相关论文: Scaffolding the Mitochondrial Disease Ontology fro…

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…

Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within…

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…

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…

Information retrieval from distributed heterogeneous data sources remains a challenging issue. As the number of data sources increases more intelligent retrieval techniques, focusing on information content and semantics, are required.…

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…

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…

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.…

The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such caGrid, support access…

Translating biomedical ontologies is an important challenge, but doing it manually requires much time and money. We study the possibility to use open-source knowledge bases to translate biomedical ontologies. We focus on two aspects:…

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…

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…

Despite the large-scale uptake of semantic technologies in the biomedical domain, little is known about common modelling practices in published ontologies. OWL ontologies are often published only in the crude form of sets of axioms leaving…

End users of recent biomedical information systems are often unaware of the storage structure and access mechanisms of the underlying data sources and can require simplified mechanisms for writing domain specific complex queries. This…

Rapid growth of documents, web pages, and other types of text content is a huge challenge for the modern content management systems. One of the problems in the areas of information storage and retrieval is the lacking of semantic data.…

Despite the large number of patients in Electronic Health Records (EHRs), the subset of usable data for modeling outcomes of specific phenotypes are often imbalanced and of modest size. This can be attributed to the uneven coverage 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…

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…

In this work we address the issue of generic automated disease incidence monitoring on twitter. We employ an ontology of disease related concepts and use it to obtain a conceptual representation of tweets. Unlike previous key word based…

This paper studies the role that ontologies can play in establishing conceptual data models during the process of information systems development. A mapping algorithm has been proposed and embedded in a special purpose Transformation-Engine…