DeltaBreed small updates

[ci skip]

This build is based on
8609ef8.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/8609ef849b6801b17c55efffc7885e50849e0315/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/10427088197

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/58c3f231058f92728f1c67af88dc26730ecca656/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/8609ef849b6801b17c55efffc7885e50849e0315/>.
 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
-[`58c3f231058f92728f1c67af88dc26730ecca656`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/58c3f231058f92728f1c67af88dc26730ecca656).
+[`8609ef849b6801b17c55efffc7885e50849e0315`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/8609ef849b6801b17c55efffc7885e50849e0315).

index.html

@@ -81,7 +81,7 @@
   <meta name="author" content="Stephan Weise" />
   <meta name="author" content="Shawn C. Yarnes" />
   <meta name="author" content="The BrAPI Consortium" />
-  <meta name="dcterms.date" content="2024-08-14" />
+  <meta name="dcterms.date" content="2024-08-16" />
   <meta name="keywords" content="brapi, breeding, api, standards, community" />
   <title>BrAPI Success Stories</title>
   <style>
@@ -126,11 +126,11 @@
   <meta name="citation_title" content="BrAPI Success Stories" />
   <meta property="og:title" content="BrAPI Success Stories" />
   <meta property="twitter:title" content="BrAPI Success Stories" />
-  <meta name="dc.date" content="2024-08-14" />
-  <meta name="citation_publication_date" content="2024-08-14" />
-  <meta property="article:published_time" content="2024-08-14" />
-  <meta name="dc.modified" content="2024-08-14T16:34:52+00:00" />
-  <meta property="article:modified_time" content="2024-08-14T16:34:52+00:00" />
+  <meta name="dc.date" content="2024-08-16" />
+  <meta name="citation_publication_date" content="2024-08-16" />
+  <meta property="article:published_time" content="2024-08-16" />
+  <meta name="dc.modified" content="2024-08-16T22:34:23+00:00" />
+  <meta property="article:modified_time" content="2024-08-16T22:34:23+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -368,9 +368,9 @@
   <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/58c3f231058f92728f1c67af88dc26730ecca656/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/58c3f231058f92728f1c67af88dc26730ecca656/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/58c3f231058f92728f1c67af88dc26730ecca656/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8609ef849b6801b17c55efffc7885e50849e0315/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8609ef849b6801b17c55efffc7885e50849e0315/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8609ef849b6801b17c55efffc7885e50849e0315/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" />
@@ -387,10 +387,10 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/58c3f231058f92728f1c67af88dc26730ecca656/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/8609ef849b6801b17c55efffc7885e50849e0315/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/58c3f231058f92728f1c67af88dc26730ecca656">plantbreeding/BrAPI-Manuscript2@58c3f23</a>
-on August 14, 2024.
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/8609ef849b6801b17c55efffc7885e50849e0315">plantbreeding/BrAPI-Manuscript2@8609ef8</a>
+on August 16, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
@@ -1289,10 +1289,8 @@ <h4 id="breedbase">Breedbase</h4>
 <p>The BrAPI interface is crucial for Breedbase. Breedbase uses BrAPI to connect with the data collection apps, other projects such as CLIMMOB<span class="citation" data-cites="LCpCba21"><sup><a href="#ref-LCpCba21" role="doc-biblioref">6</a></sup></span>, and native BrAPPs built into the Breedbase webpage. Users also appreciate the ability to connect to Breedbase instances using packages such as <a href="https://icarda-git.github.io/QBMS">QBMS</a><span class="citation" data-cites="a9uPTJgO"><sup><a href="#ref-a9uPTJgO" role="doc-biblioref">44</a></sup></span> for data import into R for custom analyses. The Breedbase team has been part of the BrAPI community since its inception and has continuously adopted and contributed to the BrAPI standard.</p>
 <h4 id="deltabreed">DeltaBreed</h4>
 <!-- Shawn Y.-->
-<p><a href="https://app.breedinginsight.net/">DeltaBreed</a> is an open-source breeding data management system designed and developed by <a href="https://breedinginsight.org/">Breeding Insight</a> to support U.S. Department of Agriculture - Agricultural Research Service (USDA-ARS) specialty crop and animal breeders. DeltaBreed differs from other related systems in that is customizable to small breeding teams and generalized enough to support the workflows of diverse niche species. DeltaBreed is a unified system that connects a variety of BrAPI applications (see list below). BrAPI integration allows the complexity underlying interoperability to be hidden, shielding users from multifactorial differences between various applications. DeltaBreed, adhering to the BrAPI model, establishes data standards and validations for users and provides a singular framework for data management and user training.</p>
-<p>DeltaBreed users need not be aware of BrAPI or the specifics of underlying applications but will notice that BrAPI interoperability reduces the need for human-mediated file transfers and data manipulation. Field Book users, for example, can connect to their DeltaBreed program, authenticate, and pull studies and traits directly from DeltaBreed to Field Book on their data collection device. The subsequent step of pushing observations from Field Book to DeltaBreed is straightforward via BrAPI, but is pending implementation until some enhancements can be made to ensure quality data is being transferred. These enhancements include improved data transaction handling, differentiation of intentional and inadvertent repeated measures, and a data staging area is implemented for quality control.</p>
-<!-- Submission is expected July 2024. We may need to trim this aspirational list down to reality in final edits.-->
-<p>DeltaBreed is integrated with at least eight other BrAPI community tools, and plans are in place to integrate with several more as the project continues. There is a BrAPI enabled connection, either in development or production, with all of the following tools: <a href="https://test-server.brapi.org/brapi/v2/">BrAPI Java Test Server</a>, <a href="https://breedbase.org/">BreedBase</a>, <a href="https://play.google.com/store/apps/details?id=com.fieldbook.tracker">Field Book</a>, <a href="https://gigwa.southgreen.fr/gigwa/">Gigwa</a>, <a href="https://icarda-git.github.io/QBMS">QBMS</a>, <a href="https://github.com/AparicioJohan/MrBeanApp">Mr Bean</a>, <a href="https://helium.hutton.ac.uk/#/">Helium</a> and the <a href="https://github.com/solgenomics/BrAPI-Pedigree-Viewer">Pedigree Viewer</a> BrAPP.</p>
+<p><a href="https://app.breedinginsight.net/">DeltaBreed</a> is an open-source breeding data management system designed and developed by <a href="https://breedinginsight.org/">Breeding Insight</a> to support U.S. Department of Agriculture - Agricultural Research Service (USDA-ARS) specialty crop and animal breeders. DeltaBreed differs from other related systems in that it is customizable to small breeding teams and generalized enough to support the workflows of diverse species. DeltaBreed is a unified system that connects a variety of BrAPI applications. BrAPI integration allows the complexity underlying interoperability to be hidden, shielding users from multifactorial differences between various applications. DeltaBreed, adhering to the BrAPI model, establishes data standards and validations for users and provides a singular framework for data management and user training. BrAPI enabled connections are being used with all of the following tools: <a href="https://test-server.brapi.org/brapi/v2/">BrAPI Java Test Server</a>, <a href="https://breedbase.org/">BreedBase</a>, <a href="https://play.google.com/store/apps/details?id=com.fieldbook.tracker">Field Book</a>, <a href="https://gigwa.southgreen.fr/gigwa/">Gigwa</a>, <a href="https://icarda-git.github.io/QBMS">QBMS</a>, <a href="https://github.com/AparicioJohan/MrBeanApp">Mr Bean</a>, <a href="https://helium.hutton.ac.uk/#/">Helium</a> and the <a href="https://github.com/solgenomics/BrAPI-Pedigree-Viewer">Pedigree Viewer</a> BrAPP.</p>
+<p>DeltaBreed users may not be aware of BrAPI or the specifics of underlying tools, but will notice that BrAPI interoperability reduces the need for human-mediated file transfers and data manipulation. Field Book users, for example, can connect to their DeltaBreed program, authenticate, and pull studies and observation variables directly from DeltaBreed to Field Book on their data collection device. The subsequent step of pushing observations from Field Book to DeltaBreed is straightforward via BrAPI, but is pending implementation until data quality validations are put in place; these include improved data transaction handling and differentiation of intentional and inadvertent repeated measures.</p>
 <h4 id="faidare">FAIDARE</h4>
 <!-- Cyril P, first draft-->
 <p><a href="https://urgi.versailles.inrae.fr/faidare/">FAIDARE</a><span class="citation" data-cites="HC5no0wP"><sup><a href="#ref-HC5no0wP" role="doc-biblioref">45</a></sup></span> is a data discovery portal providing a biologist-friendly search system over a global federation of 40 plant research databases.