Related papers: SBtab - Conventions for structured data tables in …
In software system design, one of the purposes of diagrammatic modeling is to explain something (e.g., data tables) to others. Very often, syntax of diagrams is specified while the intended meaning of diagrammatic constructs remains…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
Over the past decade, there has been a steep rise in the data-driven analysis in major areas of medicine, such as clinical decision support system, survival analysis, patient similarity analysis, image analytics etc. Most of the data in the…
Case definitions are essential for effectively communicating public health threats. However, the absence of a standardized, machine-readable format poses significant challenges to interoperability, epidemiological research, the exchange of…
Recent work on database application development platforms has sought to include a declarative formulation of a conceptual data model in the application code, using annotations or attributes. Some recent work has used metadata to include the…
Querying is one of the basic functionality expected from a database system. Query efficiency is adversely affected by increase in the number of participating tables. Also, querying based on syntax largely limits the gamut of queries a…
We consider the problem of statistical inference on unknown quantities structured as a multiway table. We show that such multiway tables are naturally formed by arranging regression coefficients in complex systems of linear models for…
Brain Imaging Data Structure (BIDS) allows the user to organise brain imaging data into a clear and easy standard directory structure. BIDS is widely supported by the scientific community and is considered a powerful standard for…
The paradigm of Big Data has been established as a solid field of studies in many areas such as healthcare, science, transport, education, government services, among others. Despite widely discussed, there is no agreed definition about the…
Relational databases are central to modern data management, yet most data exists in unstructured forms like text documents. To bridge this gap, we leverage large language models (LLMs) to automatically synthesize a relational database by…
Biological and biomedical imaging datasets record the constitution, architecture and dynamics of living organisms across several orders of magnitude of space and time. Imaging technologies are now used throughout the life and biomedical…
The advent of data-driven science in the 21st century brought about the need for well-organized structured data and associated infrastructure able to facilitate the applications of Artificial Intelligence and Machine Learning. We present an…
Relational databases play a central role in many information systems. Their schema contains structural (e.g. tables and columns) and behavioral (e.g. stored procedures or views) entity descriptions. Then, just like for ``normal'' software,…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
In the burgeoning era of big data, selecting the optimal database solution has become a critical decision for organizations across every industry. Big data demands a powerful database solution. Traditionally, SQL Database, Database ruled,…
Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
As the use of technology increases and data analysis becomes integral in many businesses, the ability to quickly access and interpret data has become more important than ever. Information retrieval technologies are being utilized by…
Database Management System (DBMS) is designed to help store and process large collections of data, and is incredibly flexible to perform various kinds of optimizations as long as it achieves serializability with a high-level interface…