Biomedical data, computational methods and tools for evaluating disease–disease associations

J Xiang, J Zhang, Y Zhao, FX Wu… - Briefings in …, 2022 - academic.oup.com
In recent decades, exploring potential relationships between diseases has been an active
research field. With the rapid accumulation of disease-related biomedical data, a lot of …

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction

FZ Smaili, X Gao, R Hoehndorf - Bioinformatics, 2019 - academic.oup.com
Motivation Ontologies are widely used in biology for data annotation, integration and
analysis. In addition to formally structured axioms, ontologies contain meta-data in the form …

[HTML][HTML] AgroPortal: A vocabulary and ontology repository for agronomy

C Jonquet, A Toulet, E Arnaud, S Aubin… - … and Electronics in …, 2018 - Elsevier
Many vocabularies and ontologies are produced to represent and annotate agronomic data.
However, those ontologies are spread out, in different formats, of different size, with different …

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

E Ong, Z Xiang, B Zhao, Y Liu, Y Lin… - Nucleic acids …, 2017 - academic.oup.com
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified
Resource Identifiers (URIs), and sharing information using Resource Description …

Building IoT-based applications for smart cities: How can ontology catalogs help?

A Gyrard, A Zimmermann… - IEEE Internet of Things …, 2018 - ieeexplore.ieee.org
The Internet of Things (IoT) plays an ever-increasing role in enabling smart city applications.
An ontology-based semantic approach can help improve interoperability between a variety …

DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes

W Liu-Wei, Ş Kafkas, J Chen, NJ Dimonaco… - …, 2021 - academic.oup.com
Motivation Infectious diseases caused by novel viruses have become a major public health
concern. Rapid identification of virus–host interactions can reveal mechanistic insights into …

Unifying the identification of biomedical entities with the Bioregistry

CT Hoyt, M Balk, TJ Callahan, D Domingo-Fernández… - Scientific data, 2022 - nature.com
The standardized identification of biomedical entities is a cornerstone of interoperability,
reuse, and data integration in the life sciences. Several registries have been developed to …

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation

M Martínez-Romero, C Jonquet, MJ O'connor… - Journal of biomedical …, 2017 - Springer
Background Ontologies and controlled terminologies have become increasingly important in
biomedical research. Researchers use ontologies to annotate their data with ontology terms …

The anatomy of phenotype ontologies: principles, properties and applications

GV Gkoutos, PN Schofield… - Briefings in …, 2018 - academic.oup.com
The past decade has seen an explosion in the collection of genotype data in domains as
diverse as medicine, ecology, livestock and plant breeding. Along with this comes the …

Ontology engineering: Current state, challenges, and future directions

T Tudorache - Semantic Web, 2020 - content.iospress.com
In the last decade, ontologies have become widely adopted in a variety of fields ranging
from biomedicine, to finance, engineering, law, and cultural heritage. The ontology …