BACKGROUND: Recent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific resources, such as ontologies. I...
BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association stu...
The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent experiments, spectral and derived data, and s...
AMIA ... Annual Symposium proceedings. AMIA Symposium
Dec 5, 2018
Rare diseases, although individually rare, collectively affect one in ten Americans. Because of their rarity, patients with rare diseases are typically left misdiagnosed or undiagnosed, which leads to a prolonged medical journey. The diagnosis pathwa...
AMIA ... Annual Symposium proceedings. AMIA Symposium
Dec 5, 2018
Disease-symptom relation is an important biomedical relation that can be used for clinical decision support including building medical diagnostic systems. Here we present a study on mining disease-symptom relation from massive biomedical literature a...
AMIA ... Annual Symposium proceedings. AMIA Symposium
Dec 5, 2018
Regardless of potential benefits and better outcomes, adoption of shared decision-making between a patient and providers involved in his/her care is still in its infancy. This paper intends to fill this gap by formalizing shared decision-making, situ...
AMIA ... Annual Symposium proceedings. AMIA Symposium
Dec 5, 2018
BioPortal is widely regarded to be the world's most comprehensive repository of biomedical ontologies. With a coverage of many biomedical subfields by 716 ontologies (June 27, 2018), BioPortal is an extremely diverse repository. BioPortal maintains e...
This study was undertaken to evaluate the use of ontology-based semantic mapping (OS-Mapping) in chemical toxicity assessment. Nineteen chemical-species phenotypic profiles (CSPPs) were constructed by ontologically annotating the toxicity responses r...
BACKGROUND: Despite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet a majority of natural language processing or semantic tools as well as domain terminologies or ont...
International journal of medical informatics
Nov 3, 2018
OBJECTIVE: Reproducibility of research studies is key to advancing biomedical science by building on sound results and reducing inconsistencies between published results and study data. We propose that the available data from research studies combine...
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