AIMC Topic: Biological Ontologies
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An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD).
Journal of biomedical semantics
Nov 12, 2020
BACKGROUND: The Genetic and Rare Diseases (GARD) Information Center was established by the National Institutes of Health (NIH) to provide freely accessible consumer health information on over 6500 genetic and rare diseases. As the cumulative scientif...
List-wise learning to rank biomedical question-answer pairs with deep ranking recursive autoencoders.
PloS one
Nov 9, 2020
Biomedical question answering (QA) represents a growing concern among industry and academia due to the crucial impact of biomedical information. When mapping and ranking candidate snippet answers within relevant literature, current QA systems typical...
PCLiON: An Ontology for Data Standardization and Sharing of Prostate Cancer Associated Lifestyles.
International journal of medical informatics
Nov 7, 2020
BACKGROUND: Researches on Lifestyle medicine (LM) have emerged in recent years to garner wide attention. Prostate cancer (PCa) could be prevented and treated by positive lifestyles, but the association between lifestyles and PCa is always personalize...
Correlations Between Phenotypes and Biological Process Ontologies in Monogenic Human Diseases.
Interdisciplinary sciences, computational life sciences
Oct 28, 2020
A substantial body of research is focused to improve the understanding of the relationship between genotypes and phenotypes. Genotype-phenotype studies have shown promise in improving disease diagnosis in humans and identification of specific clinica...
Concept placement using BERT trained by transforming and summarizing biomedical ontology structure.
Journal of biomedical informatics
Oct 22, 2020
The comprehensive modeling and hierarchical positioning of a new concept in an ontology heavily relies on its set of proper subsumption relationships (IS-As) to other concepts. Identifying a concept's IS-A relationships is a laborious task requiring ...
A realism-based approach to an ontological representation of symbiotic interactions.
BMC medical informatics and decision making
Oct 8, 2020
BACKGROUND: The symbiotic interactions that occur between humans and organisms in our environment have a tremendous impact on our health. Recently, there has been a surge in interest in understanding the complex relationships between the microbiome a...
Multi-Ontology Refined Embeddings (MORE): A hybrid multi-ontology and corpus-based semantic representation model for biomedical concepts.
Journal of biomedical informatics
Oct 1, 2020
OBJECTIVE: Currently, a major limitation for natural language processing (NLP) analyses in clinical applications is that concepts are not effectively referenced in various forms across different texts. This paper introduces Multi-Ontology Refined Emb...
Analysis of COVID-19 clinical trials: A data-driven, ontology-based, and natural language processing approach.
PloS one
Sep 30, 2020
With the novel COVID-19 pandemic disrupting and threatening the lives of millions, researchers and clinicians have been recently conducting clinical trials at an unprecedented rate to learn more about the virus and potential drugs/treatments/vaccines...
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project.
Nature reviews. Nephrology
Sep 16, 2020
An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medic...
Ontology and values anchor indigenous and grey nomenclatures: a case study in lichen naming practices among the SamÃ, Sherpa, Scots, and Okanagan.
Studies in history and philosophy of biological and biomedical sciences
Sep 10, 2020
Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of d...
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