Related papers: Creation and unification of development and life s…
Being heavily reliant on animals, it is our ethical obligation to improve their well-being by understanding their needs. Several studies show that animal needs are often expressed through their faces. Though remarkable progress has been…
Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge. Here, we review current cell ontology efforts to…
Background: Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support…
To present the biodiversity information, a semantic model is required that connects all kinds of data about living creatures and their habitats. The model must be able to encode human knowledge for machines to be understood. Ontology offers…
Mappings between related ontologies are increasingly used to support data integration and analysis tasks. Changes in the ontologies also require the adaptation of ontology mappings. So far the evolution of ontology mappings has received…
Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research…
Ontologies are built on systems that conceptually evolve over time. In addition, techniques and languages for building ontologies evolve too. This has led to numerous studies in the field of ontology versioning and ontology evolution. This…
The Zebrafish Model Organism Database (ZFIN) provides a Web resource of zebrafish genomic, genetic, developmental, and phenotypic data. Four different ontologies are currently used to annotate data to the most specific term available…
The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspects of biology in a "species independent manner", the fact…
Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks…
Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation of one pathway from another. Conversely,…
This study presents a versatile ontology and a useful codification scheme for describing all kinds of engineered living materials (ELMs). The different components of the ontology, namely: families according to the taxonomy for ELMs,…
Ontologies such as taxonomies, product catalogs or web directories are heavily used and hence evolve frequently to meet new requirements or to better reflect the current instance data of a domain. To effectively manage the evolution of…
Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies…
Big Data architectures allow to flexibly store and process heterogeneous data, from multiple sources, in their original format. The structure of those data, commonly supplied by means of REST APIs, is continuously evolving. Thus data…
Life cycle assessment (LCA) plays a critical role in assessing the environmental impacts of a product, technology, or service throughout its entire life cycle. Nonetheless, many existing LCA tools and methods lack adequate metadata…
Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Background. Most tutorial ontologies focus on illustrating one aspect of ontology development, notably language features and automated reasoners, but ignore ontology development factors, such as emergent modelling guidelines and ontological…