# Glossary ```{glossary} Action A generic term to describe a {term}`Method`, {term}`Visualizer`, or {term}`Pipeline`. Actions accept parameters and/or {term}`Artifacts ` and/or {term}`Metadata`) as input, and generate one or more {term}`Results ` as output. Archive The directory structure of a QIIME 2 {term}`Result`. Contains *at least* a root directory (named by {term}`UUID`) and a ``VERSION`` file within that directory. Artifact A QIIME 2 {term}`Result` that contains data to operate on. Artifact class A kind of {term}`Artifact` that can exist. This is defined by a plugin developer by associating a {term}`semantic type` with a {term}`directory format` when registering an artifact class. Artifact API See {term}`Python 3 API`. Conda metapackage A metapackage is a package with no files, only metadata. They are typically used to collect several packages together into a single package via dependencies. ([source](https://docs.conda.io/projects/conda-build/en/stable/resources/commands/conda-metapackage.html)) Deployment An installation of QIIME 2 as well as zero-or-more {term}`interfaces ` and {term}`plugins `. The collection of interfaces and plugins in a deployment can be defined by a {term}`distribution` of QIIME 2. Directory Format An object that is a subclass of `qiime2.plugin.DirectoryFormat`. A Directory Format represents a particular layout of a directory that contains files and/or arbitrarily nested sub-directories, and defines how the contents must be structured. Distribution A collection of QIIME 2 plugins that are installed together through a single {term}`conda metapackage`. These are generally grouped by a theme. For example, the *amplicon distribution* provides a collection of plugins for analysis of microbiome amplicon data, while MOSHPIT (previously the *metagenome distribution*) provides a collection of plugins for analysis of microbiome shotgun metagenomics data. When a distribution is installed, that particular installation of QIIME 2 is an example of a {term}`deployment`. DRY An acronym of *Don't Repeat Yourself*, and a critical principle of software engineering. For more information on DRY and software engineering in general, see {cite:t}`pragprog20`. The {cite:t}`pragprog20` content on DRY is available in a [free example chapter here](https://media.pragprog.com/titles/tpp20/dry.pdf). File Format An object which subclasses either `qiime2.plugin.TextFileFormat` or `qiime2.plugin.BinaryFileFormat`. File formats define the particular format of a file, and define a process for validating the format. Format See {term}`file format` and {term}`directory format`. Framework The engine of orchestration that enables QIIME 2 to function together as a cohesive unit. Galaxy [Galaxy](https://usegalaxy.org) is a browser-based graphical interface used to access bioinformatics (and other data science tools) without having to write command line or other code. QIIME 2 provides a Galaxy interface to support access to plugins through a web browser. Identifier A unique value that denotes an individual sample or feature. Identity Distinguishes a piece of data. QIIME 2 does not consider a rename (like UNIX ``mv``) to change identity, however re-running a command, would change identity. Input Data provided to an {term}`action`. Can be an {term}`artifact` or {term}`metadata`. Interface A user-interface responsible for coordinating user-specified intent into {term}`framework`-driven action. Metadata Columnar data for annotating additional values to existing data. Operates along Sample IDs or Feature IDs. Method A method accepts some combination of QIIME 2 {term}`artifacts ` and {term}`parameters ` as {term}`input`, and produces one or more QIIME 2 artifacts as {term}`output`. Output Objects returned by an {term}`action`. Can be {term}`artifact(s) ` or {term}`visualization(s) `. Pairwise sequence alignment 1. (noun) A hypothesis about which positions in a pair of biological sequences (i.e., a DNA, RNA, or protein sequence) were derived from a common ancestral sequence position. 2. (verb) The process of generating a pairwise sequence alignment (noun). For additional detail, see the *Pairwise Sequence Alignment* chapter of [*An Introduction to Applied Bioinformatics*](https://readiab.org) {cite}`iab-2`. Parameter A value that alters the behavior of an {term}`action`. Payload Data that is meant for primary consumption or interpretation (in contrast to *metadata* which may be useful retrospectively, but is not primarily useful). Pipeline A pipeline accepts some combination of QIIME 2 {term}`artifacts ` and {term}`parameters ` as {term}`input`, and produces one or more QIIME 2 {term}`artifacts ` and/or {term}`visualizations ` as {term}`output`. Plugin A discrete module that registers some form of additional functionality with the {term}`framework`, including new {term}`methods `, {term}`visualizers `, {term}`formats `, or {term}`transformers `. Plugin Manager An instance of the `qiime2.sdk.PluginManager` object. This object provides access to all plugins, actions, artifact classes, and transformers that are registered to all plugins in a given {term}`deployment`, and are therefore central to the functioning of interfaces. Primitive Type A {term}`type` that is used to communicate parameters to an {term}`interface`. These are predefined by the {term}`framework` and cannot be extended. Provenance In the context of QIIME 2, provenance or data provenance refers to the history of how a given {term}`result` was generated. Provenance information describes the host system, the computing environment, Actions performed, parameters passed, primary sources cited, and more. Provenance Replay The QIIME 2 functionality that enables new executable code to be generated from an existing QIIME 2 {term}`result's ` {term}`provenance`. For additional detail, refer to {cite}`Keefe2023-oy`. Python 3 API When *the Python 3 API* is referred to in the context of QIIME 2, this refers to the interface that allows users to work with QIIME 2 plugins and actions natively in Python 3 (for example in a Jupyter Notebook environment). This was formerly referred to as the Artifact API. q2cli [q2cli](https://github.com/qiime2/q2cli) is the original (and still primary, as of March 2024) command line interface for QIIME 2. Result A generic term for either a {term}`Visualization` or an {term}`Artifact`. Semantic Type An identifier that is used to describe what some data is intended to represent, and when and where they can be used. When associated with a {term}`directory format`, the combination defines an {term}`artifact class`. These types may be extended by {term}`plugins`. Single-Use Plugin (SUP) A plugin that is intended for one specific use case, such as generating figures for a single manuscript, as opposed to a plugin that is intended for general widespread usage. tl;dr "Too long; didn't read." In other words, a quick summary of the content that follows. Transformer A function registered on the {term}`framework` capable of converting data in one {term}`format` into data of another {term}`format`. Type A term that is used to represent several different ideas in QIIME 2, and which is therefore ambiguous when used on its own. More specific terms are *file type*, *semantic type*, and *data type*. See [](types-of-types) for more information. UUID Universally Unique IDentifier, in the context of QIIME 2, almost certainly refers to a *Version 4* UUID, which is a randomly generated ID. See this [RFC](https://tools.ietf.org/html/rfc4122) or this [wikipedia entry](https://en.wikipedia.org/wiki/Universally_unique_identifier) for details. View A particular representation of data. This includes on-disk formats and in-memory data structures (objects). Visualization A QIIME 2 {term}`Result` that contains an interactive visualization. Visualization (Type) The {term}`type` of a {term}`visualization`. There are no subtyping relations between this type and any other (it is a singleton) and cannot be extended (because it is a singleton). Visualizer A visualizer accepts some combination of QIIME 2 {term}`artifacts ` and {term}`parameters ` as {term}`input`, and produces exactly one {term}`visualization` as {term}`output`. ```