Related papers: The Karyotype Ontology: a computational representa…

Ontologies present an attractive technology for describing bio-medicine, because they can be shared, and have rich computational properties. However, they lack the rich expressivity of English and fit poorly with the current scientific…

Ontology development relates to software development in that they both involve the production of formal computational knowledge. It is possible, therefore, that some of the techniques used in software engineering could also be used for…

Developing ontologies can be expensive, time-consuming, as well as difficult to develop and maintain. This is especially true for more expressive and/or larger ontologies. Some ontologies are, however, relatively repetitive, reusing design…

The SemanticWeb emerged as an extension to the traditional Web, towards adding meaning to a distributed Web of structured and linked data. At its core, the concept of ontology provides the means to semantically describe and structure…

We addressed the problem of a lack of semantic representation for user-centric explanations and different explanation types in our Explanation Ontology (https://purl.org/heals/eo). Such a representation is increasingly necessary as…

Ontology development is a non-trivial task requiring expertise in the chosen ontological language. We propose a method for making the content of ontologies more transparent by presenting, through the use of natural language generation,…

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…

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…

This paper presents a software component that generates a user interface structure for populating a domain ontology. The core of this work is an algorithm that takes an ontology and returns a structure describing the user interface. The…

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…

Bio-medical ontologies can contain a large number of concepts. Often many of these concepts are very similar to each other, and similar or identical to concepts found in other bio-medical databases. This presents both a challenge and…

Ontologies order and interconnect knowledge of a certain field in a formal and semantic way so that they are machine-parsable. They try to define allwhere acceptable definition of concepts and objects, classify them, provide properties as…

The Tawny-OWL library provides a fully-programmatic environment for ontology building; it enables the use of a rich set of tools for ontology development, by recasting development as a form of programming. It is built in Clojure - a modern…

The information retrieval systems that are present nowadays are mainly based on full text matching of keywords or topic based classification. This matching of keywords often returns a large number of irrelevant information and this does not…

This paper is based on and advocates the trend in software engineering of extending the use of software patterns as means of structuring solutions to software development problems (be they motivated by best practice or by company interests…

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…

Model card reports provide a transparent description of machine learning models which includes information about their evaluation, limitations, intended use, etc. Federal health agencies have expressed an interest in model cards report for…

Typology is a subfield of linguistics that focuses on the study and classification of languages based on their structural features. Unlike genealogical classification, which examines the historical relationships between languages, typology…

Today, we can find many search engines which provide us with information which is more operational in nature. None of the search engines provide domain specific information. This becomes very troublesome to a novice user who wishes to have…

Explainability has been a goal for Artificial Intelligence (AI) systems since their conception, with the need for explainability growing as more complex AI models are increasingly used in critical, high-stakes settings such as healthcare.…