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Ontologies in the biomedical domain are numerous, highly specialized and very expensive to develop. Thus, a crucial prerequisite for ontology adoption and reuse is effective support for exploring and finding existing ontologies. Towards…
Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…
Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a…
Because of the increasing number of electronic data, designing efficient tools to retrieve and exploit documents is a major challenge. Current search engines suffer from two main drawbacks: there is limited interaction with the list of…
Motivation: Ontologies are widely used in biology for data annotation, integration, and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of…
Ontology alignment is the task of identifying semantically equivalent entities from two given ontologies. Different ontologies have different representations of the same entity, resulting in a need to de-duplicate entities when merging…
Despite the overwhelming quantity of health information that is available online today, finding reliable and trustworthy information is still challenging, even when advanced recommender systems are used. To tackle this challenge and improve…
There is a large number of online documents data sources available nowadays. The lack of structure and the differences between formats are the main difficulties to automatically extract information from them, which also has a negative…
The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently there has…
In this article, we investigate our early attempts at building an ontology describing rehabilitation therapies following brain injury. These therapies are wide-ranging, involving interventions of many different kinds. As a result, these…
Generative artificial intelligence (AI), exemplified by the release of GPT-3.5 in 2022, has significantly advanced the potential applications of large language models (LLMs), including in the realms of ontology development and knowledge…
Taking advantage of the widespread use of ontologies to organise and harmonize knowledge across several distinct domains, this paper proposes a novel approach to improve an embedding-Large Language Model (embedding-LLM) of interest by…
Many platforms for benchmarking optimization algorithms offer users the possibility of sharing their experimental data with the purpose of promoting reproducible and reusable research. However, different platforms use different data models…
Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the…
This work presents the architecture used in the ongoing OntologyNavigator project. It is a research tool to help advanced learners to find adapted IT papers to create scientific bibliographies. The purpose is the use of an IT representation…
Biomedical ontologies, which comprehensively define concepts and relations for biomedical entities, are crucial for structuring and formalizing domain-specific information representations. Biomedical code mapping identifies similarity or…
Many optimization algorithm benchmarking platforms allow users to share their experimental data to promote reproducible and reusable research. However, different platforms use different data models and formats, which drastically complicates…
Ever-expanding volumes of biomedical text require automated semantic annotation techniques to curate and put to best use. An established field of research seeks to link mentions in text to knowledge bases such as those included in the UMLS…
The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a…
Successful biomedical relation extraction can provide evidence to researchers and clinicians about possible unknown associations between biomedical entities, advancing the current knowledge we have about those entities and their inherent…