AIMC Topic: Biological Ontologies
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OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.
JCO clinical cancer informatics
Mar 1, 2020
PURPOSE: The purpose of OncoMX knowledgebase development was to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types.
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain.
Database : the journal of biological databases and curation
Jan 1, 2020
The ability to compare entities within a knowledge graph is a cornerstone technique for several applications, ranging from the integration of heterogeneous data to machine learning. It is of particular importance in the biomedical domain, where seman...
FOBI: an ontology to represent food intake data and associate it with metabolomic data.
Database : the journal of biological databases and curation
Jan 1, 2020
Nutrition research can be conducted by using two complementary approaches: (i) traditional self-reporting methods or (ii) via metabolomics techniques to analyze food intake biomarkers in biofluids. However, the complexity and heterogeneity of these t...
Using clinical reasoning ontologies to make smarter clinical decision support systems: a systematic review and data synthesis.
Journal of the American Medical Informatics Association : JAMIA
Jan 1, 2020
OBJECTIVE: The study sought to describe the literature describing clinical reasoning ontology (CRO)-based clinical decision support systems (CDSSs) and identify and classify the medical knowledge and reasoning concepts and their properties within the...
Whole-brain death and integration: realigning the ontological concept with clinical diagnostic tests.
Theoretical medicine and bioethics
Oct 1, 2019
For decades, physicians, philosophers, theologians, lawyers, and the public considered brain death a settled issue. However, a series of recent cases in which individuals were declared brain dead yet physiologically maintained for prolonged periods o...
Provenance for Biomedical Ontologies with RDF and Git.
Studies in health technology and informatics
Sep 3, 2019
The German Center for Lung Research (DZL) is a research network with the aim of researching respiratory diseases. In order to enable consortium-wide retrospective research and prospective patient recruitment, we perform data integration into a centra...
Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.
Current protocols in human genetics
Sep 1, 2019
The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnost...
Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits.
Systematic biology
Sep 1, 2019
Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. Thes...
Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis.
Studies in health technology and informatics
Aug 21, 2019
Exposomics is a field of research which is receiving growing attention. In this work, we characterize the exposome research landscape and update our previous study of formal knowledge representation approaches to this field. We applied a deductive an...
Semantic Provenance Graph for Reproducibility of Biomedical Research Studies: Generating and Analyzing Graph Structures from Published Literature.
Studies in health technology and informatics
Aug 21, 2019
OBJECTIVE: To characterize the scientific reproducibility of biomedical research studies by query and analysis of semantic provenance graphs generated from provenance metadata terms extracted from PubMed articles.
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