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Substructure search in chemical compound databases is a fundamental task in cheminformatics with critical implications for fields such as drug discovery, materials science, and toxicology. However, the increasing size and complexity of…
Materials science workflows rely on structured and unstructured data from the vast body of available scientific literature. However, most of the experimental details remain buried in text, tables, graphs and figures. Thus, constructing…
The article presents a systematic review of the results of the development of the theoretical basis and the pilot implementation of data storage technology with automatic replenishment of data from sources belonging to different thematic…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
Bio image analysis has recently become one keystone of biological research but biologists tend to get lost in a plethora of available software and the way to adjust available tools to their own image analysis problem. We present BIII,…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Researchers in biomedical research, public health, and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and…
The web, through many search engine sites, has popularized the keyword-based search paradigm, where a user can specify a string of keywords and expect to retrieve relevant documents, possibly ranked by their relevance to the query. Since a…
Species distribution models (SDMs), which aim to predict species occurrence based on environmental variables, are widely used to monitor and respond to biodiversity change. Recent deep learning advances for SDMs have been shown to perform…
Real-time databases deal with time-constrained data and time-constrained transactions. The design of this kind of databases requires the introduction of new concepts to support both data structures and the dynamic behaviour of the database.…
Property graphs often contain tree-shaped substructures, yet they are not captured by existing proposals for graph schemas; likewise, query languages and query engines offer little-to-no native support for managing them systematically. As a…
This paper presents a tool, TyDI, and methods experimented in the building of a termino-ontology, i.e. a lexicalized ontology aimed at fine-grained indexation for semantic search applications. TyDI provides facilities for knowledge…
Indexing massive data sets is extremely expensive for large scale problems. In many fields, huge amounts of data are currently generated, however extracting meaningful information from voluminous data sets, such as computing similarity…
Massive Multi-Omics Microbiome Database (M3DB) is a data warehousing and analytics solution designed to handle diverse, complex, and unprecedented volumes of sequence and taxonomic classification data obtained in a typical microbiome…
There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in…
Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on…
The purpose of data warehouses is to enable business analysts to make better decisions. Over the years the technology has matured and data warehouses have become extremely successful. As a consequence, more and more data has been added to…
The technological landscape changes daily, making it nearly impossible for a single person to be aware of all trends or available tools that may or may not be suitable for their software project. This makes tool selection and architectural…
Designing novel proteins with desired characteristics remains a significant challenge due to the large sequence space and the complexity of sequence-function relationships. Efficient exploration of this space to identify sequences that meet…
During genomics life science research, the data volume of whole genomics and life science algorithm is going bigger and bigger, which is calculated as TB, PB or EB etc. The key problem will be how to store and analyze the data with…