Related papers: Primer on the Gene Ontology
Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies…
A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often…
We present DINGO (Data INtegration for Grants Ontology), an ontology that provides a machine readable extensible framework to model data for semantically-enabled applications relative to projects, funding, actors, and, notably, funding…
The present gap between the amount of available protein sequence due to the development of next generation sequencing technology (NGS) and slow and expensive experimental extraction of useful information like annotation of protein sequence…
Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data.…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
We applied machine learning to predict whether a gene is involved in axon regeneration. We extracted 31 features from different databases and trained five machine learning models. Our optimal model, a Random Forest Classifier with 50…
Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysis that measures the over- or under-representation of…
Ontologies order and interconnect knowledge of a certain field in a formal and semantic way so that they are machine-parsable. They try to define allwhere acceptable definition of concepts and objects, classify them, provide properties as…
Retrieve information resources made by the machine processing may refer to multiple sources. A personal web as part of information resources in the Internet requires a feature that can be understood by computer machines. Therefore, in this…
Software testing is a prime factor in software industry. Besides knowing the importance of testing, only limited time is allocated for teaching it. It will be more efficient if testing is taught simultaneously with programming foundations.…
Ontology-based approaches for predicting gene-disease associations include the more classical semantic similarity methods and more recently knowledge graph embeddings. While semantic similarity is typically restricted to hierarchical…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
Many platforms for benchmarking optimization algorithms offer users the possibility of sharing their experimental data with the purpose of promoting reproducible and reusable research. However, different platforms use different data models…
In semantic technologies, the shared common understanding of the structure of information among artifacts (people or software agents) can be realized by building an ontology. To do this, it is imperative for an ontology builder to answer…
We present KNOW--the Knowledge Navigator Ontology for the World--the first ontology designed to capture everyday knowledge to augment large language models (LLMs) in real-world generative AI use cases such as personal AI assistants. Our…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
Generative artificial intelligence (AI), exemplified by the release of GPT-3.5 in 2022, has significantly advanced the potential applications of large language models (LLMs), including in the realms of ontology development and knowledge…
Big Data architectures allow to flexibly store and process heterogeneous data, from multiple sources, in their original format. The structure of those data, commonly supplied by means of REST APIs, is continuously evolving. Thus data…
The information retrieval systems that are present nowadays are mainly based on full text matching of keywords or topic based classification. This matching of keywords often returns a large number of irrelevant information and this does not…