Related papers: Primer on the Gene Ontology
Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental…
Ontology development methodologies emphasise knowledge gathering from domain experts and documentary resources, and knowledge representation using an ontology language such as OWL or FOL. However, working ontologists are often surprised by…
Ontology (and more generally: Knowledge Graph) Matching is a challenging task where information in natural language is one of the most important signals to process. With the rise of Large Language Models, it is possible to incorporate this…
The construction of an ontology of scientific knowledge objects, presented here, is part of the development of an approach oriented towards the visualization of scientific knowledge. It is motivated by the fact that the concepts that are…
We propose a novel framework to facilitate the on-demand design of data-centric systems by exploiting domain knowledge from an existing ontology. Its key ingredient is a process that we call focusing, which allows to obtain a schema for a…
In ontology development, there is a gap between domain ontologies which mostly use the web ontology language, OWL, and foundational ontologies written in first-order logic, FOL. To bridge this gap, we present Gavel, a tool that supports the…
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…
Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information…
Genetic Algorithm (GA) is a popular meta-heuristic evolutionary algorithm that uses stochastic operators to find optimal solution and has proved its effectiveness in solving many complex optimization problems (such as classification,…
This paper describes a methodology for analyzing the evolutionary dynamics of genetic programming (GP) using genealogical information, diversity measures and information about the fitness variation from parent to offspring. We introduce a…
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…
This article presents the top-level of an ontology categorizing and generalizing best practices and quality criteria or measures for Linked Data. It permits to compare these techniques and have a synthetic organized view of what can or…
The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although…
Ontologies are a popular way of representing domain knowledge, in particular, knowledge in domains related to life sciences. (Semi-)automating the process of building an ontology has attracted researchers from different communities into a…
Ontologies comprising of concepts, their attributes, and relationships are used in many knowledge based AI systems. While there have been efforts towards populating domain specific ontologies, we examine the role of document structure in…
With the adoption of Semantic Web technologies, an increasing number of vocabularies and ontologies have been developed in different domains, ranging from Biology to Agronomy or Geosciences. However, many of these ontologies are still…
The General Formal Ontology (GFO) is a top-level ontology that is designed to formally describe different domains of reality. Most recent advancements within GFO have been made in defining its modules of space and material objects, defining…
Due to the emergence of the semantic Web and the increasing need to formalize human knowledge, ontologie engineering is now an important activity. But is this activity very different from other ones like software engineering, for example ?…
This paper discusses the use of `ontologies' in Natural Language Processing. It classifies various kinds of ontologies that have been employed in NLP and discusses various benefits and problems with those designs. Particular focus is then…
In applied mathematics and related disciplines, the modeling-simulation-optimization workflow is a prominent scheme, with mathematical models and numerical algorithms playing a crucial role. For these types of mathematical research data,…