantial promise in addressing biomedical data challenges and shows increasing adoption in biomedical research. This study systematically reviews recent advances…
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to…
Tabular data is difficult to analyze and to search through, yielding for new tools and interfaces that would allow even non tech-savvy users to gain insights from open datasets without resorting to specialized data analysis tools or even…
SynDiffix is a new open-source tool for structured data synthesis. It has anonymization features that allow it to generate multiple synthetic tables while maintaining strong anonymity. Compared to the more common single-table approach,…
The explosion of scientific literature has made the efficient and accurate extraction of structured data a critical component for advancing scientific knowledge and supporting evidence-based decision-making. However, existing tools often…
Structured Query Language (SQL) has remained the standard query language for databases. SQL is highly optimized for processing structured data laid out in relations. Meanwhile, in the present application development landscape, it is highly…
Table extraction from PDF and image documents is a ubiquitous task in the real-world. Perfect extraction quality is difficult to achieve with one single out-of-box model due to (1) the wide variety of table styles, (2) the lack of training…
The information in tables can be an important complement to text, making table-based question answering (QA) systems of great value. The intrinsic complexity of handling tables often adds an extra burden to both model design and data…
In this paper, we define a category DB, called the category of simplicial databases, whose objects are databases and whose morphisms are data-preserving maps. Along the way we give a precise formulation of the category of relational…
Spreadsheets are the go-to tool for computerized calculation and modelling, but are hard to comprehend and adapt after reaching a certain complexity. In general, cognition of complex systems is facilitated by having a higher order mental…