TY - JOUR
T1 - Ontologies, Knowledge Representation, and Machine Learning for Translational Research
T2 - Recent Contributions
AU - Robinson, Peter N.
AU - Haendel, Melissa A.
N1 - Publisher Copyright:
Georg Thieme Verlag KG Stuttgart.
PY - 2020/8/1
Y1 - 2020/8/1
N2 - OBJECTIVES: To select, present, and summarize the most relevant papers published in 2018 and 2019 in the field of Ontologies and Knowledge Representation, with a particular focus on the intersection between Ontologies and Machine Learning. METHODS: A comprehensive review of the medical informatics literature was performed to select the most interesting papers published in 2018 and 2019 and that document the utility of ontologies for computational analysis, including machine learning. RESULTS: Fifteen articles were selected for inclusion in this survey paper. The chosen articles belong to three major themes: (i) the identification of phenotypic abnormalities in electronic health record (EHR) data using the Human Phenotype Ontology ; (ii) word and node embedding algorithms to supplement natural language processing (NLP) of EHRs and other medical texts; and (iii) hybrid ontology and NLP-based approaches to extracting structured and unstructured components of EHRs. CONCLUSION: Unprecedented amounts of clinically relevant data are now available for clinical and research use. Machine learning is increasingly being applied to these data sources for predictive analytics, precision medicine, and differential diagnosis. Ontologies have become an essential component of software pipelines designed to extract, code, and analyze clinical information by machine learning algorithms. The intersection of machine learning and semantics is proving to be an innovative space in clinical research.
AB - OBJECTIVES: To select, present, and summarize the most relevant papers published in 2018 and 2019 in the field of Ontologies and Knowledge Representation, with a particular focus on the intersection between Ontologies and Machine Learning. METHODS: A comprehensive review of the medical informatics literature was performed to select the most interesting papers published in 2018 and 2019 and that document the utility of ontologies for computational analysis, including machine learning. RESULTS: Fifteen articles were selected for inclusion in this survey paper. The chosen articles belong to three major themes: (i) the identification of phenotypic abnormalities in electronic health record (EHR) data using the Human Phenotype Ontology ; (ii) word and node embedding algorithms to supplement natural language processing (NLP) of EHRs and other medical texts; and (iii) hybrid ontology and NLP-based approaches to extracting structured and unstructured components of EHRs. CONCLUSION: Unprecedented amounts of clinically relevant data are now available for clinical and research use. Machine learning is increasingly being applied to these data sources for predictive analytics, precision medicine, and differential diagnosis. Ontologies have become an essential component of software pipelines designed to extract, code, and analyze clinical information by machine learning algorithms. The intersection of machine learning and semantics is proving to be an innovative space in clinical research.
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U2 - 10.1055/s-0040-1701991
DO - 10.1055/s-0040-1701991
M3 - Article
C2 - 32823310
AN - SCOPUS:85089817953
SN - 0943-4747
VL - 29
SP - 159
EP - 162
JO - Yearbook of medical informatics
JF - Yearbook of medical informatics
IS - 1
ER -