MED-RT Documentation

[rtni20]

This issue aims to provide an overview of the MED-RT data

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Concept and link description

In the xml we have elements which can take names: CTY, NUI. NUI is a unique alphanumeric value (N#) assigned only to every concept owned by MED-RT. CTY is a concept type, a category or label assigned only to every concept owned by MED-RT. Examples of possible valid CTY values that are used in relations are MoA, PE, TC, PK.

There exist a lot of association types/relationships (page 7 in documentation). The documentation mentions ingredients a lot when describing the association types. For example "may_prevent - preventative use or indication of an ingredient" which we understand as: An ingredient in the drug may prevent the disease.

• Synonym Of: Almost always refers to "self". Self-loop.
• has_MoA: Mechanism of Action refers to the specific way in which a drug produces its effect on the body or a specific target. drug -> MoA. (REPHRASE)
• has_SC: Structural Classification. Classification of chemical structure of an ingredient.
• has_PE: Physiological Effect. The impact that an ingredient has on the body's physiological processes. drug/EPC -> PE.
• has_TC: Therapeutic Category is based on the intended therapeutic outcome or goal. Therapeutic outcome is the intended result of the use of a drug. drug -> TC.
• CI_with: Contraindication. The use of a particular ingredient may not be safe or efficient for a specific patient or group of patients, based on their health status and medial history. (REPHRASE)
• may_prevent. drug -> disease.
• may_treat. drug -> disease.
• may_diagnose. drug -> disease.
• induces: State caused by the use of a drug. drug -> disease.
• has_PK: Pharmacokinetics. Refers to the way the body absorbs, distributes, metabolizes, and eliminate the drug over time. drug -> PK.
• has_active_metabolites: A substance that is produced by the body as a result of using the drug.
• site_of_metabolism: Where the metabolism takes place in the human anatomy; A specific part or organ of the body. drug -> PK.
• effect_may_be_inhibited_by: Interference between two ingredients. Interaction between ingredients in drugs.

There exist three other relation types labeled: CI_ChemClass, CI_MoA (drug -> MoA), CI_PE (drug -> PE).

Inside tags are namespace, name, code, status, tags, tags. Inside property tags are namespace, name, and value. Value can either be a CTY or an NUI; name indicates this. Synonym tags includes namespace, name, and to_name; Often a self-loop.

Inside tags are namespace, name, from_namespace, from_name, from_code, to_namespace, to_name, to_code, and a tag. A qualifier includes namespace, name, and value; name is often Authority and value is the acronym of the asserting source authority (which authority recommended the relationship/association).

HC concept types has a hierarchy that has drugs as leaf nodes. Depth=4. Start from root: Pharmaceutical and Biological Preparations -> 3 other sub categories -> A [Preparations], B, C, .... -> drugs.

parent_of associations can also go from EPC to APC but APC are simply additions of pharmalogical classes and exist in the EPC hierarchy.

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Important information from videos

RxNorm is the primary accepted and most ubiquitous drug terminology (video 1 around 1:30). MED-RT is an upgrade to to NDF-RT due to evolution in the clinical medical field.

• RxNorm: Source of drug ingredients.
• Mesh: Source of diseases and source of chemicals and drugs (use for chemical structure classification hierarchies for active ingredients)
• SNOMED CT: Extends drug classification, via the EPCs, into the SNOMED CT substance or product hierarchies.
• MED-RT: Six different concept types are represented in MED-RT.

Synonym Of relations map ingredients from one terminology to another :)

Pyramid hierarchy at 5:00 in video 1. Apelon Open Source Distributed Terminology System (DTS) Editor tool is used for the MED-RT browser to look up a concept or anything in the MED-RT world.