Related papers: Primer on the Gene Ontology
This document describes the Gloss Ontology. The ontology and associated class model are organised into several packages. Section 2 describes each package in detail, while Section 3 contains a summary of the whole ontology.
Understanding large, structured documents like scholarly articles, requests for proposals or business reports is a complex and difficult task. It involves discovering a document's overall purpose and subject(s), understanding the function…
In recent years, deep learning algorithms have outperformed the state-of-the art methods in several areas thanks to the efficient methods for training and for preventing overfitting, advancement in computer hardware, the availability of…
Ontologies are critical sources of semantic information for many application domains. Hence, there are ontologies proposed and utilized for domains such as medicine, chemical engineering, and electrical energy. In this paper, we present an…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language…
Explainable Artificial Intelligence (AI) focuses on helping humans understand the working of AI systems or their decisions and has been a cornerstone of AI for decades. Recent research in explainability has focused on explaining the…
The study of biological processes can greatly benefit from tools that automatically predict gene functions or directly cluster genes based on shared functionality. Existing data mining methods predict protein functionality by exploiting…
Today, we can find many search engines which provide us with information which is more operational in nature. None of the search engines provide domain specific information. This becomes very troublesome to a novice user who wishes to have…
The purpose of this work is to find out how different library classification systems and linguistic ontologies arrange a particular domain of interest and what are the limitations for information retrieval. We use knowledge representation…
This paper describes the software implementation of genetic algorithm for identifying and selecting most relevant results received during sequentially executed subject search operations. Simulated evolutionary process generates sustainable…
Research on neural networks has gained significant momentum over the past few years. Because training is a resource-intensive process and training data cannot always be made available to everyone, there has been a trend to reuse pre-trained…
In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as…
Over the last several decades, there has been rapid growth in the number and scope of agricultural genetics, genomics and breeding (GGB) databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44…
High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental…
Disease Intelligence (DI) is based on the acquisition and aggregation of fragmented knowledge of diseases at multiple sources all over the world to provide valuable information to doctors, researchers and information seeking community. Some…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
This Ontologies are widely used as a means for solving the information heterogeneity problems on the web because of their capability to provide explicit meaning to the information. They become an efficient tool for knowledge representation…
gUFO is a lightweight implementation of the Unified Foundational Ontology (UFO) suitable for Semantic Web OWL 2 DL applications. UFO is a mature foundational ontology with a rich axiomatization and that has been employed in a significant…
Deep learning models, while effective and versatile, are becoming increasingly complex, often including multiple overlapping networks of arbitrary depths, multiple objectives and non-intuitive training methodologies. This makes it…