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This paper presents ForestQB, a SPARQL query builder, to assist Bioscience and Wildlife Researchers in accessing Linked-Data. As they are unfamiliar with the Semantic Web and the data ontologies, ForestQB aims to empower them to benefit…
Most existing Knowledge Graph Question Answering (KGQA) approaches are designed for a specific KG, such as Wikidata, DBpedia or Freebase. Due to the heterogeneity of the underlying graph schema, topology and assertions, most KGQA systems…
We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data.…
Schema matching is a critical task in data integration, particularly in the medical domain where disparate Electronic Health Record (EHR) systems must be aligned to standard models like OMOP CDM. While Large Language Models (LLMs) have…
Query classification, including multiple subtasks such as intent and category prediction, is vital to e-commerce applications. E-commerce queries are usually short and lack context, and the information between labels cannot be used,…
RDF query optimization is a challenging problem. Although considerable factors and their impacts on query efficiency have been investigated, this problem still needs further investigation. We identify that decomposing query into a series of…
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic…
Sustainable agricultural production aligns with several sustainability goals established by the United Nations (UN). However, there is a lack of studies that comprehensively examine sustainable agricultural practices across various products…
Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased…
With recent emerging technologies such as the Internet of Things (IoT), information collection on our physical world and environment can be achieved at a much higher granularity and such detailed knowledge will play a critical role in…
Mammalian gut microbiomes are essential for host functions like digestion, immunity, and nutrient utilization. This study examines the gut microbiome of horses, donkeys, and their hybrids, mules and hinnies, to explore the role of…
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…
Nowadays, a huge amount of knowledge has been amassed in digital agriculture. This knowledge and know-how information are collected from various sources, hence the question is how to organise this knowledge so that it can be efficiently…
To address the requirement of enabling a comprehensive perspective of life-sciences data, Semantic Web technologies have been adopted for standardized representations of data and linkages between data. This has resulted in data warehouses…
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…
Microorganisms employ sophisticated mechanisms for intercellular communication and environmental sensing, with quorum sensing serving as a fundamental regulatory process. Dysregulation of quorum sensing has been implicated in various…
The purpose of this paper is to describe and analyze the development of a knowledge-based infrastructure to support MSP decision-making processes. The paper emerged from a study to define specifications for a knowledge-based infrastructure…
Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of…
Single-cell foundation models such as scGPT represent a significant advancement in single-cell omics, with an ability to achieve state-of-the-art performance on various downstream biological tasks. However, these models are inherently…
Precision soil greenhouse gas (GHG) flux prediction is essential in agricultural systems for assessing environmental impacts, developing emission mitigation strategies and promoting sustainable agriculture. Due to the lack of advanced…