AIMC Topic: Biological Ontologies

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KGen: a knowledge graph generator from biomedical scientific literature.

BMC medical informatics and decision making
BACKGROUND: Knowledge is often produced from data generated in scientific investigations. An ever-growing number of scientific studies in several domains result into a massive amount of data, from which obtaining new knowledge requires computational ...

COVID-19 Surveillance in a Primary Care Sentinel Network: In-Pandemic Development of an Application Ontology.

JMIR public health and surveillance
BACKGROUND: Creating an ontology for COVID-19 surveillance should help ensure transparency and consistency. Ontologies formalize conceptualizations at either the domain or application level. Application ontologies cross domains and are specified thro...

Natural language processing algorithms for mapping clinical text fragments onto ontology concepts: a systematic review and recommendations for future studies.

Journal of biomedical semantics
BACKGROUND: Free-text descriptions in electronic health records (EHRs) can be of interest for clinical research and care optimization. However, free text cannot be readily interpreted by a computer and, therefore, has limited value. Natural Language ...

An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD).

Journal of biomedical semantics
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
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
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
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
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
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
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...