Related papers: Primer on the Gene Ontology
Generic Ontology Design Patterns, GODPs, are defined in Generic DOL, an extension of DOL, the Distributed Ontology, Model and Specification Language, and implemented using Heterogeneous Tool Set. Parameters such as classes, properties,…
By leveraging GPT-4 for ontology narration, we developed GPTON to infuse structured knowledge into LLMs through verbalized ontology terms, achieving accurate text and ontology annotations for over 68% of gene sets in the top five…
Ontology citation, the practice of referring the ontology in a similar fashion the scientific community routinely follows in providing the bibliographic references to other scholarly works, has not received enough attention it supposed to.…
In this paper, we describe an approach to populate an existing ontology with instance information present in the natural language text provided as input. An ontology is defined as an explicit conceptualization of a shared domain. This…
Ontologies are known for their ability to organize rich metadata, support the identification of novel insights via semantic queries, and promote reuse. In this paper, we consider the problem of automated planning, where the objective is to…
Reusing ontologies in practice is still very challenging, especially when multiple ontologies are (jointly) involved. Moreover, despite recent advances, the realization of systematic ontology quality assurance remains a difficult problem.…
Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, discovering new functions largely relies on expensive and…
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…
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…
We tackle the task of enriching ontologies by automatically translating natural language sentences into Description Logic. Since Large Language Models (LLMs) are the best tools for translations, we fine-tuned a GPT-3 model to convert…
In the knowledge engineering community "ontology" is usually defined in the tradition of Gruber as an "explicit specification of a conceptualization". Several variations of this definition exist. In the paper we argue that (with one notable…
An ontology makes a special vocabulary which describes the domain of interest and the meaning of the term on that vocabulary. Based on the precision of the specification, the concept of the ontology contains several data and conceptual…
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…
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…
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…
Semantic Web is actually an extension of the current one in that it represents information more meaningfully for humans and computers alike. It enables the description of contents and services in machine-readable form, and enables…
Extracting relevant and structured knowledge from large, complex technical documents within the Reliability and Maintainability (RAM) domain is labor-intensive and prone to errors. Our work addresses this challenge by presenting OntoKGen, a…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
We propose an effective method to improve Protein Function Prediction (PFP) utilizing hierarchical features of Gene Ontology (GO) terms. Our method consists of a language model for encoding the protein sequence and a Graph Convolutional…
Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for…