An educational playlist (including 11 videos) covering the key essentials for using machine learning as part of a data science analysis pipeline. While topics are primarily framed around applications in biomedicine, this content is broadly applicable to other domains. This series was prepared at the Cedars Sinai Medical Center in Los Angeles by Dr. Ryan Urbanowicz of the Department of Computational Biomedicine.
View ResourceNCBO BioPortal
March 5, 2023
by
Ray
BioPortal is an open repository of biomedical ontologies that stores ontologies developed in various formats, that provides for automatic updates by user submissions of new versions, and that provides access via Web browsers and through Web services. This is a great place to explore and search for ontologies related to different types of data and fields of biomedical study.
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RxNorm
March 5, 2023
by
Ray
RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, Multum, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary.
View ResourceSemi-automated Term Harmonization Pipeline
March 5, 2023
by
Ray
This repository includes a set of Python-based Jupyter notebooks that comprise a semi-automated term harmonization pipeline applied to harmonize medical history terms across 28 clinical trials of pulmonary arterial hypertension. These notebooks pair with the paper ‘A Semi-Automated Term Harmonization Pipeline Applied to Pulmonary Arterial Hypertension Clinical Trials’. Below, we offer an overview of these pipelines and provide guidance for users on how to adapt these notebooks to their own target harmonization tasks.
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SNOMED
March 5, 2023
by
Ray
SNOMED CT is one of a suite of designated standards for use in U.S. Federal Government systems for the electronic exchange of clinical health information and is also a required standard in interoperability specifications of the U.S. Healthcare Information Technology Standards Panel. The clinical terminology is owned and maintained by SNOMED International, a not-for-profit association.
View ResourceThe Gene Ontology Resource
March 5, 2023
by
Ray
The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
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