glossary

VHP4Safety Glossary

This work is licensed under the CC-BY 4.0 International.

This VHP4Safety Glossary ontology is collected by (in alphabetical order) Ozan Çınar, Marvin Martens, Egon Willighagen, and others from the VHP4Safety project.

DEVELOPMENT VERSION

This glossary is under development. For example, many definitions do not meet the community standards yet [1].

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.

Toxicology in General

Term Abbreviation Definition
3 Rs Principle 3Rs Replacement, Reduction, and Refinement. Used in the context of performing more humane animal research.
Benchmark dose BMD See Benchmark dose modeling
Benchmark dose modeling 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 anin vitrotest system.
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.
Developmental and Reproductive Toxicology DART
Developmental Neurotoxicity DNT
(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.
induced Embryonic 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.
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.
Monte Carlo Risk Assessment MCRA See Monte Carlo Risk Assessment calculation model.
Monte Carlo Risk Assessment calculation model 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.
New Approach Methodology NAM A collection of various methods (e.g., high-throughput screening and high-content methods) in a wide set of contexts includingin chemicoandin vitroto 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
Non-Animal 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
High Throughput Screening HTS
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.
Read accross 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.
Teratology Scientific field that studies the causes, mechanisms, and classes of congenital malformations in animals and plants. ref1
nan NOEL
Absorption, Distribution, Metabolism, and Excretion ADME Absorption, distribution, metabolism, and excretion of a substance (toxic or not) in a living organism, following exposure to this substance
Term Abbreviation Definition
Apical Endpoint
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 An agency of the European Union which manages the technical and administrative aspects of the implementation of the European Union regulation called Registration, Evaluation, Authorisation and Restriction of Chemicals. ref1
European Food Safety Authority EFSA Legislator
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).
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.
Integrated Approaches to Testing and Assessment IATA
Mode of Action MoA
The legislation of 'Registration, Evaluation, Authorisation and Restriction of Chemicals' REACH Regulation (EC) No 1907/2006 of the European Parliament and of the Council concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH). ref1
Risk Assessment The process of assessing human health risks in a historic, current or emerging exposure scenario for which a concern has risen.
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.
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
Bioactivity The affinity and/or potency of a compound for a protein target.
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.
Term Abbreviation Definition
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
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.
Kubernetes K8s A computer tool to orchesterize and manage Docker containers.
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
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.
Strato An internet hosting service provider that supplies the servers where the virtual platform is built. ref1
VHP server 1 The server provided by Strato where the Docker containers used in the project are deployed.
VHP server 2 The server provided by Strato where the Kubernetes structure is formed for orchestration of the Docker containers on VHP server 1.
VHP server 3 The server provided by Strato that is used for experimentation, learning, and testing the work that is carried out on VHP servers 1 and 2.
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.
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
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.
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 teammember to be completed before the end of that sprint.
Catalog A systemic collection of items of the same type. ref1
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.
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.
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.
Explainability The ability to interpret and understand the output of an LLM, including why certain predictions or answers were generated.
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.
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
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
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
Knowledge Graphs 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
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
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.
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
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
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
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
Pharmacokinetics PK see ADME (these terms are equivalent)
Physiologically based biokinetic model PBBK see PBPK model (these terms are equivalent)
Physiologically based kinetic model PBK model see PBPK model (these terms are equivalent)
Physiologically based pharmacokinetic model PBPK Mechanistic representation of ADME processes for a chemical in a living organism, based on physiological and chemical properties
Physiologically based toxicokinetic model PBTK see PBPK model (these terms are equivalent)
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.
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.
Research Output Management Plan ROMP Descriprion of the process of organising and documenting the diverse range of outputs generated during the research lifecycle. 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.
Resource Description Framework RDF A globally-accepted framework for data and knowledge representation that is intended to be read and interpreted by machines. ref1
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
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 teammember 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.
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 TK see ADME (these terms are equivalent, although TK is used exclusively for toxic substances)
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
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
Workflow An orchestrated and repeatable multi-step process to coordinate multiple tasks and their data dependencies. ref1
Standardization A process of developing, implementing, and maintaining technical standards to ensure consistency, uniformity, and compatibility across products, processes, or services.
Term Abbreviation Definition
Research Line RL Formal structure within a project to reach some goal.
Research Line 1 RL1 Building the Virtual Human Platform.
Research Line 2 RL2 Feeding the Virtual Human Platform.
Research Line 3 RL3 Implementing the Virtual Human Platform.
Stakeholder A person or a group of people who hold(s) a stake and/or can influence decision-making on a specific issue.
Task Force TF Cross work package effort to reach some goal.
Work Package WP Formal structure within a project to reach some goal.
Work Package 1.1 WP1.1 Building the ICT infrastructure for the VHP: objectives to develop the technical infrastructure, setting up a predictive platform, developing analysis workflows, making services and data available and interoperable.
Work Package 1.2 WP1.2 In silico toxicokinetics: objectives to define parameters required for PBPK modelling, developing PBK models and providing guidance forin vitrotoin vivoextrapolations.
Work Package 1.3 WP1.3 Computational toxicodynamics: objectives to develop QSAR and MIE prediction models, develop qAOPs, testing the platform and generating safety estimates.
Work Package 2.1 WP2.1 In vitromodels to provide toxicokinetics & toxicodynamics parameters: objectives to verifyin vitromodels for ADME and local toxicity, obtaining parameters for PBK modelling, test chemicals on iPSC models.
Work Package 2.2 WP2.2 Disease state - Case study chronic kidney disease: objectives to identify critical physiological pathways, develop AOP networks, test toxicity of selected drugs, and assess the safety of selected drugs.
Work Package 2.3 WP2.3 Life course exposure - Case study neurodegenerative disease and life course exposure to chemicals: objectives to identify critical physiological pathways, model life time exposure, develop AOP networks, test toxicity and assess the safety of selected chemicals.
Work Package 2.4 WP2.4 Age and gender specific safety - Case study Thyroid mediated developmental neurotoxicity: objectives to collect mechanistic physiological data, determine critical pathways, establish quantitative AOP network, identify gender-specific sentitivities and compounds that discriminate, and assess the safety of compound exposure.
Work Package 3.1 WP3.1 Technology Assessment of VHP: objectives to perform technology assessment, study and analyse the initiation, development and implementation of VHP, and specify performance criteria.
Work Package 3.2 WP3.2 Acceptance of VHP for safety assessment: objectives to position the VHP in the transition to animal-free safety assessment, raise awareness, investigate uncertainties and acceptance of safety assessments.
Work Package 3.3 WP3.3 Training and Education: objectives to promote collaboration, facilitate transferability of methods and models, implementing new teaching modules, promote capacity building and awareness of stakeholders, improve skills regarding risk communication.
Work Package 4 WP4 Project Coordination, Impact and Data Management: objectives to ensure that project objectives are achieved, deliverables are completed, manage overall knowledge utilisation, and provide effective and sustainable data management.
User

Organizations

Term Abbreviation Definition
European Medicines Agency EMA
nan CBG
nan ZIN
nan CTBG
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

References

  1. 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.

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