Related papers: Primer on the Gene Ontology

Domain experts often rely on most recent knowledge for apprehending and disseminating specific biological processes that help them design strategies for developing prevention and therapeutic decision-making in various disease scenarios. A…

Ontologies provide formal representation of knowledge shared within Semantic Web applications. Ontology learning involves the construction of ontologies from a given corpus. In the past years, ontology learning has traversed through shallow…

Useful information about scientific collaboration structures and patterns can be inferred from computer databases of published papers. The genetic programming bibliography is the most complete reference of papers on GP\@. In addition to…

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…

Generative answer engines expose content through selective citation rather than ranked retrieval, fundamentally altering how visibility is determined. This shift calls for new optimization methods beyond traditional search engine…

OTTR is a language for representing ontology modeling patterns, which enables to build ontologies or knowledge bases by instantiating templates. Thereby, particularities of the ontological representation language are hidden from the domain…

Ontology reuse aims to foster interoperability and facilitate knowledge reuse. Several approaches are typically evaluated by ontology engineers when bootstrapping a new project. However, current practices are often motivated by subjective,…

With a strong motivational background in search engine optimization the amount of structured data on the web is growing rapidly. The main search engine providers are promising great increase in visibility through annotation of the web…

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…

This paper discusses the representation of ontologies in the first-order logical environment {\ttfamily FOLE}. An ontology defines the primitives with which to model the knowledge resources for a community of discourse. These primitives…

Retrieval-Augmented Generation (RAG) systems combine Large Language Models (LLMs) with external knowledge, and their performance depends heavily on how that knowledge is represented. This study investigates how different Knowledge Graph…

All living organisms use the same genetic languages in their molecular biology machinery. They can be understood as the optimal solutions to the replication tasks involving DNA and proteins. These solutions perfectly fit the pattern…

Ontology engineering (OE) in large projects poses a number of challenges arising from the heterogeneous backgrounds of the various stakeholders, domain experts, and their complex interactions with ontology designers. This multi-party…

The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for…

SOTA coreference resolution produces increasingly impressive scores on the OntoNotes benchmark. However lack of comparable data following the same scheme for more genres makes it difficult to evaluate generalizability to open domain data.…

Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…

This paper presents a systematic survey on existing literature and seminal works relevant to the application of ontologies in different aspects of Cloud computing. Our hypothesis is that ontologies along with their reasoning capabilities…

This paper provides an insight into the possibility of how to find ontologies most relevant to scientific texts using artificial neural networks. The basic idea of the presented approach is to select a representative paragraph from a source…

Starting from an unsolved problem of information retrieval this paper presents an ontology-based model for indexing and retrieval. The model combines the methods and experiences of cognitive-to-interpret indexing languages with the…

The Gene Ontology (GO) provides a knowledge base to effectively describe proteins. However, measuring similarity between proteins based on GO remains a challenge. In this paper, we propose a new similarity measure, information coefficient…