intro wip

[ci skip]

This build is based on
d7f5f15.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/6165102723

README.md

@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/gh-pages) branch hosts the contents of this directory at <https://plantbreeding.github.io/BrAPI-Manuscript2/>.
-The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/3fe174bb696987086eef7951278374563e92521b/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://plantbreeding.github.io/BrAPI-Manuscript2/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`3fe174bb696987086eef7951278374563e92521b`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/3fe174bb696987086eef7951278374563e92521b).
+[`d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc).

index.html

@@ -54,8 +54,8 @@
   <meta name="dc.date" content="2023-09-12" />
   <meta name="citation_publication_date" content="2023-09-12" />
   <meta property="article:published_time" content="2023-09-12" />
-  <meta name="dc.modified" content="2023-09-12T16:00:02+00:00" />
-  <meta property="article:modified_time" content="2023-09-12T16:00:02+00:00" />
+  <meta name="dc.modified" content="2023-09-12T21:36:14+00:00" />
+  <meta property="article:modified_time" content="2023-09-12T21:36:14+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -74,9 +74,9 @@
   <meta name="citation_fulltext_html_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta name="citation_pdf_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3fe174bb696987086eef7951278374563e92521b/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3fe174bb696987086eef7951278374563e92521b/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3fe174bb696987086eef7951278374563e92521b/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -93,9 +93,9 @@ <h1 class="title">BrAPI 2</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3fe174bb696987086eef7951278374563e92521b/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/3fe174bb696987086eef7951278374563e92521b">plantbreeding/BrAPI-Manuscript2@3fe174b</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/d7f5f15a59f46f0de8a83f1d89d9951fcaff83dc">plantbreeding/BrAPI-Manuscript2@d7f5f15</a>
 on September 12, 2023.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -151,15 +151,18 @@ <h2 id="introduction">Introduction</h2>
 <h3 id="how-it-works">How it works</h3>
 <p>An Application Programming Interface (API) is a technical connection between two pieces of software. Just as a Graphical User Interface (GUI) or a Command Line Interface (CLI) allows a human user to interact with a piece of software, an API allows one software application to interact with another. A GUI or CLI might allow a user to input data, read data, and start processes within an application. An API allows one piece of software (sometimes called a client, user agent, or service consumer) to programmatically input data, read data, and start process within another piece of software (sometimes called a server or service provider).</p>
 <p>A Representational State Transfer (REST) web service is a type of API commonly used in today’s modern web infrastructure. REST is a technical architecture that describes the stateless transmission of data between applications. Typically, REST systems are implemented using the standard HTTP protocol that most of the modern internet is built upon. REST implementations also generally use JavaScript Object Notation (JSON) to represent the data being transferred. Both HTTP and JSON are programming language agnostic, very stable, and very flexible. This means BrAPI can be implemented in almost any piece of software, and can solve a wide range of use cases.</p>
+<p>Data repositories and service providers can choose to represent their data as a BrAPI compatible API. By mapping the internal data structures to the standard models, data repositories can easily expose data to the outside world. Similarly, they can accept new data from external sources and automatically map the new data into the existing database. Client application developers can take advantage of this standardization by building tools that can easily integrate with all other BrAPI compatible data repositories. Visualization, reporting, analytics, data collection, and quality control tools can be built once and shared with other organizations following the standards. As the number of BrAPI compatible databases, tools, and organizations grows, so does the value added by implementing the standard into a given application.</p>
 <h3 id="project-updates">Project Updates</h3>
-<p>Over its lifetime, the BrAPI project has grown and changed substantially. The latest stable version of the specification (v2.1) looks vastly different from the original version (v1.0) 51 released in 2017. The total size of the specification has almost quadrupled in that time, going from 51 endpoints documented in v1.0 to 201 endpoints documented in v2.1. Because of this growth, the specification documents were reorganized into four modules: BrAPI-Core, BrAPI-Germplasm, BrAPI-Genotyping, and BrAPI-Phenotyping. Figure <a href="#fig:domains">1</a>1 shows a simplified domain map of the whole BrAPI v2.1 data model, divided into the organizational modules.</p>
+<p>Over its lifetime, the BrAPI project has grown and changed substantially. The latest stable version of the specification (v2.1) looks vastly different from the original version (v1.0) released in 2017. The total size of the specification has almost quadrupled in that time, going from 51 endpoints documented in v1.0 to 201 endpoints documented in v2.1. Because of this growth, the specification documents were reorganized into four modules: BrAPI-Core, BrAPI-Germplasm, BrAPI-Genotyping, and BrAPI-Phenotyping. Figure <a href="#fig:domains">1</a> shows a simplified domain map of the whole BrAPI v2.1 data model, divided into the organizational modules. The early versions of the specification focused on read-only phenotype data, with a small consideration to the other domains. Now the specification has a full representation of most of the major concepts applicable to the breeding process. The new specification is also internally consistent, easier to navigate, and allows for read, write, and update capabilities. None of those qualities were a guarantee for the earlier versions.</p>
 <div id="fig:domains" class="fignos">
 <figure>
-<img src="images/BrAPI_Domains_v2-1_vertical.png" alt="Figure 1: Figure 1: A simplified domain map of the whole BrAPI data model, divided into organizational modules" />
-<figcaption aria-hidden="true"><span>Figure 1:</span> Figure 1: A simplified domain map of the whole BrAPI data model, divided into organizational modules</figcaption>
+<img src="images/BrAPI_Domains_v2-1_vertical.png" alt="Figure 1: A simplified domain map of the whole BrAPI data model, divided into organizational modules. A more detailed Entity Relationship Diagram (ERD) is available on brapi.org." />
+<figcaption aria-hidden="true"><span>Figure 1:</span> A simplified domain map of the whole BrAPI data model, divided into organizational modules. A more detailed Entity Relationship Diagram (ERD) is available on brapi.org.</figcaption>
 </figure>
 </div>
+<p>As the specification has matured, so have the tools, services, and libraries available to the community to work with the specification.</p>
 <h3 id="community-growth">Community Growth</h3>
+<p>Community</p>
 <h2 id="success-stories">Success Stories</h2>
 <p>6+/- success stories highlighting BrAPI usefulness in breeding cycle</p>
 <h3 id="field-book-for-starting-data-collection">Field Book for starting data collection</h3>