Related papers: Primer on the Gene Ontology
Efficiency and scalability are obstacles that have not yet received a viable response from the human activity recognition research community. This paper proposes an activity recognition method. The knowledge model is in the form of…
Ontohub is a repository engine for managing distributed heterogeneous ontologies. The distributed nature enables communities to share and exchange their contributions easily. The heterogeneous nature makes it possible to integrate…
A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product.…
We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a…
In recent years ontologies enjoyed a growing popularity outside specialized AI communities. System engineering is no exception to this trend, with ontologies being proposed as a basis for several tasks in complex industrial implements,…
Modeling an ontology is a hard and time-consuming task. Although methodologies are useful for ontologists to create good ontologies, they do not help with the task of evaluating the quality of the ontology to be reused. For these reasons,…
This paper presents an ontology-driven treatment article retrieval system developed and experimented using the data and ground truths provided by the TREC 2017 precision medicine track. The key aspects of our system include: meaningful…
Existing data-centric methods for protein science generally cannot sufficiently capture and leverage biology knowledge, which may be crucial for many protein tasks. To facilitate research in this field, we create ProteinKG65, a knowledge…
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…
Obtaining an implementation of a data warehouse is a complex task that forces designers to acquire wide knowledge of the domain, thus requiring a high level of expertise and becoming it a prone-to-fail task. Based on our experience, we have…
A widely used approach for extracting information from gene expression data employ the construction of a gene co-expression network and the subsequent application of algorithms that discover network structure. In particular, a common goal…
Machine Learning (ML) systems are capable of reproducing and often amplifying undesired biases. This puts emphasis on the importance of operating under practices that enable the study and understanding of the intrinsic characteristics of ML…
The article presents an overview of current specialized ontology engineering tools, as well as texts' annotation tools based on ontologies. The main functions and features of these tools, their advantages and disadvantages are discussed. A…
Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of…
Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them. The topological alignment of two Protein-Protein Interaction (PPI) networks should thus…
Recently there has been significant interest in using causal modelling techniques to understand the structure of physical theories. However, the notion of `causation' is limiting - insisting that a physical theory must involve causal…
This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect…
Community annotation of biological entities with concepts from multiple bio-ontologies has created large and growing repositories of ontology-based annotation data with embedded implicit relationships among orthogonal ontologies.…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
The study proposes a framework of ONTOlogy-based Group Decision Support System (ONTOGDSS) for decision process which exhibits the complex structure of decision-problem and decision-group. It is capable of reducing the complexity of problem…