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Research papers in the biomedical field come with large and complex data sets that are shared with the scientific community as unstructured data files via public data repositories. Examples are sequencing, microarray, and mass spectroscopy…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
To turn environmentally derived metabarcoding data into community matrices for ecological analysis, sequences must first be clustered into operational taxonomic units (OTUs). This task is particularly complex for data including large…
As scientific discovery becomes increasingly data-driven, software platforms are needed to efficiently organize and disseminate data from disparate sources. This is certainly the case in the field of materials science. For example,…
An increasing amount of research is being devoted to applying machine learning methods to electronic health record (EHR) data for various clinical purposes. This growing area of research has exposed the challenges of the accessibility of…
AOtools is a Python package which is open-source and aimed at providing tools for adaptive optics users and researchers. We present version 1.0 which contains tools for adaptive optics processing, including analysing data in the pupil…
This article presents the OpenCitations Index, a collection of open citation data maintained by OpenCitations, an independent, not-for-profit infrastructure organisation for open scholarship dedicated to publishing open bibliographic and…
Cybersecurity is a very challenging topic of research nowadays, as digitalization increases the interaction of people, software and services on the Internet by means of technology devices and networks connected to it. The field is broad and…
Biobanks advance biomedical and clinical research by collecting and offering data and biological samples for numerous studies. However, the impact of these repositories varies greatly due to differences in their purpose, scope, governance,…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
To enable materials databases supporting computational and experimental research, it is critical to develop platforms that both facilitate access to the data and provide the tools used to generate/analyze it - all while considering the…
Biomedical ontology refers to a shared conceptualization for a biomedical domain of interest that has vastly improved data management and data sharing through the open data movement. The rapid growth and availability of biomedical data make…
Consolidated access to current and reliable terms from different subject fields and languages is necessary for content creators and translators. Terminology is also needed in AI applications such as machine translation, speech recognition,…
Business Intelligence constitutes a set of methodologies and tools aiming at querying, reporting, on-line analytic processing (OLAP), generating alerts, performing business analytics, etc. When in need to perform these tasks collectively by…
Keeping track of the ever-increasing body of scientific literature is an escalating challenge. We present PubTree a hierarchical search tool that efficiently searches the PubMed/MEDLINE dataset based upon a decision tree constructed using…
High-quality data on existing bicycle infrastructure are a requirement for evidence-based bicycle network planning, which supports a green transition of human mobility. However, this requirement is rarely met: Data from governmental…
The MIMIC-IV dataset is a large, publicly available electronic health record (EHR) resource widely used for clinical machine learning research. It comprises multiple modalities, including structured data, clinical notes, waveforms, and…
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers…
Biomedical research increasingly relies on heterogeneous, high-dimensional datasets, yet effective visualization remains hindered by fragmented code resources, steep programming barriers, and limited domain-specific guidance. Bizard is an…
Despite the wealth of single-cell multi-omics data, it remains challenging to predict the consequences of novel genetic and chemical perturbations in the human body. It requires knowledge of molecular interactions at all biological levels,…