Table 1. Definitions.

Compiled based on references [19,31–37]

Biomarker	A characteristic objectively measured and evaluated as an indicator of normal biological processes or pharmacological responses to a therapeutic intervention. Type 0 biomarker: a marker of the natural history of a disease that correlates longitudinally with known clinical indices Type I biomarker: a marker that captures the effects of a therapeutic intervention in context with its mechanism of action Context independent: developed for general clinical and pre-clinical testing Context specific: developed in association with a drug development program and, accordingly, to study and monitor the effects of specific drugs. They may enter the market together with a specific drug as a “companion diagnostic device” [65]. Antecedent: Identifying the risk of developing an illness Screening: screening for subclinical disease Diagnostic: recognizing overt disease Staging: categorizing disease severity Monitoring: assessing disease progression, therapeutic efficacy and adverse effects Prognostic: predicting future disease course/response to therapy
Clinical end point	A characteristic or variable that reflects how a patient feels, functions or survives. Intermediate (non-ultimate) end point: a true clinical endpoint, a symptom or measure of function but not the ultimate end-point of the disease Ultimate end point: survival or the rate of other or irreversible morbid events
Surrogate end point	A biomarker intended to substitute for a clinical endpoint aiming to predict clinical benefit or harm or lack of benefit or lack of harm on the basis of epidemiological, therapeutic, pathophysiological or other scientific evidence.
Metabolome	A quantitative descriptor of all endogenous low-molecular-weight components in a biological sample such as urine or plasma. Each cell type and biological fluid has a characteristic set of metabolites that reflects the organism under a particular set of environmental conditions and that fluctuates according to physiological demands. The metabolome can be divided into the primary metabolome (as controlled by the host genome) and the co-metabolome (dependent on the microbiome).
Metabonome	Theoretical combinations, sums and products of the interactions of multiple metabolomes (primary, symbiotic, parasitic, environmental, and co-metabolic) in complex systems.
Metabolomics	The comprehensive quantitative analysis of all the metabolites of an organism or a specific biological sample.
Metabonomics	The quantitative measurement over time of the metabolic responses of an individual or population to a disease, drug treatment or other challenge.
Microbiolome	The consortium of microorganisms, bacteria, protozoa, and fungi that live commensally or symbiotically with a host.
Xenometabolome	Characteristic profile of non-endogenous compounds such as drugs, their metabolites and their excipients, dietary components, herbal medicines and environmental exposure.
Proteome	The expressed protein and peptide complement of a cell, organ or organism, including all isoforms and post-translational variants.
Proteomics	The systematic analysis of proteins for their identity, quantity and function.
Genomics	Genomics is the study of the genome (approx. 25,000 genes). It is static and allows for estimate the risk for an individual to develop a disease, may modify the efficacy or tolerability of a drug, or influence its tissue distribution and pharmacokinetics.
Transcriptomics	Transcriptomics is also known as functional genomics and is the study of expression patterns of all gene transcripts (approx. 85,000).