Glossary
========

The following is a list of definitions used in vantage6.

**A**

-  **Algorithm**: a piece of code executed at the node to perform a specific task.
   The most well-known usage is to compute an analysis on the local date, but algorithm
   functions are also used to extract data from the node data sources and to preprocess
   the data.
-  **Algorithm store**: A repository of algorithms, which can be coupled to specific
   collaborations or all collaborations on a vantage6 HQ.
-  **API**: Application Programming Interface, a set of routines, protocols, and tools
   for building software applications.
-  **Authentication**: the process of verifying the identity of a user.
-  **Authorization**: the process of verifying the permissions of a user.
-  **Autonomy:** the ability of a party to be in charge of the control and management of
   its own data.

**C**

-  **Central function**: The orchestration part of an algorithm that coordinates and
   aggregates results from partial functions.
-  **Child container**: A container created by an algorithm container to perform
   subtasks, typically a *federated function*
-  **Client**: A vantage6 user or application that communicates with the
   vantage6 hub.
-  **Collaboration**: an agreement between two or more parties to participate in a
   project (i.e., to answer a research question).
-  **Computation task**: A task that performs a computation on a DataFrame.
-  **Container**: A lightweight, standalone, executable package of software that
   includes everything needed to run it.

**D**

-  **Dataframe**: A standardized representation of data in a session that can be used
   for computation tasks.
-  **Data extraction task**: A task that extracts data from a database.
   This data can be used for computation tasks (e.g., a preprocessing task or a
   computation task).
-  **Data Station**: A vantage6 *node* that has access to the local data.
-  **Distributed learning**: see *Federated Learning* and *Federated Analytics*
-  **Docker:** a platform that uses operating system virtualization to deliver software
   in packages called *containers*. It is worth noting that although they are often
   confused, `Docker containers are not virtual machines <https://www.docker.com/blog/containers-are-not-vms/>`__.
-  **Docker registry**: A repository of *images*. In vantage6, both algorithms and
   the infrastructure itself are stored as *images* in the *Docker registry*. Images
   are used to create *containers*.


**E**

-  **End-to-end encryption**: A method of encoding data so that it can only be decoded
   by the intended recipient. In vantage6, end-to-end encryption is used to encrypt
   data in transit between two nodes or between a node and a client.

**F**

-  **FAIR data**: data that are Findable, Accessible, Interoperable, and
   Reusable. For more information, see `the original
   paper <https://www.nature.com/articles/sdata201618.pdf?origin=ppub>`__.
-  **Federated analytics**: an approach for analyzing data that are
   spread across different parties using traditional statistical methods. The main
   idea is that parties run computations on their local data, yielding aggregated
   parameters. These are then shared to generate a global (statistical) model.
-  **Federated learning**: an approach for analyzing data that are
   spread across different parties using machine learning methods. The main
   idea is that parties run computations on their local data, yielding
   aggregated parameters. These are then shared to generate a global (statistical)
   model.
-  **Federated function**: A function that is executed on the local data of a party.
   It is a part of a *federated analytics* or *federated learning* algorithm.

**H**

-  **Heterogeneity**: the condition in which in a federated learning scenario, parties
   are allowed to have differences in hardware and software (e.g., operating systems).
-  **Horizontally-partitioned data**: data spread across different parties where the
   latter have the same features of different instances (e.g., patients). See also
   vertically-partitioned data.

.. figure:: /images/horizontal_partition.png
   :alt: Horizontally partitioned data
   :align: center

   Horizontally-partitioned data

-  **Horizontal scaling**: the ability of a system to handle an increasing amount of
   requests by creating more instances of itself.
-  **HQ**: Public access point of the vantage6 infrastructure. Contains at
   least the **vantage6-hq** application. Optional components such as RabbitMQ message
   broker and Prometheus monitoring can be made available in the same deployment.
-  **Headquarters**: see *HQ*
-  **Hub**: All central components of the vantage6 infrastructure. Together with the
   nodes, it forms the vantage6 network. The Hub always contains the vantage6 HQ
   application and an authentication service. It may also contain other components,
   such as the algorithm store and the user interface.

**I**

- **Image** (as in *container* image). A blueprint for a *container*, which can be
  stored in an *image registry* (e.g. a *Docker registry*).

**J**

-  **JWT Token**: A JSON Web Token used for authentication and authorization in the
   system.

**K**

- **Kubernetes**: An open-source system for automating deployment, scaling, and
  operations of application containers across clusters of hosts. Vantage6 uses
  Kubernetes' container orchestration capabilities to deploy the hub and the nodes.

**N**

-  **Node**: vantage6 node application that runs at a **Data Station** which has access
   to the local data.

**M**

-  **Multi-party computation**: an approach to perform analyses across
   different parties by performing operations on encrypted data.

**P**

-  **Partial function**: The federated part of an algorithm that runs on local data
   at nodes.
-  **Party**: an entity that takes part in one (or more) collaborations. In vantage6
   a party is an organization.
-  **Permission scope**: The level of access granted to users for viewing and modifying
   dataframes (personal, organization, or collaboration level).
-  **Preprocessing task**: A task that modifies dataframes by adding or removing
   columns, or filtering rows.
-  **Privacy-enhancing Technology (PET)**: Technologies that enable privacy-preserving
   analyses on federated data. This includes technologies such as differential
   privacy, secure multi-party computation, and federated analytics/learning.
-  **Python**: a high-level general purpose programming language. It
   aims to help programmers write clear, logical code. Vantage6 is mostly
   `written in Python <https://github.com/vantage6/vantage6>`__.

**R**

-  **RSA keys**: Cryptographic keys used for encryption and decryption of data between
   organizations.

**S**

-  **Secure multi-party computation**: see *Multi-party computation*
-  **Session**: A way to prepare a dataset that can be reused in many computation
   tasks, especially useful for large datasets and flexible preprocessing.
-  **Study**: A study is a subgroup of organizations within a collaboration.

**T**

-  **Task**: A task is a request from a client to the vantage6 HQ to execute an
   algorithm. Is is the main unit of work in vantage6.
-  **TOTP (Time-based One-Time Password)**: A form of two-factor authentication where
   users generate time-based codes using an authenticator app.
-  **Two-factor authentication**: A method of authentication that requires two
   forms of identification.

**U**

-  **UI**: User Interface, the web application that allows users to interact with the
   vantage6 hub.

**V**

-  **vantage6**: an infrastructure for executing federated learning analyses. It can
   also be used as a FAIR data station and as a model repository.
-  **Vertically-partitioned data**: data spread across different parties
   where the latter have different features of the same instances (i.e.,
   patients). See also horizontally-partitioned data.

.. figure:: /images/vertical_partition.png
   :alt: Vertically partitioned data
   :align: center

   Vertically partitioned data

**W**

-  **Wrapper**: A library that simplifies and standardizes the interaction between the
   node and algorithm container, handling data reading and writing operations.
-  **Whitelist**: A list of allowed domains, ports, and IP addresses that algorithms
   can access.

.. todo Add references to sections of the docs where to find info on them