What is MED-RT and why you should download it
If you are a health care professional, a researcher, or a student interested in medication terminology, pharmacologic classifications, and their relationships, you might want to download MED-RT. MED-RT stands for Medication Reference Terminology, and it is a comprehensive and authoritative source of information on drugs, substances, and pharmacologic classes. In this article, you will learn what MED-RT is, how it works, what are its benefits, and how to download and use it.
MED-RT overview
What is MED-RT
MED-RT is a formal ontological representation of medication terminology, pharmacologic classifications, and asserted authoritative relationships between them. It is produced by the Veterans Health Administration (VHA), a division of the U.S. Department of Veteran Affairs. It is a replacement and successor to NDF-RT, which was discontinued in 2018. MED-RT incorporates data from other terminologies, such as RxNorm, MeSH, and SNOMED CT International. It also maintains the National Committee on Vital and Health Statistics (NCVHS) standards for describing medication pharmacologic classification.
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How MED-RT works
MED-RT consists primarily of named relationships between concept pairs, each asserted by an explicit authoritative source. Either concept in the relationship may be a native MED-RT pharmacologic class or some concept in an external terminology. Relationships asserted by one explicit source are not necessarily endorsed by another source. For example, a drug may have different mechanisms of action or physiologic effects according to different sources. MED-RT allows users to explore these differences and similarities among sources.
What are the benefits of MED-RT
MED-RT has several benefits for users who need to access, analyze, or integrate medication information from various sources. Some of these benefits are:
It provides a comprehensive and consistent representation of medication terminology and pharmacologic classifications.
It supports interoperability and mapping between different terminologies and standards.
It enables semantic reasoning and inference based on the ontological structure and relationships.
It facilitates drug safety surveillance and quality improvement by identifying potential drug-drug interactions, contraindications, adverse effects, and other clinical issues.
It supports research and education by providing a rich source of knowledge on drugs, substances, and pharmacologic classes.
How to download MED-RT
Where to find MED-RT
MED-RT is available for download from the National Cancer Institute (NCI) Enterprise Vocabulary Services (EVS) website. Users need to register for a free account and agree to the terms of use before downloading the files. The files are updated monthly and include documentation, data files, and XML schema definitions.
What are the requirements for MED-RT
MED-RT is compatible with any system that can process XML files. However, users may need additional tools or software to view, query, or manipulate the data. For example, users may use Protégé, an open-source ontology editor and framework, to browse and edit the MED-RT ontology. Users may also use UMLS Metathesaurus Browser, a web-based tool that allows users to search for concepts and relationships in various terminologies, including MED-RT. Users need a free UMLS license to access this tool.</ How to install MED-RT
Installing MED-RT is a simple process that involves extracting the downloaded files and loading them into the desired system or tool. Users can follow these steps to install MED-RT:
Download the latest version of MED-RT from the NCI EVS website. The files are compressed in a ZIP format.
Extract the ZIP file to a folder of your choice. The folder will contain several files, such as medrt.owl, medrt.xml, medrt.xsd, and readme.txt.
Load the medrt.owl or medrt.xml file into your system or tool of choice. For example, you can use Protégé to open the medrt.owl file and view the ontology. You can also use UMLS Metathesaurus Browser to search for concepts and relationships in MED-RT.
How to use MED-RT
How to search for concepts and relationships in MED-RT
One of the main ways to use MED-RT is to search for concepts and relationships that are relevant to your needs. You can use different tools or methods to perform this task, depending on your preferences and objectives. Here are some examples of how to search for concepts and relationships in MED-RT:
You can use UMLS Metathesaurus Browser to search for concepts and relationships in MED-RT by entering a term or code in the search box. You can also filter the results by source, semantic type, or relationship type. You can view the details of each concept or relationship, such as its definition, synonyms, attributes, and sources.
You can use Protégé to search for concepts and relationships in MED-RT by opening the medrt.owl file and using the search function. You can also browse the ontology by expanding the classes and properties in the hierarchy. You can view the details of each concept or relationship, such as its label, description, annotations, and axioms.
You can use SPARQL, a query language for RDF data, to search for concepts and relationships in MED-RT by writing and executing queries against the medrt.owl or medrt.xml file. You can use various SPARQL endpoints or tools to run your queries, such as Apache Jena Fuseki or RDF4J Workbench. You can specify the criteria and parameters of your queries, such as filters, patterns, variables, and operators.
How to browse the MED-RT hierarchy
Another way to use MED-RT is to browse the hierarchy of pharmacologic classes and their relationships. The hierarchy is organized according to the NCVHS standards for describing medication pharmacologic classification. The hierarchy consists of four levels: therapeutic intent, mechanism of action, physiologic effect, and chemical structure. Each level has a number of subclasses that represent more specific or granular concepts. For example, under the therapeutic intent level, there are subclasses such as anti-infective agents, cardiovascular agents, central nervous system agents, etc. Each subclass may have further subclasses or individual drugs or substances as members.
You can browse the MED-RT hierarchy using different tools or methods, depending on your preferences and objectives. Here are some examples of how to browse the MED-RT hierarchy:
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You can use UMLS Metathesaurus Browser to browse the MED-RT hierarchy by selecting MED-RT as the source and clicking on the "View Hierarchy" button. You can then expand or collapse the nodes in the tree view and see the concepts and relationships under each node.
You can use Protégé to browse the MED-RT hierarchy by opening the medrt.owl file and selecting the "Entities" tab. You can then expand or collapse the classes and properties in the tree view and see the concepts and relationships under each node.
You can use a spreadsheet program, such as Microsoft Excel or Google Sheets, to browse the MED-RT hierarchy by importing the medrt.csv file that is included in the download package. You can then sort, filter, or manipulate the data in the spreadsheet according to your needs.
How to export and import MED-RT data
A third way to use MED-RT is to export and import data from or into other systems or formats. This can be useful for integrating MED-RT with other terminologies or standards, creating custom reports or analyses, or sharing data with others. You can export and import data from or into MED-RT using different tools or methods, depending on your preferences and objectives. Here are some examples of how to export and import data from or into MED-RT:
You can use Protégé to export and import data from or into MED-RT by using the "File" menu and selecting the appropriate options. You can export or import data in various formats, such as RDF/XML, OWL/XML, Turtle, Manchester Syntax, etc. You can also use plugins or extensions to export or import data in other formats, such as CSV, JSON, Excel, etc.
You can use SPARQL to export and import data from or into MED-RT by writing and executing queries against the medrt.owl or medrt.xml file. You can use various SPARQL endpoints or tools to run your queries, such as Apache Jena Fuseki or RDF4J Workbench. You can specify the output or input format of your queries, such as XML, JSON, CSV, TSV, etc.
You can use a programming language, such as Python, Java, or R, to export and import data from or into MED-RT by using libraries or packages that can parse and manipulate XML or RDF data. For example, you can use Python's lxml or rdflib modules to read and write MED-RT data in XML or RDF formats. You can also use other libraries or packages to convert MED-RT data to other formats, such as pandas for CSV or Excel, json for JSON, etc.
Conclusion
Summary of the main points
In conclusion, MED-RT is a valuable resource for anyone who needs to access, analyze, or integrate medication information from various sources. It is a formal ontological representation of medication terminology, pharmacologic classifications, and asserted authoritative relationships between them. It provides a comprehensive and consistent representation of medication information that supports interoperability, semantic reasoning, drug safety surveillance, research, and education. It is available for download from the NCI EVS website and can be used with various tools and methods.
Call to action and resources
If you are interested in downloading and using MED-RT, you can visit the NCI EVS website and register for a free account. You can also find more information and documentation on the website. If you have any questions or feedback about MED-RT, you can contact the NCI EVS team or join the MED-RT listserv. You can also check out some of the following resources that may help you learn more about MED-RT and related topics:
[MED-RT User Guide]: A detailed guide on how to use MED-RT with Protégé and UMLS Metathesaurus Browser.
[MED-RT Webinar]: A recorded webinar that introduces MED-RT and demonstrates its features and functionalities.
[MED-RT FAQ]: A list of frequently asked questions and answers about MED-RT.
[MED-RT Publication]: A peer-reviewed article that describes the development and evaluation of MED-RT.
[MED-RT Tutorial]: A self-paced tutorial that teaches the basics of MED-RT and how to use it with Protégé.
FAQs
What is the difference between MED-RT and RxNorm?
RxNorm is another terminology that provides normalized names for clinical drugs and links them to other drug vocabularies. RxNorm focuses on drugs that are commonly prescribed in the U.S., while MED-RT covers a broader range of drugs and substances. RxNorm also does not provide pharmacologic classifications or relationships among drugs, while MED-RT does. MED-RT incorporates data from RxNorm as one of its sources.
How often is MED-RT updated?
MED-RT is updated monthly by the VHA Pharmacy Benefits Management Services (PBMS). The updates reflect changes in the source terminologies, such as RxNorm, MeSH, SNOMED CT International, etc., as well as changes in the pharmacologic classifications and relationships based on new evidence or feedback.
How can I contribute to MED-RT?
You can contribute to MED-RT by providing feedback, suggestions, corrections, or additions to the NCI EVS team or the MED-RT listserv. You can also submit requests for new concepts or relationships through the NCI Term Suggestion Portal. Your input will be reviewed and considered by the VHA PBMS and NCI EVS teams.
What are some use cases for MED-RT?
Some possible use cases for MED-RT are Some possible use cases for MED-RT are:
You can use MED-RT to create a drug formulary or a medication list that is consistent and interoperable with other terminologies and standards.
You can use MED-RT to perform drug utilization review or pharmacovigilance by identifying potential drug-drug interactions, contraindications, adverse effects, and other clinical issues based on the pharmacologic classifications and relationships.
You can use MED-RT to conduct research or education on drugs, substances, and pharmacologic classes by exploring the ontological structure and relationships and accessing the authoritative sources.
What are some limitations or challenges of MED-RT?
Some possible limitations or challenges of MED-RT are:
MED-RT may not cover all the drugs, substances, or pharmacologic classes that exist or are used in different countries or regions. Users may need to supplement MED-RT with other terminologies or sources that are more specific or comprehensive for their needs.
MED-RT may not reflect the latest evidence or consensus on the pharmacologic classifications or relationships of some drugs or substances. Users may need to verify the accuracy and currency of the data with the original sources or other references.
MED-RT may not provide sufficient granularity or specificity for some use cases or applications. Users may need to customize or extend MED-RT with additional concepts or relationships that are more relevant or useful for their purposes.
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