transition glossary from qiime2/dev-docs, create back-matter section

book/_toc.yml

@@ -66,4 +66,6 @@ parts:
 
   - caption: "Back Matter"
     chapters:
-      - file: bibliography
+      - file: back-matter/glossary
+      - file: back-matter/bibliography
+      - file: back-matter/genindex

book/back-matter/genindex.md

@@ -0,0 +1 @@
+# Index

book/back-matter/glossary.md

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+# Glossary
+
+```{glossary}
+Action
+  A generic term to describe a concrete {term}`method`, {term}`visualizer`, or {term}`pipeline`.
+  Actions accept parameters and/or files ({term}`artifacts <Artifact>` or {term}`metadata`) as input, and generate some kind of 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.
+
+Deployment
+  An installation of QIIME 2 as well as zero-or-more {term}`interfaces <Interface>` and {term}`plugins <Plugin>`.
+  The collection of interfaces and plugins in a deployment can be defined by a {term}`distribution` of QIIME 2.
+
+Directory Format
+  A string that represents a particular layout of files and or directories as well as how their contents will be structured.
+
+Distribution
+  A collection of QIIME 2 plugins that are designed to be installed together.
+  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 Shotgun 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`.
+
+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 {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 <Artifact>` and {term}`parameters <Parameter>` 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) <Artifact>` or {term}`visualization(s) <Visualization>`.
+
+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 <Artifact>` and {term}`parameters <Parameter>` as {term}`input`, and produces one or more QIIME 2 {term}`artifacts <Artifact>` and/or {term}`visualizations <Visualization>` as {term}`output`.
+
+Plugin
+  A discrete module that registers some form of additional functionality with the {term}`framework`, including new {term}`methods <Method>`, {term}`visualizers <Visualizer>`, {term}`formats <Format>`, or {term}`transformers <Transformer>`.
+
+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.
+
+Result
+  A generic term for either a {term}`Visualization` or an {term}`Artifact`.
+
+Provenance
+  Data describing how an analysis was performed, captured automatically whenever users perform a QIIME 2 {term}`Action`.
+  Provenance information describes the host system, the computing environment, Actions performed, parameters passed, primary sources cited, and more.
+
+Semantic Type
+  A {term}`type` that is used to classify {term}`artifacts<Artifact>` and how they can be used.
+  These types may be extended by {term}`plugins<Plugin>`.
+
+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 <Artifact>` and {term}`parameters <Parameter>` as {term}`input`, and produces exactly one {term}`visualization` as {term}`output`.
+```