glossary
VHP4Safety Glossary
Welcome to the VHP4Safety Glossary!
The Virtual Human Platform for Safety Assessment (VHP4Safety) is a project to support chemical and pharmaceutical safety testing without using laboratory animals and animal testing, and funded by the Netherlands Research Council (NWO). For more information on the funding, please see the Funding section at the end this page.
On this page, you can find (a set of) the terminology and their definitions in the context the terms are used in the project. The terms are categorized below based on the context that the term is used, such as risk assessment, chemicals, or computer infrastructure. In addition, the abbreviations, references, and some supplementary information depending on the category that the term belongs to are presented below.
The VHP4Safety Glossary has been created and maintained by (in alphabetical order) Ozan Çınar, Marvin Martens, Javier Millán Acosta, Egon Willighagen. The terms, their descriptions and other additional information have been provided by the members and partners of the VHP4Safety project.
This work is licensed under the CC-BY 4.0 International.
Development Version and Contribution
This glossary has been under development since 2022 and is still continuously developed. This means that new terms can be added in the future depending on their prevalence and frequency of use among the project members. In addition, unfortunately, not all the terms and their definitions currently meet the community standards1, although our goal is to achieve this status.
This glossary is developedt as a GitHub repository. The readers and users of the platform are welcome to contribute. To make new entry queries, please create an issue here using the issue template. For other issues, suggestions, or problems, please create an issue here. Experienced GitHub users are encouraged to submit pull requests. More information can be found in the project README.
Case Studies & Process Flow Steps
| Term | Abbreviation | Definition | related_to |
| Adverse Outcome (Process Flow Step) | A process flow step that is named after adverse outcome, although specifically refers to clinical and epidemiological effects. It categorizes services that provide information on the toxicological endpoints and adverse outcomes at a clinical or epidemiological level of chemical exposures. | VHP0000025 | |
| Case Study | A human-health scenario used as a guiding use case within the VHP4Safety Project to integrate data, models, and tools, and to formulate specific regulatory questions that the Virtual Human Platform should be able to answer. | ||
| Exposure (Process Flow Step) | A process flow step that is named after exposure assessment and categorizes services that evaluate and analyze the route, duration, magnitude and frequency of exposure of an organism or (sub)population to one or multiple chemicals. | VHP0000104 | |
| Chemical Characteristics and Hazard identification (Process Flow Step) | A process flow step that is named after hazard assessment and considered to be cheminformatics-based. It categorizes services that use molecular structures, chemical descriptors, and databases to predict or analyze the properties, behavior, and potential risks of chemical substances. | VHP0000102 | |
| Process Flow Step | One of the generic stages in the VHP4Safety human-based risk-assessment workflow, used to structure tools, data and models along the risk assessment process. | ||
| Regulatory Question | RQ | A concrete, decision-oriented risk-assessment question, formulated for a given case study, that the Virtual Human Platform should help to answer step-by-step. | |
| Toxicodynamics (Process Flow Step) | A process flow step that is named after Toxicodynamics and categorizes services that use or extend the (quantitative) AOP framework to analyze and assess the interaction of chemicals with biological targets. | VHP0000102 | |
| Toxicokinetics (Process Flow Step) | A process flow step that is named after toxicokinetics and categorizes services that analyze the kinetics (absorption, distribution, metabolism and excretion) of chemicals and how these processes influence the internal dose. The kinetics step contains four physiological processes substeps: Absorption, Distribution, Metabolism, and Excretion which can be captured in PBK models. | VHP0000102 |
Chemicals
| Term | Abbreviation | Definition | SMILES |
| bisphenol A | BPA | chemical compound, InChIKey IISBACLAFKSPIT-UHFFFAOYSA-N, CAS registry number 80-05-7 ref1 ref2 | |
| bisphenol AF | BPAF | chemical compound, InChIKey ZFVMWEVVKGLCIJ-UHFFFAOYSA-N, CAS registry number 1478-61-1 ref1 ref2 | |
| bisphenol F | BPF | chemical compound, InChIKey PXKLMJQFEQBVLD-UHFFFAOYSA-N, CAS registry number 620-92-8 ref1 ref2 | |
| bisphenol S | BPS | chemical compound, InChIKey VPWNQTHUCYMVMZ-UHFFFAOYSA-N, CAS registry number 80-09-1 ref1 ref2 | |
| bisphenol Z | BPZ | chemical compound, InChIKey SDDLEVPIDBLVHC-UHFFFAOYSA-N, CAS registry number 843-55-0 ref1 ref2 | |
| caffeine | chemical compound used as a stimulant, InChIKey RYYVLZVUVIJVGH-UHFFFAOYSA-N, CAS registry number 58-08-2 ref1 ref2 | ||
| calcineurin inhibitor | compound that inhibits or blocks the phosphatase activity of calcineurin ref1 | ||
| cisplatin | pharmaceutical drug, InChIKey LXZZYRPGZAFOLE-UHFFFAOYSA-L, CAS registry number 15663-27-1 ref1 ref2 | ||
| creatinine | chemical compound, InChIKey DDRJAANPRJIHGJ-UHFFFAOYSA-N, CAS registry number 60-27-5 ref1 ref2 | ||
| diclofenac | chemical compound, InChIKey DCOPUUMXTXDBNB-UHFFFAOYSA-N, CAS registry number 15307-86-5 ref1 ref2 | ||
| dietary supplement | Product intended to supplement the diet with vitamins, minerals, herbs, amino acids, or enzymes ref1 | ||
| dimethyl sulfoxide | DMSO | organosulfur chemical compound used as a solvent, InChIKey IAZDPXIOMUYVGZ-UHFFFAOYSA-N, CAS registry number 67-68-5 ref1 ref2 | |
| dopamine | organic chemical that functions both as a hormone and a neurotransmitter, InChIKey VYFYYTLLBUKUHU-UHFFFAOYSA-N, CAS registry number 51-61-6 ref1 ref2 | ||
| endocrine disrupting chemicals | EDCs | chemicals that can interfere with endocrine or hormonal systems at certain doses ref1 | |
| ethyl-parathion | chemical compound, InChIKey LCCNCVORNKJIRZ-UHFFFAOYSA-N, CAS registry number 56-38-2 ref1 ref2 | ||
| fenitrothion | chemical compound, InChIKey ZNOLGFHPUIJIMJ-UHFFFAOYSA-N, CAS registry number 122-14-5 ref1 ref2 | ||
| flavonolignan | class of chemical compounds, any lignan condensed with a 2-aryl-1-benzopyran skeleton and its substituted derivatives ref1 | ||
| folpet | chemical compound, InChIKey HKIOYBQGHSTUDB-UHFFFAOYSA-N, CAS registry number 133-07-3 ref1 ref2 | ||
| immunosuppressant | agent that suppresses immune function by one of several mechanisms of action (e.g. inhibiting DNA synthesis, inhibiting activation of T-cells, or inhibiting the activation of helper cells) ref1 | ||
| indocyanine green | chemical compound, InChIKey MOFVSTNWEDAEEK-UHFFFAOYSA-M, CAS registry number 3599-32-4 ref1 ref2 | ||
| methyl-parathion | chemical compound, InChIKey RLBIQVVOMOPOHC-UHFFFAOYSA-N, CAS registry number 298-00-0 ref1 ref2 | ||
| milk thistle (Silybum marianum) | species of plant of genus Silybum in family Asteraceae ref1 | ||
| organophosphate pesticides | |||
| paraquat | chemical compound, InChIKey INFDPOAKFNIJBF-UHFFFAOYSA-N, CAS registry number 4685-14-7 ref1 ref2 | ||
| pentachlorophenol | chemical compound, InChIKey IZUPBVBPLAPZRR-UHFFFAOYSA-N, CAS registry number 87-86-5 ref1 ref2 | ||
| perfluorooctanesulfonic acid | PFOS | chemical compound, InChIKey YFSUTJLHUFNCNZ-UHFFFAOYSA-N, CAS registry number 1763-23-1 ref1 ref2 | |
| perfluorooctanoic acid | PFOA | chemical compound, InChIKey SNGREZUHAYWORS-UHFFFAOYSA-N, CAS registry number 335-67-1 ref1 ref2 | |
| pesticide | Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests. ref1 ref2 | ||
| probenecid | chemical compound, InChIKey DBABZHXKTCFAPX-UHFFFAOYSA-N, CAS registry number 57-66-9 ref1 ref2 | ||
| pyraclostrobin | chemical compound, InChIKey HZRSNVGNWUDEFX-UHFFFAOYSA-N, CAS registry number 175013-18-0 ref1 ref2 | ||
| quercetin | polyphenol of the family of flavonoids, InChIKey REFJWTPEDVJJIY-UHFFFAOYSA-N, CAS registry number 117-39-5 ref1 ref2 | ||
| (R)-dinoseb | type of a chemical entity, InChIKey OWZPCEFYPSAJFR-ZCFIWIBFSA-N ref1 | ||
| rifampicin | pharmaceutical drug, InChIKey JQXXHWHPUNPDRT-WLSIYKJHSA-N, CAS registry number 13292-46-1 ref1 ref2 | ||
| (S)-dinoseb | type of a chemical entity, InChIKey OWZPCEFYPSAJFR-LURJTMIESA-N ref1 | ||
| amiodarone | chemical compound, InChIKey IYIKLHRQXLHMJQ-UHFFFAOYSA-N, CAS registry number 1951-25-3 ref1 | ||
| amiodarone hydrochloride | type of a chemical entity, InChIKey ITPDYQOUSLNIHG-UHFFFAOYSA-N, CAS registry number 19774-82-4 ref1 | ||
| cefuroxime | type of a chemical entity, InChIKey JFPVXVDWJQMJEE-IZRZKJBUSA-N, CAS registry number 55268-75-2 ref1 | ||
| chlorpyrifos | type of a chemical entity, InChIKey SBPBAQFWLVIOKP-UHFFFAOYSA-N, CAS registry number 2921-88-2 ref1 | ||
| diazinon | type of a chemical entity, InChIKey FHIVAFMUCKRCQO-UHFFFAOYSA-N, CAS registry number 333-41-5 ref1 | ||
| dinoseb | mixture ref1 | ||
| endosulfan | mixture, InChIKey RDYMFSUJUZBWLH-AZVNHNRSSA-N ref1 | ||
| ethylenebis(dithiocarbamate) | type of a chemical entity, InChIKey AWYFNIZYMPNGAI-UHFFFAOYSA-L ref1 | ||
| iopanoic acid | group of stereoisomers, InChIKey OIRFJRBSRORBCM-UHFFFAOYSA-N, CAS registry number 96-83-3 ref1 | ||
| lesinurad | chemical compound, InChIKey FGQFOYHRJSUHMR-UHFFFAOYSA-N, CAS registry number 878672-00-5 ref1 | ||
| mancozeb | mixture ref1 | ||
| Mn²⁺ | type of a chemical entity, InChIKey WAEMQWOKJMHJLA-UHFFFAOYSA-N ref1 | ||
| monobutyl phthalate | MBP | type of a chemical entity, InChIKey YZBOVSFWWNVKRJ-UHFFFAOYSA-N, CAS registry number 131-70-4 ref1 | |
| NH-3 | chemical compound, InChIKey IXMROOKFPWGDGF-UHFFFAOYSA-N, CAS registry number 447415-26-1 ref1 | ||
| PBDE-99 | type of a chemical entity, InChIKey WHPVYXDFIXRKLN-UHFFFAOYSA-N, CAS registry number 60348-60-9 ref1 | ||
| rotenone | chemical compound, InChIKey JUVIOZPCNVVQFO-HBGVWJBISA-N, CAS registry number 83-79-4 ref1 | ||
| Silibinin | mixture ref1 | ||
| silychristin A | chemical compound, InChIKey BMLIIPOXVWESJG-LMBCONBSSA-N, CAS registry number 33889-69-9 ref1 | ||
| silymarin | extract of the milk thistle (Silybum marianum) that contains a mixture of flavonolignans, including silibinin isomers, silychristin isomers, and others. ref1 | ||
| staurosporine | chemical compound, InChIKey HKSZLNNOFSGOKW-FYTWVXJKSA-O ref1 ref2 | ||
| sulfobromophthalein | type of a chemical entity, InChIKey OHTXTCNTQJFRIG-UHFFFAOYSA-N, CAS registry number 297-83-6 ref1 | ||
| sulfobromophthalein sodium | type of a chemical entity, InChIKey CDTNUNQQEUGDSD-UHFFFAOYSA-L, CAS registry number 123359-42-2 ref1 | ||
| tacrolimus | immunosuppressive Rx drug, InChIKey QJJXYPPXXYFBGM-LFZNUXCKSA-N, CAS registry number 104987-11-3 ref1 ref2 | ||
| triclosan | antimicrobial agent, InChIKey XEFQLINVKFYRCS-UHFFFAOYSA-N, CAS registry number 3380-34-5 ref1 ref2 | ||
| triiodothyronine | T3 | type of a chemical entity, InChIKey AUYYCJSJGJYCDS-LBPRGKRZSA-N ref1 | |
| thyroxine | T4 | type of a chemical entity, InChIKey XUIIKFGFIJCVMT-LBPRGKRZSA-N ref1 | |
| tetrabromobisphenol A | TBBPA | bisphenol, InChIKey VEORPZCZECFIRK-UHFFFAOYSA-N, CAS registry number 79-94-7 ref1 | |
| verapamil hydrochloride | chemical compound, InChIKey DOQPXTMNIUCOSY-UHFFFAOYSA-N, CAS registry number 152-11-4 ref1 ref2 | ||
| xanthohumol | type of a chemical entity, InChIKey ORXQGKIUCDPEAJ-YRNVUSSQSA-N, CAS registry number 6754-58-1 ref1 | ||
| Zn²⁺ | type of a chemical entity, InChIKey PTFCDOFLOPIGGS-UHFFFAOYSA-N ref1 | ||
| α-endosulfan | type of a chemical entity, InChIKey RDYMFSUJUZBWLH-BEJSPLBDSA-N ref1 | ||
| β-endosulfan | type of a chemical entity, InChIKey RDYMFSUJUZBWLH-LLXUDWAZSA-N ref1 |
Toxicology in General
| Term | Abbreviation | Definition |
| 3 Rs Principle | 3Rs | Replacement, Reduction, and Refinement. Used in the context of performing more humane animal research. |
| Absorption, Distribution, Metabolism, and Excretion synonyms: PK, TK |
ADME | Absorption, distribution, metabolism, and excretion of a substance (toxic or not) in a living organism, following exposure to this substance |
| Acute Kidney Injury | Abrupt loss of kidney function that develops within 48 hours ref1 | |
| Alamar Blue assay | Bioassay for ell viability, proliferation, and cytotoxicity ref1 | |
| Allan-Herndon-Dudley Syndrome | AHDS | A syndrome with neuromuscular involvement characterized by infantile hypotonia, muscular hypoplasia, spastic paraparesis with dystonic/athetoic movements, and severe cognitive deficiency. ref1 ref2 |
| Apoptosis | A regulated cell death mechanism characterized by distinctive morphologic changes in the nucleus and cytoplasm, including the endonucleolytic cleavage of genomic DNA, at regularly spaced, internucleosomal sites, i.e., DNA FRAGMENTATION. It is genetically programmed and serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth. ref1 ref2 | |
| Apparent Permeability | Papp | A biochemical parameter representing the apparent permeability of a compound specifically between the compartments. ref1 |
| Area Under the Curve | AUC | A statistical means of summarizing information from a series of measurements on one individual. It is frequently used in clinical pharmacology where the AUC from serum levels can be interpreted as the total uptake of whatever has been administered. As a plot of the concentration of a drug against time, after a single dose of medicine, producing a standard shape curve, it is a means of comparing the bioavailability of the same drug made by different companies. (From Winslade, Dictionary of Clinical Research, 1992) ref1 |
| Bioassay | Analytical method to determine concentration or potency of a substance by its effect on living cells or tissues ref1 | |
| Blood Brain Barrier | BBB | A tissue to protect the brain and spinal cord from both toxic and pathogenic agents in the blood. It is formed by extensive tight junctions between vascular epithelial cells, which are polarized into luminal (blood-facing) and abluminal (brain-facing) plasma membrane domains. |
| Benchmark Dose see also: Benchmark Dose Modeling |
BMD | See Benchmark dose modeling |
| Benchmark Dose Modeling see also: Benchmark Dose |
BMD | An approach to determine the toxicological limit values for human health, such as the acceptable daily intake (ADI), of all chemical substances (e.g., food) regardless of type or origin. BMD modeling (possibly in combination with PBK modeling) analyzes in conjunction with multiple test systems and organ systems, to study how exposure variation has on the outcome of an in vitro test system. |
| Blood-Cerebrospinal Fluid Barrier | BCSFB | Functional component of the vertebrate central nervous system ref1 |
| Blood-to-Plasma Ratio | BPR | The ratio of the concentration of molecule in whole blood (i.e. contains both red blood cells and plasma) to the concentration of molecule in plasma, namely CB/CP. ref1 |
| Brain-Derived Neurotrophic Factor | BDNF | Brain-derived neurotrophic factor (247 aa, ~28 kDa) is encoded by the human BDNF gene. This protein plays a role in both the development of the nervous system and neuronal survival. ref1 ref2 |
| Caco-2 | Cell line ref1 | |
| CD44 | CD44 antigen (742 aa, ~82 kDa) is encoded by the human CD44 gene. This protein is involved in cell-cell adhesion and cell-matrix adhesion. ref1 ref2 | |
| Cell line | Population of cells that originates from a primary culture, adapted to grow and divide under laboratory conditions ref1 | |
| CellTiter-Fluor assay | The CellTiter-Fluor Cell Viability Assay measures the relative number of viable cells in a population. The assay is based on measurement of a conserved and constitutive protease activity within live cells and therefore serves as a biomarker of cell viability. The live-cell protease activity is restricted to intact viable cells and is measured using a fluorogenic, cell-permeant, peptide substrate (Gly-Phe-AFC). The substrate enters intact cells, where it is cleaved by the live-cell protease activity to generate a fluorescent signal proportional to the number of living cells. The live-cell protease becomes inactive upon loss of membrane integrity and leakage into the surrounding culture medium. (description adapted from vendor Promega) ref1 | |
| CellTiter-Glo assay | ||
| CFDA assay | ||
| CHO-K1 | Chinese hamster ovary cells, subclone from parental CHO cell line that was initiated from an ovary biopsy of an adult Chinese hamster in 1957. ref1 ref2 | |
| Cholestasis | Impairment of the bile flow caused by obstruction within the liver, or outside the liver in the bile duct system. ref1 ref2 | |
| Co-culture | Techniques of culturing mixed cell types in vitro to allow their synergistic or antagonistic interactions ref1 | |
| Concentration-response relationship | ||
| Cytotoxicity | It is the toxic or cell-death inducing property of a perturbagen. Known cytotoxic agents mediate cell death commonly by necrosis, apoptosis, or autophagy. Cytotoxicity can be detected by measuring various aspects of the death process: e.g. membrane permeability, ATP concentration, DNA fragmentation, etc. ref1 ref2 | |
| Deiodinase | DIO | Class of enzymes ref1 |
| Developmental and Reproductive Toxicology | DART | |
| Developmental Neurotoxicity | DNT | |
| Dopaminergic neurons | Neurons whose primary neurotransmitter is DOPAMINE. ref1 ref2 | |
| Dose-response relationship | Relationship between the dose of an administered drug and the response of the organism to the drug ref1 | |
| Endocrine disruption | ||
| Endoplasmic Reticulum Stress | ER stress | Physiological or molecular disturbances that impair endoplasmic reticulum function ref1 |
| Endothelial-Like Cells | ELC | |
| Endpoint | The endpoint is a quantitive or qualitative interpretable standardized representation of a perturbation (a change from a defined reference state of a "closed" model system) that is measured by the bioassay. An endpoint consists of a series of data points, one for each perturbing agent (screened entity) tested the assay. ref1 | |
| Enzyme-Linked Immunosorbent Assay | ELISA | An immunoassay utilizing an antibody labeled with an enzyme marker such as horseradish peroxidase. While either the enzyme or the antibody is bound to an immunosorbent substrate, they both retain their biologic activity; the change in enzyme activity as a result of the enzyme-antibody-antigen reaction is proportional to the concentration of the antigen and can be measured spectrophotometrically or with the naked eye. Many variations of the method have been developed. ref1 ref2 |
| Fibrosis | Formation of excess fibrous connective tissue in an organ or tissue in a reparative or reactive process ref1 | |
| Fraction Unbound in Plasma | fup | An unbound fraction parameter specifically for plasma. ref1 |
| Gene Set Enrichment Analysis | GSEA | An inferential statistical data analysis that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). ref1 ref2 |
| H2DCFDA assay | ||
| Half Maximal Inhibitory Concentration | IC50 | The effective concentration of an inhibitor, which produces 50% of the maximum possible response for that inhibitor. ref1 ref2 |
| HepG2 | human hepatocellular carcinoma (HCC) cells (p53-wt). ref1 ref2 | |
| High Throughput Screening | HTS | |
| Human Brain Microvascular Endothelial Cells | hBMEC | Any microvascular endothelial cell that is part of a brain. ref1 |
| (human) Embryonic Stem Cell | (h)ESCs | Pluripotent stem cells derived from the inner cell mass of a blastocyst (an early-stage pre-implantation embryo). These cells are characterised by their ability to differentiate into any cell type of the three germ layers: ectoderm, mesoderm, and endoderm. They are also known for their self-renewal capability, meaning they can proliferate indefinitely in culture while maintaining their pluripotency. |
| Human Neural Progenitor Test | hNPT | |
| In silico | On a computer or via computer simulation software ref1 | |
| In vitro | Outside a natural biological environment ref1 | |
| In vivo | Studies in which the effects of various biological entities are tested on whole, living organisms ref1 | |
| induced Pluripotent Stem Cell | iPSCs | A type of pluripotent stem cell that can be generated directly from adult cells. The process of creating iPSCs involves reprogramming differentiated somatic cells (such as skin or blood cells) by introducing specific genes that reset the cells to a pluripotent state. This reprogramming allows iPSCs to develop into almost any cell type in the body, similarly to hESCs, making them highly valuable for regenerative medicine, disease modelling, and drug discovery. |
| Integrated Approaches to Testing and Assessment | IATA | An assessment method puts together information from multiple sources used for toxicity assessment of chemical substances in regulatory context. IATA is coined by the OECD, for which case studies are conducted to establish IATAs. ref1 |
| Intrinsic Clearance | CLint | Intrinsic metabolic clearance is defined as ratio of maximum metabolism rate, Vmax, and the Michaelis-Menten constant, Km. ref1 |
| Kidney Injury Molecule 1 | KIM-1 | Hepatitis A virus cellular receptor 1 (359 aa, ~39 kDa) is encoded by the human HAVCR1 gene. This protein is involved in the modulation of asthma and allergic reactions. ref1 ref2 |
| KLF9 | Protein-coding gene in the species Homo sapiens ref1 | |
| Lactate Dehydrogenase Assay | LDH | A quantitative measurement of the amount of lactate dehydrogenase present in a sample. ref1 |
| Liquid Chromatography-Mass Spectrometry | LC-MS | Analytical chemistry technique with on-line coupling of liquid chromatography to mass spectrometry ref1 |
| Lowest Observed Adverse Effect Level | LOAEL | The lowest exposure level of a chemical stressor evaluated in a toxicity test that shows harmful effects on a plant or animal. |
| LUHMES | Cell line ref1 | |
| Markov Chain Monte Carlo | MCMC | Class of algorithms ref1 |
| Maximum Plasma Concentration | Cmax | This is a measurement that quantifies the maximum concentration of an experimental substance or drug in the plasma or a target organ after dose administration. ref1 |
| MDCK1 | Cell line ref1 | |
| Microelectrode Array | MEA | Devices that contain multiple microelectrodes through which neural signals are obtained or delivered, essentially serving as neural interfaces that connect neurons to electronic circuitry ref1 |
| Mitochondrial dysfunction | Mitochondrial dysfunction is a subtype of dysfunctioning: A process that performs an abnormal and incomplete mitochondrial function. ref1 | |
| MO3.13 | Human hybrid cell line that express phenotypic characteristics of primary oligodendrocytes ref1 ref2 | |
| Molecular docking | Attempt to predict the structure of the intermolecular complex formed between two or more molecules ref1 | |
| Monocarboxylate Transporter 8 | MCT8 | Monocarboxylate transporter 8 (539 aa, ~60 kDa) is encoded by the human SLC16A2 gene. This protein is involved in cellular uptake of thyroxine (T4), triiodothyronine (T3), reverse triiodothyronine (rT3) and diiodothyronine. ref1 ref2 |
| Monte Carlo Risk Assessment see also: Monte Carlo Risk Assessment Calculation Model |
MCRA | See Monte Carlo Risk Assessment calculation model. |
| Monte Carlo Risk Assessment Calculation Model see also: Monte Carlo Risk Assessment |
A modeling technique for realistically possible calculation of the intake of risk substances by humans, for example via food, where the exposure can also be linked to the hazard, with which a risk assessment can be carried out. | |
| Nephrotoxicity | Toxicity that causes injury to the kidney or damages its function. This can include nephritis, renal failure, injury to kidney. ref1 ref2 | |
| Neural Progenitor Cells | NPCs | An undifferentiated cell derived from a neural stem cell, with a limited capacity to self-renew (Dibajnia and Morshead, 2013) and the ability to generate multiple types of lineage-restricted progenitors, contributing to the formation of neurons, astrocytes, and oligodendrocytes. ref1 ref2 |
| Neurodegeneration | Progressive loss of neural cells and tissue. ref1 ref2 | |
| Neurodevelopment | The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state ref1 | |
| Neuronal network activity | ||
| Neurotoxicity | Toxicity that causes injury to the central or peripheral nervous system or damages its function. This can include stroke, multiple sclerosis, encephalopathy, dementia, Alzheimer's disease, amnesia, dyskinesia, Parkinson's disease, tremor, convulsions and Guillain Barre syndrome. ref1 ref2 | |
| New Approach Methodology see also: Non-Animal Methodology |
NAM | A collection of various methods (e.g., high-throughput screening and high-content methods) in a wide set of contexts including in chemico and in vitro to improve knowledge over the toxicokinetic or toxicodynamic attributes of chemical substances, and in turn to improve the chemical safety assessment (see also Non-Animal Methodology). ref1 ref2 |
| No Observed Adverse Effect Level | NOAEL | The highest exposure level of a chemical stressor evaluated in a toxicity test that shows no harmful effects on a plant or animal. |
| No Observed Effect Level | NOEL | The highest exposure level of a chemical stressor evaluated in a toxicity test that shows no effects on a plant or animal. |
| Non-Animal Methodology see also: New Approach Methodology |
A collection of methods to evaluate the potential for a chemical to cause systematic toxicity without using tests on animals (see also New Approach Methodology). ref1 | |
| Ordinary Differential Equation | ODE | Differential equation containing one or more functions of one independent variable and its derivatives ref1 |
| Organ-on-a-chip | Devices designed to recapitulate tissue or organ-level physiology and architect by combining MICROFLUIDICS; MICROFABRICATION; and 3D CELL CULTURE. Microphysiological systems mimic interconnections important in physiological or pathophysiological states of organ(s) and are often used for instance in HIGH THROUGHPUT SCREENING of drugs and factors important in disease modeling. ref1 ref2 | |
| Organic Anion-Transporting Polypeptide 1C1 | OATP1C1 | Protein-coding gene in the species Homo sapiens ref1 |
| Organic Cation Transporter 2 | OCT2 | Organic cation transporter consisting of twelve transmembrane domains and expressed primarily in the kidney. It transports a wide range of metabolites, drugs, and neurotransmitters from the blood to the KIDNEY TUBULES, including DOPAMINE; SEROTONIN; CHOLINE; and CISPLATIN. ref1 ref2 |
| Organoid | Miniaturized and simplified version of an organ ref1 | |
| Oxidative stress | A disturbance in the prooxidant-antioxidant balance in favor of the former, leading to potential damage. Indicators of oxidative stress include damaged DNA bases, protein oxidation products, and lipid peroxidation products (Sies, Oxidative Stress, 1991, pxv-xvi). ref1 ref2 | |
| P-glycoprotein | P-gp | A 170-kDa transmembrane glycoprotein from the superfamily of ATP-BINDING CASSETTE TRANSPORTERS. It serves as an ATP-dependent efflux pump for a variety of chemicals, including many ANTINEOPLASTIC AGENTS. Overexpression of this glycoprotein is associated with multidrug resistance (see DRUG RESISTANCE, MULTIPLE). ref1 ref2 |
| Parkinson's Disease | PD | A progressive, degenerative neurologic disease characterized by a TREMOR that is maximal at rest, retropulsion (i.e. a tendency to fall backwards), rigidity, stooped posture, slowness of voluntary movements, and a masklike facial expression. Pathologic features include loss of melanin containing neurons in the substantia nigra and other pigmented nuclei of the brainstem. LEWY BODIES are present in the substantia nigra and locus coeruleus but may also be found in a related condition (LEWY BODY DISEASE, DIFFUSE) characterized by dementia in combination with varying degrees of parkinsonism. (Adams et al., Principles of Neurology, 6th ed, p1059, pp1067-75) ref1 ref2 |
| pCHEMBL | A value that allows a number of roughly comparable measures of half-maximal response concentration/potency/affinity to be compared on a negative logarithmic scale. ref1 | |
| Proximal Tubular-Like Cells | PTL | |
| Proximal tubule | In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. ref1 ref2 | |
| Quantitative In Vitro to In Vivo Extrapolation | QIVIVE | |
| Reactive Oxygen Species | ROS | Molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers. ref1 ref2 |
| Read Across | A common approach in the risk assessment in order to examine structural similarities between the source and the target substances when there is a lack of information on their physical-chemical, toxicological properties, or environmental fate. | |
| Reverse Transcription Quantitative PCR | RT-qPCR | A method in which amplification of a specific RNA/cDNA sequence by a reverse transcription polymerase chain reaction is monitored by detection of fluorescent probes or intercalating dyes that indicate the (absolute or relative) amount of product being produced in real time. ref1 |
| RNA Sequencing | RNA-seq | High-throughput nucleotide sequencing techniques for RNA ref1 |
| RPTEC/TERT1 | Cell line ref1 | |
| SH-SY5Y | Cell line ref1 | |
| SK-N-AS | Cell line ref1 | |
| Substantia nigra | A large cell mass extending forward, over the dorsal surface of the crus cerebri, from the rostral border of the pons into the subthalamic region. It is composed of a dorsal stratum of closely spaced pigmented cells, the pars compacta, and a larger ventral region of widely scattered cells, the pars reticulata. The pars compacta includes numerous cells that project forward to the striatum (caudate nucleus and putamen) and contain dopamine, which acts as the primary neurotransmitter at the synaptic endings. Other, apparently non-dopaminergic cells project to portions of the ventral nucleus of thalamus, the superior colliculus and reticular formation. The nigrostriatal projection is reciprocated by a striatonigral fiber system with multiple neurotransmitters, chief among which is gamma-aminobutyric acid (GABA). The substantia nigra is involved in the metabolic disturbances associated with Parkinson's disease and Huntington's disease. ref1 ref2 | |
| Synaptogenesis | Formation of synapses between neurons in the nervous system ref1 | |
| TempO-Seq | ||
| Teratology | Scientific field that studies the causes, mechanisms, and classes of congenital malformations in animals and plants. ref1 | |
| Thyroid Hormone | TH | Any of several closely related compounds that are produced by the thyroid gland and are active metabolically. ref1 ref2 |
| Thyroid Hormone Receptor | TR | A nuclear receptor that specifically binds to and is activated by thyroid hormone. ref1 |
| Tissue-blood partition coefficient | ||
| Toxicodynamics | TD | Study of interactions between the toxicant and a biological target ref1 |
| Transcriptomics | The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. ref1 ref2 | |
| Tubuloid |
Risk Assessment
| Term | Abbreviation | Definition |
| Alternative Safety Profiling Algorithm | ASPA | a risk assessment workflow to combine information required for Next Generation Risk Assessment (NGRA), coined by Animal-free Safety assessment of chemicals: Project cluster for Implementation of novel Strategies (ASPIS; joint collaboration ONTOX, PrecisionTox, RISK-HUNT3R) ref1 |
| Benchmark Concentration | BMC | |
| Benchmark Dose Lower Confidence Limit | BMDL | |
| Bioactivity-Exposure Ratio | BER | |
| Dietary exposure | Exposure to potentially harmful factors or substances in contaminated food or drinking water ref1 | |
| Environmental exposure | The exposure to potentially harmful chemical, physical, or biological agents in the environment or to environmental factors that may include ionizing radiation, pathogenic organisms, or toxic chemicals. ref1 | |
| European Centre for the Validation of Alternative Methods | ECVAM | The EU Reference Laboratory for alternatives to animal testing, located in Ispra, Italy. |
| European Chemical Agency | ECHA | The European Chemicals Agency (ECHA) is responsible for, among other things, implementing European Union legislation on chemicals, such as REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) and CLP (Classification, Labelling and Packaging of substances and mixtures). ref1 |
| European Food Safety Authority | EFSA | The European Food Safety Authority (EFSA) is responsible for providing scientific advice on risks related to food and animal feed throughout the entire supply chain in the European Union. |
| Exposome | The measure of all the exposures of an individual from all sources, including environmental and occupational sources, in a lifetime and how those exposures relate to health. (from https://www.cdc.gov/niosh/topics/exposome/ on 06/06/2019) ref1 ref2 | |
| Exposure | Contact between a toxicological agent and an outer boundary of an organism. | |
| Exposure Assessment | The process of assessing the magnitude, frequency and duration of exposure of a certain organism to a certain agent; OF the process of assessing the total external (or internal) exposure following one or more exposure/use scenarios that are described in terms of route, extent, frequency and duration of exposure, including exposure via more than one exposure route (aggregated exposure) and exposure to multiple chemicals (cumulative exposure). | |
| Exposure scenario | ||
| External exposure | ||
| Hazard Assessment | The process of assessing the intrinsic hazard a substance poses to human health and/or the environment. This provides information on potential human health effects such that a safe production and use of a chemical can be assured. Two types can be generally distinguished, i.e. with the purpose to classify the chemical to a certain category of toxicity (mostly qualitative assessment) or to derive an exposure limit, such as a health-based guidance value or product limit, that ensures safe use. | |
| Hazard characterization | ||
| Hazard identification | First step of risk assessment and management in systematically discovering, recognizing and documenting potential risks which may negatively impact the objectives of an organization or individual ref1 | |
| Human biomonitoring | Measurement of the body burden of toxic chemical compounds, elements, or their metabolites, in biological substances ref1 | |
| Internal (Exposure) | The amount of a chemical (or its active metabolites) present in human tissues or biological fluids over time, typically expressed as concentration-time profiles or dose metrics, resulting from external exposure after ADME/TK processes, and used as the input for the Toxicodynamics/AOP step. | |
| Lowest Observed Effect Concentration | LOEC | |
| Mode of Action | MoA | A functional or anatomical change, resulting from the exposure of a living organism to a substance. |
| Monte Carlo simulation | Broad class of computational algorithms using random sampling to obtain numerical results ref1 | |
| Next Generation Risk Assessment | NGRA | |
| Occupational exposure | Exposure to a hazard in the workplace ref1 | |
| Pharmacovigilance | The pharmacological science relating to the collection, detection, assessment, monitoring, and prevention of adverse effects with pharmaceutical product ref1 | |
| Point of Departure | PoD | |
| Population variability | Differences in measurable biological values, characteristics, or traits, among individuals of a population or between population groups. ref1 | |
| Raw Primary Commodity | RPC | |
| Recommended Daily Intake | RDI | The amounts of various substances in the diet recommended by governmental guidelines as needed to sustain healthy life. ref1 |
| The legislation of 'Registration, Evaluation, Authorization and Restriction of Chemicals' | REACH | Regulation (EC) No 1907/2006 of the European Parliament and of the Council concerning the Registration, Evaluation, Authorization and Restriction of Chemicals (REACH). ref1 |
| Risk Assessment | The process of assessing human health and environmental risks in a historic, current or emerging exposure scenario for which a concern has risen. | |
| Risk characterization | A process to combine information for a substance about the hazard and exposure to determine how much risk there is. | |
| Safety Assessment | The overarching term for hazard and risk assessment in toxicology. For pharmaceuticals, this term is generally used for assessments of the safety of a certain application of pharmaceuticals, including the determination of the therapeutic window and risk/benefit analysis. | |
| Therapeutic Drug Monitoring | TDM | Observing, recording, or detecting the effects of a chemical substance administered to an individual ref1 |
| Weight of evidence | ||
| WHO Human Health Risk Assessment Toolkit: Chemical Hazards | A publication that provides guidance on how to identify, gather, and use the information needed to assess chemical hazards, exposures, and related health risks. It was developed by the International Programme on Chemical Safety. ref1 |
Adverse Outcome Pathway
| Term | Abbreviation | Definition |
| Adverse Outcome | AO | A specialised type of key event that is generally accepted as being of regulatory significance on the basis of correspondence to an established protection goal or equivalence to an apical endpoint in an accepted regulatory guideline toxicity test. ref1 |
| Adverse Outcome Pathway | AOP | An AOP describes a sequence of events commencing with initial interaction(s) of a stressor with a biomolecule within an organism that causes a perturbation in its biology (i.e., molecular initiating event, MIE), which can progress through a dependent series of intermediate key events (KEs) and culminate in an adverse outcome (AO) considered relevant to risk assessment or regulatory decision-making. ref1 |
| Apical Endpoint | The outcomes that can be proven by observation or experiment after exposure to a chemical substances. ref1 | |
| Bioactivity | The affinity and/or potency of a compound for a protein target. | |
| Bradford-Hill criteria | Principles for establishing a causal relationship ref1 | |
| Key Event | KE | A change in biological or physiological state that is both measurable and essential to the progression of a defined biological perturbation leading to a specific adverse outcome. ref1 |
| Key Event Relationship | KER | A scientifically-based relationship that connects one key event to another, defines a causal and predictive relationship between the upstream and downstream event, and thereby facilitates inference or extrapolation of the state of the downstream key event from the known, measured, or predicted state of the upstream key event. ref1 |
| Molecular Adverse Outcome Pathways | mAOP | Metapathway, similar to conventional AOPs, but connected events as e.g. WikiPathways pathways. Their function is to expand KEs with molecular pathways and allow analyses of omics data. |
| Molecular Initiating Event | MIE | A specialised type of key event that represents the initial point of chemical/stressor interaction at the molecular level within the organism that results in a perturbation that starts the AOP. ref1 |
| Quantitative Adverse Outcome Pathway | qAOP | Quantitative AOPs, "Leiden approach" to connect events using differential equations. |
| Stressor | ||
| TXG-MAPr R package | TXG-MAPr | Statistical quantitative AOP approach using known coexpression changes in tissue toxicity. |
Computer Infrastructure
| Term | Abbreviation | Definition |
| Artificial Intelligence | AI | Field that develops and studies software enabling machines to exhibit intelligent behavior ref1 |
| BioAssay Ontology | BAO | Ontology to annotate experiments in the field of the life sciences ref1 |
| Cell Line Ontology | CLO | Ontology which describes anatomic origin and nature of eukaryotic cell lines ref1 |
| Cell Ontology | CL | An ontology for cell types ref1 |
| Cloud computing | A computer infrastructure that provides access to data resources, analysis software, and computer power to conduct analyses specific to a use case or research community. ref1 | |
| Controlled vocabulary | Standardized and organized sets of words and phrases for retrieval and disambiguation of information, distinguishing preferred terms from non-preferred terms ref1 | |
| CSV | Tabular data represented as comma-separated values in a text file. ref1 ref2 | |
| Digital Object Identifier | DOI | ISO standard unique string identifier for a digital object ref1 |
| Docker | A service to create a virtual computer environment which can include the required software/tools to conduct a scientific work. | |
| Dockerfile | A file that includes the commands to build a Docker image. | |
| Docker container | The virtual environment that has been initiated to run based on its Docker image. | |
| Docker image | A representative file from which a docker container can be run and executed. | |
| eNanoMapper Ontology | ENM | Application ontology for the nanomaterial safety assessment domain ref1 |
| Exposure Ontology | ExO | Ontology for environmental and chemical exposure assessment ref1 |
| Gene Ontology | GO | Ontology for describing the function of genes and gene products ref1 |
| GitHub | Hosting service for software projects using Git ref1 | |
| JSON | Text-based open standard designed for human-readable data interchange ref1 | |
| Jupyter Notebook | Web-based interactive computational environment for creating Jupyter notebook documents ref1 | |
| Kubernetes | K8s | A computer tool to orchesterize and manage Docker containers. |
| Machine learning | Scientific study of algorithms and statistical models that computer systems use to perform tasks without explicit instructions ref1 | |
| Medical Subject Headings | MeSH | Controlled vocabulary for the purpose of indexing journal articles and books in the life sciences ref1 |
| Model Context Protocol | MCP | Protocol for applications to provide context to LLMs ref1 |
| NCBI Taxonomy | NCBITaxon | Curated classification and nomenclature for all of the organisms in the public sequence databases ref1 |
| Ontology for Biomedical Investigations | OBI | An ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. ref1 ref2 |
| Open source | Practice of publishing digital resources publicly alongside their source code or source files ref1 | |
| OpenAPI | Specification language for APIs ref1 | |
| ORCID | Nonproprietary alphanumeric code to uniquely identify scientific and other academic authors ref1 | |
| Platform | A computer environment where a set of software and tools are hosted and made available for the use of others over the internet. ref1 | |
| R Shiny | Web-application on R -language ref1 | |
| Research Organization Registry | ROR | Community-led database of research organizations maintained by the ROR community ref1 |
| Research Resource Identifier | RRID | Persistent and unique identifier for referencing a research resource ref1 |
| REST API | Architectural style for distributed hypermedia systems ref1 | |
| RO-Crate | Method to aggregate and describing research data with associated metadata ref1 | |
| Scalability | The property of a (cloud) infrastructure to be able to handle a growing amount of data and work related to it with additions. ref1 | |
| Secure Shell | ssh | A network protocol to access a network service remotely and securely. |
| SPARQL | SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format. ref1 ref2 | |
| Strato | An internet hosting service provider that supplies the servers where the virtual platform is built. ref1 | |
| Uberon | Cross-species anatomy ontology for metazoan structures and development ref1 | |
| User Interface | UI | Means by which a user interacts with and controls a machine ref1 |
| VHP server 1 | The server hosted in Strato where the Docker containers used in the project are deployed. | |
| VHP server 2 | The server hosted in Strato where the Kubernetes structure is formed for orchestration of the Docker containers on VHP server 1. | |
| VHP server 3 | The server hosted in Strato that is used for experimentation, learning, and testing the work that is carried out on VHP servers 1 and 2. | |
| Wikibase | Collection of software (applications and libraries) for creating, managing and sharing structured data ref1 | |
| Wikidata | Free multilingual online knowledge graph ref1 |
Tool & Service
| Term | Abbreviation | Definition |
| Accessible | One needs to know how data can be accessed, possibly including authentication and authorisation. ref1 | |
| Adapter | A framework to fine-tune (large language) models by adding a small number of external parameters without the need of the entire (large language) model. ref1 ref2 | |
| Agent | A software entity that uses a language model to autonomously perform specific tasks by interpreting prompts, interacting with data or systems, and generating results. | |
| AOP-Builder | ||
| AOP-Suite | ||
| AOP-Wiki API | ||
| AOP-Wiki RDF | ||
| AOP-Wiki RDF Dashboard | ||
| AOP-Wiki Snorql UI | ||
| Application Programming Interface | API | A type of software interface that provides a way for two or more computer programs to communicate with each other. ref1 |
| ArrayAnalysis | ||
| ASReview | ||
| Atomic Site of Metabolism | SOM | The atomic site in a molecule which is prone to metabolism by Cytochrome P450s (or other enzymes) as referred in the SOM Prediction tool. |
| AutoDock Vina | Molecular Docking Software ref1 | |
| Backlog | A prioritized list of all the tasks the team still wants to complete, used in the SCRUM method of working. Each added task is clearly described and preferably linked to an epic and a user story. At the beginning of a sprint, tasks will be selected from the backlog and assigned to team member to be completed before the end of that sprint. | |
| bio.tools | Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences ref1 | |
| BioModels | Database of biological reactions ref1 | |
| BioStudies | Data repository from EMBL-EBI ref1 | |
| BioTransformer | ||
| BMDExpress-3 | ||
| BridgeDb | Framework to map identifiers between various biological databases ref1 | |
| BROWSE model | ||
| Catalog | A systemic collection of items of the same type. ref1 | |
| CDK Depict | Web application for generating chemical structure depictions from SMILES ref1 | |
| CellDesigner | ||
| Cellosaurus | Online knowledge resource on cell lines ref1 | |
| Central Access Point | CAP | A website that provides toxicological risk assessors an easily accessible and structured analysis framework including tools developed within VHP4Safety. ref1 |
| Chemical Information Tool | Software used to transform and process chemical information items. | |
| Chemistry Development Kit | CDK | Java library for chem- and bioinformatics ref1 |
| Compound Wiki ID | Identifier used by the VHP4Safety Compound Wiki (see compoundcloud.wikibase.cloud/wiki/Item:Q1 where Q1 is the Compound Wiki ID for aflatoxin B1). | |
| CompTox | Chemical database ref1 | |
| COPASI | Biochemical System Simulator ref1 | |
| cpLogD | ||
| Cytoscape | Open source software platform for visualizing molecular interaction networks and biological pathways ref1 | |
| Danish (Q)SAR Database | ||
| Data steward | A data steward is an oversight or data governance role within an organization, and is responsible for ensuring the quality and fitness for purpose of the organization's data assets, including the metadata for those data assets. ref1 | |
| Data Management Plan | DMP | Plans to serve to address the what, how, who, and where of data management by formally outlining the roles, responsibilities, and activities for managing data during and after research in alignment with FAIR principles. ref1 |
| Data modeling | DMP | The process of discovering, analyzing, and scoping data requirements, and then representing and communicating these data requirements in a precise form called the data model. This process is iterative and may include a conceptual, logical, and physical model. ref1 |
| Data stewardship | The work performed by a data steward. | |
| DECIMER | Open source chemical OCR tool ref1 | |
| Definition of Done | DoD | A shared understanding among the team of when a task is considered as 'done'. It ensures work is completed to a certain standard before it is accepted. This might include specific documentation, review by another team member or discussion during the Sprint Review. |
| ELIXIR TeSS | ||
| Embase | Database ref1 | |
| Endocrine Disruptome | ||
| Epic | A long-term goal or general feature of the final product. Epics are broken down into user stories, whereas user stories are broken down into tasks. By completing tasks in each sprint, the epic will gradually be reached. | |
| Europe PMC | Database of biomedical research ref1 | |
| Explainability | The ability to describe the internal logic and mechanics of a model, such as Large Language Models and machine learning systems, to understand the way the model is trained and how predictions and answers are generated by the model. ref1 | |
| FAIRDOMHub | ||
| Fairspace | ||
| Farmacotherapeutisch Kompas | ||
| Findable | Metadata and data should be easy to find for both humans and computers. Machine-readable metadata are essential for automatic discovery of datasets and services. ref1 | |
| Findable, Accessible, Interoperable, Reusable | FAIR | The FAIR principles emphasise machine-actionability (i.e., the capacity of computational systems to find, access, interoperate, and reuse data with none or minimal human intervention) because humans increasingly rely on computational support to deal with data as a result of the increase in volume, complexity, and creation speed of data. ref1 |
| Fine-Tuning | The process of training a pre-existing language model on a smaller, domain-specific dataset to improve its performance on specific tasks or for specific industries. | |
| Flame | ||
| Gaussian plume drift model | ||
| General Tools | Support software tools that can be used at several stages of a workflow. | |
| Google Scholar | Academic search service by Google ref1 | |
| Identifier | The unique identifier for an administered item within a registration authority. ref1 | |
| Incident Postmortem | A framework for learning from incidents and turning problems into progress by bringing people together to discuss the details of the incident to explore why it happened, its impact, the actions that can be taken to mitigate and resolve it, and the actions to prevent it happen again. ref1 | |
| Interability | The ability to explain or to present a model, such as Large Language Models and machine learning systems in understandable terms to a human. ref1 | |
| Hackathon | An event in which computer programmers collaborate intensively with one another and sometimes with people in other specialties over a relatively short period of time to create code usually for a new software product or service. ref1 | |
| Human-Readable Data | A data or dataset that is in a format that can be naturally read by humans. It usually contrasts with machine-readable data. ref1 | |
| In vitro in vivo extrapolation | IVIVE | A method to conduct the qualitative or quantitative transposition of experimental results or observations made in vitro to predict phenomena in vivo, biological organisms. ref1 |
| Interoperable | To speed up discovery and uncover new insights, research data should be easily combined with other datasets, applications and workflows by humans as well as computer systems. ref1 | |
| JRC Data Catalogue | ||
| Knowledge Graphs see also: Resource Description Framework |
KGs | An organized and graphical representation of real world obejcts and their relationships, represented mostly as nodes and edges, respectively to store data entities and their interrelations. See also Resource Description Framework. ref1 ref2 |
| Large Language Model | LLM | A large language model is a computational model capable of language generation or other natural language processing tasks. ref1 |
| Llemy | ||
| Machine-Readable Data | A data or dataset that is in a format that can be read by a computer. It usually contrasts with human-readable data. ref1 | |
| Mathematical Markup Language | MathML | An Extensible Markup Language (XML) application to encode mathematical notations on the Web to capture their structure and content for their use and re-use. ref1 |
| MCT8 Docking for MIE Discovery | ||
| MEDLINE | Biomedical bibliographical database ref1 | |
| Metadata | The data that provide information about one or more aspects of the data that is used to summarize basic information about data that can make tracking and working with specific data easier. | |
| MINERVA | ||
| Model | A simplified (generally mathematical) representation of a real system (e.g. of system: an organism, an organ, a cell, etc.) | |
| Module | [Software Component]An individual component (software, dataset or in vitro method description) that is hosted, or linked to in the VHP4Safety platform. ref1 | |
| Molecular AOP Analyser | ||
| Molecular AOP Builder | ||
| Multimodal Model | A model capable of processing and generating responses from multiple types of data, such as text, images, and audio. | |
| Natural Language Processing | NLP | A multidisciplinary scientific field that focuses on the interaction between computers and human (natural) languages, enabling machines to understand, interpret, and generate human language in a meaningful way. ref1 ref2 |
| NFDI Terminology Service | ||
| NIH Dietary Supplement Label Database | DSLD | Database by the USA NIH ref1 |
| OECD QSAR Toolbox | ||
| OECD QSAR Toolbox AI Assistant | O-QT | |
| Ontology | A formal specification of the conceptualization of a set of phenomena naming and defining the elements of the set along with describing relations between the concepts, data, and entities; a way of showing the properties of a subject area and how they are related, by defining a set of concepts and categories that represent the subject. ref1 ref2 | |
| ONTOX Physiological Maps | ||
| OP PBK Model | ||
| Open Data | A (collection of) data that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions only to ensure that further recipients can also do these things. ref1 | |
| Open Parser for Systematic IUPAC Nomenclature | OPSIN | IUPAC name to structure convertor ref1 |
| PathVisio | Software for pathway editing and visualisation ref1 | |
| PeerTube | Decentralized video hosting network, based on free software ref1 | |
| Pharmacokinetics synonyms: ADME |
PK | see ADME (these terms are equivalent) |
| PhysB | ||
| Physiologically based biokinetic model synonyms: PBPK |
PBBK | See PBPK model (these terms are equivalent) |
| Physiologically based kinetic model synonyms: PBPK |
PBK model | See PBPK model (these terms are equivalent) |
| Physiologically based pharmacokinetic model synonyms: PBBK, PBK model, PBTK |
PBPK | Mechanistic representation of ADME processes for a chemical in a living organism, based on physiological and chemical properties |
| Physiologically based toxicokinetic model synonyms: PBPK |
PBTK | See PBPK model (these terms are equivalent) |
| PROAST | ||
| Product Owner | A key role in SCRUM method for people who have a clear view of the long term goals of the project and the expertise of the team members. People with this role review the epics and user stories and prioritize the tasks in the backlog. | |
| Prompt | An input provided to a model to guide its output or action. Prompts can take various forms, such as text, images, audio, or structured data, depending on the capabilities of the model. | |
| Prompt Engineering | The process of designing and refining prompts to achieve desired outputs from a model, often used to maximize performance in specific tasks. | |
| Proteochemometric | PCM | Mathematical models that can be used to predict the biological properties (mainly bioactivity) of compounds on proteins from the knowledge of their (chemical) structure. |
| PubMed | Online database with abstracts of medical articles, hosted by US National Library of Medicine ref1 | |
| qAOP-App | ||
| QSPRpred | ||
| Quantitative Structure Activity Relationships | QSAR | Mathematical models that can be used to predict the physicochemical, biological and environmental fate properties of compounds from the knowledge of their chemical structure. |
| R-ODAF | ||
| Reactome | Database of biological pathways ref1 | |
| Research Object Builder for Open Toxicology | ROBOT | |
| Research Output Management Plan | ROMP | Descriprion of the process of organising and documenting the diverse range of outputs generated during the research lifecycle. ref1 |
| Research Software Directory | ||
| Resource Description Framework see also: Knowledge Graphs |
RDF | A globally-accepted framework for data and knowledge representation that is intended to be read and interpreted by machines. ref1 |
| Retrieval-Augmented Generation | RAG | A technique that combines retrieval systems (e.g., search engines or databases) with generation models like LLMs. The retrieval system provides relevant context or data, which the generation model then uses to create accurate and context-aware responses. |
| Reusable | Research data should be ready for future research and future processing, making it self-evident that findings can be replicated and that new research effectively builds on already acquired, previous results. ref1 | |
| Scopus | Online bibliographic database ref1 | |
| SCRUM | An agile way of working as a development team that uses time-boxed iterations called sprints to focus on fully executing smaller increments of a larger product. It includes clear bite-sized tasks, regular discussions and collaborative review. It tackles issues such as vague long term goals, poor teamwork and inefficient timespending. | |
| SCRUM Board | The documentation of the tasks in the backlog, tasks in the current sprint, the user stories, the epics and the completed tasks when working in SCRUM. Usually shared and edited through GitHub Projects, Notion or similar tools. | |
| SCRUM Master | A person with the role in the SCRUM method who ensures the team follows the scrum practices and that the backlog, sprint, user stories and epics are clear. | |
| Sprint | A fixed time-box, usually 1-4 weeks, used in the SCRUM method of working. Per sprint, each team member works on selected tasks which they can (likely) finish within the sprint. Each sprint has meetings to plan the sprint, review the finished tasks and reflect to improve productivity. | |
| Sprint Planning | A meeting at the beginning of each sprint where the team selects tasks from the backlog to work on during that sprint. The team will also assign members to each task and discuss how they plan on completing them. | |
| Sprint Review | A meeting at the end of a sprint where the team presents their work and discuss any issues. The goal is to review the completed tasks and adapt the backlog accordingly. This meeting can be combined with the Sprint Retrospective. | |
| Sprint Retrospective | A meeting after the Sprint Review where the team reflects on the process of sprint that was reviewed. It focuses on the aspects of the last sprint that went well or bad, and how the team can improve their work in the next sprint. | |
| Sysrev | Ortec's literature reviewer support and curation documentationn storage system. | |
| Standardization | A process of developing, implementing, and maintaining technical standards to ensure consistency, uniformity, and compatibility across products, processes, or services. | |
| Taxila.nl | ||
| TDM monographs | ||
| Technology Readiness Levels | TRL | TRLs are a method for estimating the maturity of technologies during the acquisition phase of a program. ref1 |
| Template | A thing that is used as a model for producing other similar examples. ref1 | |
| Token | The basic unit of text processed by a language model, which can be a word, part of a word, or even a single character, depending on the model’s tokenizer. | |
| Toxicokinetics synonyms: ADME |
TK | see ADME (these terms are equivalent, although TK is used exclusively for toxic substances) |
| ToxTemp | Template standard to report toxicity test methods ref1 | |
| ToxTempAssistant | ||
| User Story | A simple, clear description of a desired feature or functionality from the perspective of the end user. Typically follows the format: 'As as [user], I want [feature], so that [benefit].'. Each task in the backlog should be contributing to as user story, each user story should be contributing to an epic. | |
| User experience | UX | The experience a user would go through when interacting with a company, its services, and its products. ref1 |
| VEGA QSAR | ||
| VHP4Safety Compound Wiki | ||
| VHP4Safety Glossary | ||
| Web Ontology Language | OWL | RDF standard for making ontologies machine readable. |
| Widget | A small software application that is designed to provide a specific piece of information (such as news, weather, or traffic updates) or a specific function (such as taking notes or controlling another application) on demand. ref1 | |
| WikiPathways | Database of biological pathways ref1 | |
| WikiPathways AOP Portal | ||
| Workflow | An orchestrated and repeatable multi-step process to coordinate multiple tasks and their data dependencies. ref1 | |
| xploreaop | ||
| Zenodo | Research data repository ref1 |
Project
Organizations
| Term | Abbreviation | Definition |
| Amsterdam University Medical Center | Amsterdam UMC | University hospitals cooperation in Amsterdam, Netherlands ref1 |
| Bayer | German multinational pharmaceutical, chemical, and agricultural biotechnology company ref1 | |
| Brunel University London | University in London, UK ref1 | |
| Certara | Company in St Louis, United States ref1 | |
| Charles River Laboratories | Major US biomedical company ref1 | |
| Cosmetics Europe | Organization in Brussels, Belgium ref1 | |
| DTU National Food Institute | ||
| Dutch Burns Foundation | ||
| Dutch Kidney Foundation | Kidney research funding body based in Bussum, Netherlands ref1 | |
| Dutch Research Council | NWO | National research council of the Netherlands ref1 |
| ELIXIR | European life-sciences infrastructure ref1 | |
| Erasmus MC | Hospital in Rotterdam, Netherlands ref1 | |
| European Commission | EC | Executive branch of the European Union ref1 |
| European Medicines Agency | EMA | An agency of the European Union (EU) in charge of the evaluation and supervision of pharmaceutical products. ref1 |
| College ter Beoordeling van Geneesmiddelen | CBG | Medicines Evaluation Board. The Dutch authority that evaluates and regulates medicines for human and veterinary use. ref1 |
| nan | ZIN | |
| College voor de toelating van gewasbeschermingsmiddelen en biociden | CTBG | Dutch Board for the Authorisation of Plant Protection Products and Biocides. ref1 |
| European Centre for Ecotoxicology and Toxicology of Chemicals | ECTOC | The European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) is a scientific, non-profit, non-commercial and non-governmental association. Established in 1978, ECETOC's main objective is to identify, evaluate, and through such knowledge help industry to minimise any potentially adverse effects on human health and the environment that may arise from the manufacture and use of chemicals, biomaterials and pharmaceuticals. ref1 |
| Institute for Risk Assessment Sciences | IRAS | Universiteit Utrecht ref1 |
| Joint Research Centre | JRC | European Commission's science and knowledge service ref1 |
| KWR Water Research Institute | ||
| Lakefront Biotherapeutics | ||
| Leiden University | Public university in the Netherlands ref1 | |
| Maastricht University | UM | Public university in Maastricht ref1 |
| Ministry of Agriculture, Nature and Food Quality | LNV | Agriculture ministry of Netherlands ref1 |
| National Institute for Public Health and the Environment | RIVM | Dutch research institute ref1 |
| National Institutes of Health | NIH | US government medical research agency ref1 |
| National Research Data Infrastructure | NFDI | ref1 |
| Organisation for Economic Co-operation and Development | OECD | Intergovernmental economic organization ref1 |
| ORTEC | ||
| Shell | British multinational oil and gas company ref1 | |
| Statistics Netherlands | CBS | Netherlands' principal government institution in charge of statistics and census data ref1 |
| Stichting Proefdiervrij | Organization ref1 | |
| TNO | Dutch organisation ref1 | |
| Unilever | British multinational consumer goods company ref1 | |
| University Medical Center Utrecht | UMC Utrecht | Academic hospital in Utrecht, Netherlands ref1 |
| University of Applied Sciences Utrecht | HU | University of applied sciences in Utrecht, the Netherlands ref1 |
| University of Konstanz | University in Konstanz, Germany ref1 | |
| Utrecht University | UU | University in the Netherlands ref1 |
| Vrije Universiteit Amsterdam | VU | University in Amsterdam, Netherlands ref1 |
| Wageningen University & Research | WUR | University in the Netherlands ref1 |
| World Health Organization | WHO | United Nations agency concerned with international public health ref1 |
For More Information on VHP4Safety
Please see the links below for various elements of the VHP4Safety Project.
- Main project website: vhp4safety.nl
- The Virtual Human Platform: platform.vhp4safety.nl
- The tool catalog: cloud.vhp4safety.nl
- The documentation website: docs.vhp4safety.nl
References
- Michie, S., West, R. & Hastings, J. Creating ontological definitions for use in science. Qeios (2022). DOI: 10.32388/YGIF9B.2.
Funding
VHP4Safety – the Virtual Human Platform for safety assessment project NWA 1292.19.272 is part of the NWA research program ‘Research along Routes by Consortia (ORC)’, which is funded by the Netherlands Organization for Scientific Research (NWO). The project started on June 1, 2021 with a budget of over 10 million Euros and will last for the duration of 5 years.