AIMC Topic: Biological Ontologies

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OHMI: the ontology of host-microbiome interactions.

Journal of biomedical semantics
BACKGROUND: Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases. Extensive HMI studies have generated large amounts of data. We propose that the logical representation o...

The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research.

Genes
Hearing impairment (HI) is a common sensory disorder that is defined as the partial or complete inability to detect sound in one or both ears. This diverse pathology is associated with a myriad of phenotypic expressions and can be non-syndromic or sy...

Exploring semantic deep learning for building reliable and reusable one health knowledge from PubMed systematic reviews and veterinary clinical notes.

Journal of biomedical semantics
BACKGROUND: Deep Learning opens up opportunities for routinely scanning large bodies of biomedical literature and clinical narratives to represent the meaning of biomedical and clinical terms. However, the validation and integration of this knowledge...

Jointly Integrating VCF-Based Variants and OWL-Based Biomedical Ontologies in MongoDB.

IEEE/ACM transactions on computational biology and bioinformatics
The development of the next-generation sequencing (NGS) technologies has led to massive amounts of VCF (Variant Call Format) files, which have been the standard formats developed with 1000 Genomes Project. At the same time, with the widespread use of...

Analysis of risk factor domains in psychosis patient health records.

Journal of biomedical semantics
BACKGROUND: Readmission after discharge from a hospital is disruptive and costly, regardless of the reason. However, it can be particularly problematic for psychiatric patients, so predicting which patients may be readmitted is critically important b...

Technical Note: Ontology-guided radiomics analysis workflow (O-RAW).

Medical physics
PURPOSE: Radiomics is the process to automate tumor feature extraction from medical images. This has shown potential for quantifying the tumor phenotype and predicting treatment response. The three major challenges of radiomics research and clinical ...

Towards an ontology for soft robots: what is soft?

Bioinspiration & biomimetics
The advent of soft robotics represents a profound change in the forms robots will take in the future. However, this revolutionary change has already yielded such a diverse collection of robots that attempts at defining this group do not reflect many ...

Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung.

Journal of biomedical semantics
BACKGROUND: Although the mouse is widely used to model human lung development, function, and disease, our understanding of the molecular mechanisms involved in alveolarization of the peripheral lung is incomplete. Recently, the Molecular Atlas of Lun...

Ontology patterns for the representation of quality changes of cells in time.

Journal of biomedical semantics
BACKGROUND: Cell tracking experiments, based on time-lapse microscopy, have become an important tool in biomedical research. The goal is the reconstruction of cell migration patterns, shape and state changes, and, comprehensive genealogical informati...

PARS, a system combining semantic technologies with multiple criteria decision aiding for supporting antibiotic prescriptions.

Journal of biomedical informatics
OBJECTIVE: Motivated by the well documented worldwide spread of adverse drug events, as well as the increased danger of antibiotic resistance (caused mainly by inappropriate prescribing and overuse), we propose a novel recommendation system for antib...