Glossary

Glossary#

action#: A general term for a method, a visualizer, or a pipeline. Actions are always defined by QIIME 2 plugins.
artifact#: Artifacts are QIIME 2 results that are generally considered to represent intermediate data in an analysis, meaning that an artifact is generated by QIIME 2 and intended to be consumed by QIIME 2 (rather than by a human). Artifacts can be generated either by importing data into QIIME 2 or as out from a QIIME 2 action. When written to file, artifacts typically have the extension qza. Artifacts can be provided as input to QIIME 2 actions or exported from QIIME 2 for use with other software.
breaking change#: A breaking change is a change to how a program works (for example, a QIIME 2 plugin or interface) that introduces an incompatibility with earlier versions of the program. This will generally require that users make some modification to how they were using some aspect of a system. For example, if a plugin method added a new required input in version 2, that would be a breaking change with respect to version 1: calling the method without that new parameter would fail in version 2, but would have succeeded with version 1. This may also be called a backward incompatible change or an API change.
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)
Deployment#: An installation of QIIME 2 as well as zero-or-more interfaces and plugins. The collection of interfaces and plugins in a deployment can be defined by a distribution of QIIME 2.
Distribution#: A collection of QIIME 2 plugins that are installed together through a single 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 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 deployment.
DRY#: An acronym of Don’t Repeat Yourself, and a critical principle of software engineering and equally applicable in research data management. For more information on DRY and software engineering in general, see Thomas and Hunt [5]. The Thomas and Hunt [5] content on DRY is available in a free example chapter here.
epoch#: An identifier referencing a release cycle of QIIME 2. Epochs identifiers represent dates (e.g., 2024.10 references the release cycle initiated in October of 2024).
Interface#: The layer of QIIME 2 that users (either humans or other computer software) interact with. q2cli and the Python 3 API are the two interfaces covered in Using QIIME 2. Other interfaces include Galaxy (see https://cancer.usegalaxy.org) and Adagio (more info on that soon!).
method#: A type of QIIME 2 action that takes one or more artifacts or parameters as input, and produces one or more artifacts as output. For example, the filter-features action in the q2-feature-table plugin is a method.
pipeline#: A type of QIIME 2 action that typically combines two or more other actions. A pipeline takes one or more artifacts or parameters as input, and produces one or more results (artifacts and/or visualizations) as output. For example, the core-metrics action in the q2-diversity plugin is a pipeline.
plugin#: A plugin provides analysis functionality in the form of actions. All plugins can be accessed through all interfaces. Plugins can be developed and distributed by anyone. As of this writing, a collection of plugins that are installed together are referred to as a distribution. Additional plugins can be installed, and the primary resource enabling discovery of additional plugins is the QIIME 2 Library.
Python 3 API#: QIIME 2’s Application Programmer Interface. This allows advanced users to access all QIIME 2 analytic functionality directly in Python. This can be very convenient for developing tools that use QIIME 2 as a component, or for performing data analysis without writing intermediary data artifacts to disk unless you specifically want to.
q2cli#: q2cli is the original (and still primary, as of March 2024) command line interface for QIIME 2.
qza#: An acronym for **Q*IIME Zipped Artifact. See artifact.
qzv#: An acronym for **Q*IIME Zipped Visualization. See visualization.
result#: A general term for an artifact or a visualization.
sample#: An individual unit of study in an analysis.
visualizer#: A type of QIIME 2 action that takes one or more artifacts or parameters as input, and produces exactly one visualization as output. For example, the summarize action in the q2-feature-table plugin is a visualizer.
visualization#: Visualizations are QIIME 2 results that represent terminal output in an analysis, meaning that they are generated by QIIME 2 and intended to be consumed by a human (as opposed to being consumed by QIIME 2 or other software). Visualizations can only be generated by QIIME 2 visualizers or pipelines. When written to file, visualizations typically have the extension qzv. See How to view Visualizations for information on how to view Visualizations.