Please mind that some of these definitions are drastic simplifications. This is not intended to be medically accurate but instead to be minimal to achieve understanding of this project's code.
- PGx
- PGx is an abbreviation for the study of how pharmacology is affected by multiple genes (pharmacogenomics) or individual genes (pharmacogenetics).
- RxNorm, RxCUI
- RxNorm is a US-specific standardized naming system for medications. RxNorm also defines IDs for medications, known as RxCUIs.
- Trivia: Rx stems from the latin word recipe meaning "take". The first doctor to use "Rx" used it as a verb with the same meaning in "Rx two aspirin." on a prescription being equivalent to today's "Take two aspirin.". RxCUI stands for "Rx concept unique identifier".
- Indication
- Defines the reason a medication is used, e.g. fever for ibuprofen.
- DNA
- DNA is the sequence of base pairs that makes up a human's genetic code.
- Gene
- A specific section of the DNA defining how one enzyme is built. The gene
CYP2D6 for example encodes the enzyme CYP2D6. A gene's name,
for example CYP2D6, is often referred to as a
GeneSymbol. - Genotype
- What exactly a specific gene looks like, i.e. which exact base pairs it's made up of, may differ for each individual. This specific sequence of base pairs or variant is referred to as the gene's genotype.
- Gene result
- In practice, the different genotypes can have different effects on the encoded enzyme. The gene result describes this effect. One possible gene result for CYP2D6 is "Normal metabolizer".
- Phenotype
- A gene along with its gene result is referred to as a phenotype
- Allele
- In theory, a person has two copies of each gene: one from each parent. These copies are called alleles. In reality, the exact number of inherited alleles by each parent may be unequal to one. The major way we express an allele's genotype is by using the star allele format, e.g. CYP2D6*1 for CYP2D6's star one variant, which is often used as the baseline or "normal" variant of a gene.
- Haplotype
- Describes the allele(s) inherited by a single parent. If an individual has multiple alleles from the same parent, the tar allele format joins them with a hyphen, e.g. CYP2D6*1-*2 for a haplotype with one CYP2D6 star one and one CYP2D6 star two allele.
- Diplotype
- Describes the allele(s) inherited by both parents, i.e. the two haplotypes. The star allele format defines diplotypes by joining the respective haplotypes with a slash, i.e. CYP2D6*1/*2 for an individual that has one CYP2D6 star one variant from one parent and one star two variant from the other.
- Implication
- For a given medication-phenotype pair, an implication describes what effects the phenotype has on use of the medication. An example for an implication is "Increased risk of side effects".
- Recommendation
- For a given medication-phenotype pair, a recommendation describes what an individual should do based on the corresponding implication, e.g. "Use a lower dose".
- Guideline
- Consists of the implication and recommendation for a given medication-phenotype pair.
- Annotation
- Describes data that is manually curated for our project, i.e. implication and recommendation for a medication-phenotype pair and indication, a patient-friendly medication class, and common brand names for a medication.
- (Text) Brick
- *Text Bricks* are predefined components that are used to create texts for annotations. The creation of annotation texts is strictly limited to combinations of Bricks to ensure consistency and enable easy multi-language support without the need of the maintainer having to know more than one supported language. Bricks can also include placeholders such as a given medication's name