Glossary

This page serves as a reference for other documents, we don’t recommend reading it without the accompanying context provided by the rest of this documentation.

Action

A generic term to describe a concrete method, visualizer, or pipeline. Actions accept parameters and/or files (artifacts or metadata) as input, and generate some kind of output.

Archive

The directory structure of a QIIME 2 Result. Contains at least a root directory (named by UUID) and a VERSION file within that directory.

Artifact

A QIIME 2 Result that countains data to operate on.

Deployment

An installation of QIIME 2 as well as zero-or-more interfaces and plugins.

Directory Format

A string that represents a particular layout of files and or directories as well as how their contents will be structured.

Format

A string that represents a particular file format.

Framework

The engine of orchestration that enables QIIME 2 to function together as a cohesive unit.

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 action. Can be an artifact or metadata.

Interface

A user-interface responsible for coordinating user-specified intent into 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 artifacts and parameters as input, and produces one or more QIIME 2 artifacts as output.

Output

Objects returned by an action. Can be artifact(s) or visualization(s).

Parameter

A value that alters the behavior of an 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 artifacts and parameters as input, and produces one or more QIIME 2 artifacts and/or visualizations as output.

Plugin

A discrete module that registers some form of additional functionality with the framework, including new methods, visualizers, formats, or transformers.

Primitive Type

A type that is used to communicate parameters to an interface. These are predefined by the framework and cannot be extended.

Result

A generic term for either a Visualization or an Artifact.

Semantic Type

A type that is used to classify artifacts and how they can be used. These types may be extended by plugins.

Transformer

A function registered on the framework capable of converting data in one format into data of another format.

Type

A name that is used to classify how a piece of data may be used. Most commonly used to refer to Semantic Type, but can also refer to Primitive Type and Visualization (Type).

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 or this wikipedia entry for details.

View

A particular representation of data. This includes on-disk formats and in-memory data structures (objects).

Visualization

A QIIME 2 Result that contains an interactive visualization.

Visualization (Type)

The type of a 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 artifacts and parameters as input, and produces exactly one visualization as output.