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Ontologies of research areas have been proven to be useful in many application for analysing and making sense of scholarly data. In this chapter, we present the Computer Science Ontology (CSO), which is the largest ontology of research…
In this paper, we present an ontology-based approach to compose applications while preserving their former look. Our composition process relies on the manipulation of User Interfaces (UI) and on several ontologies describing relationships…
Fine-grained entity typing (FET), which assigns entities in text with context-sensitive, fine-grained semantic types, is a basic but important task for knowledge extraction from unstructured text. FET has been studied extensively in natural…
Phenotyping consists in applying algorithms to identify individuals associated with a specific, potentially complex, trait or condition, typically out of a collection of Electronic Health Records (EHRs). Because a lot of the clinical…
Managing scientific names in ontologies that represent species taxonomies is challenging due to the ever-evolving nature of these taxonomies. Manually maintaining these names becomes increasingly difficult when dealing with thousands of…
Ontohub is a repository engine for managing distributed heterogeneous ontologies. The distributed nature enables communities to share and exchange their contributions easily. The heterogeneous nature makes it possible to integrate…
We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as…
Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases…
The mainstream approach to the development of ontologies is merging ontologies encoding different information, where one of the major difficulties is that the heterogeneity motivates the ontology merging but also limits high-quality merging…
Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling…
The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the…
Decision support is a probabilistic and quantitative method designed for modeling problems in situations with ambiguity. Computer technology can be employed to provide clinical decision support and treatment recommendations. The problem of…
Ontologies have been widely used in numerous and varied applications, e.g., to support data modeling, information integration, and knowledge management. With the increasing size of ontologies, ontology understanding, which is playing an…
Date and Darwen have proposed a theory of types, the latter forms the basis of a detailed presentation of a panoply of simple and complex types. However, this proposal has not been structured in a formal system. Specifically, Date and…
In this paper we present a minimal object oriented core calculus for modelling the biological notion of type that arises from biological ontologies in formalisms based on term rewriting. This calculus implements encapsulation, method…
We construct a logic-enriched type theory LTTW that corresponds closely to the predicative system of foundations presented by Hermann Weyl in Das Kontinuum. We formalise many results from that book in LTTW, including Weyl's definition of…
Ontology can be seen as a formal representation of knowledge. They have been investigated in many artificial intelligence studies including semantic web, software engineering, and information retrieval. The aim of ontology is to develop…
Experimental research publications provide figure form resources including graphs, charts, and any type of images to effectively support and convey methods and results. To describe figures, authors add captions, which are often incomplete,…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…