updates

[ci skip]

This build is based on
33af47f.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/33af47f71b3fba2a27bd70b3a00e45cf68190776/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8103147174

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/838c21cfb2bae42f8511dd75468c931bea0ed267/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/>.
 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
-[`838c21cfb2bae42f8511dd75468c931bea0ed267`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/838c21cfb2bae42f8511dd75468c931bea0ed267).
+[`33af47f71b3fba2a27bd70b3a00e45cf68190776`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/33af47f71b3fba2a27bd70b3a00e45cf68190776).

index.html

@@ -65,8 +65,8 @@
   <meta name="dc.date" content="2024-02-29" />
   <meta name="citation_publication_date" content="2024-02-29" />
   <meta property="article:published_time" content="2024-02-29" />
-  <meta name="dc.modified" content="2024-02-29T21:21:31+00:00" />
-  <meta property="article:modified_time" content="2024-02-29T21:21:31+00:00" />
+  <meta name="dc.modified" content="2024-02-29T22:00:04+00:00" />
+  <meta property="article:modified_time" content="2024-02-29T22:00:04+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -117,9 +117,9 @@
   <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/838c21cfb2bae42f8511dd75468c931bea0ed267/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/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" />
@@ -136,9 +136,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/838c21cfb2bae42f8511dd75468c931bea0ed267">plantbreeding/BrAPI-Manuscript2@838c21c</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/33af47f71b3fba2a27bd70b3a00e45cf68190776">plantbreeding/BrAPI-Manuscript2@33af47f</a>
 on February 29, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -380,7 +380,7 @@ <h4 id="breedbase">Breedbase</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p>Since the inception of BrAPI in 2014, the Breedbase group has been a heavy contributor to the BrAPI community.</p>
 <h4 id="bims">BIMS</h4>
-<p>BIMS (Breeding Information Management System) [https://doi.org/10.1093/database/baab054] is a free, secure, and online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data. BIMS enables individual breeders to have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving for their germplasm, phenotype, genotype, and image data. BIMS is currently implemented in five community databases, the Genome Database for Rosaceae [https://doi.org/10.1093/nar/gky1000], CottonGEN [https://doi.org/10.3390/plants10122805], the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, <a href="https://breedwithbims.org" class="uri">https://breedwithbims.org</a>. BIMS in these five community databases enables individual breeders to import publicly available data so that they can utilize public data in their breeding program. BIMS utilizes the Android App Field Book, enabling seamless data transfer between BIMS and the Field Book App through either files or BrAPI. Data transfer through BrAPI between BIMS and other resources such as BreedBase, GIGWA, and Breeder Genomics Hub is also on the way.</p>
+<p>BIMS (Breeding Information Management System) <span class="citation" data-cites="ArPSsaJQ">[<a href="#ref-ArPSsaJQ" role="doc-biblioref">2</a>]</span> is a free, secure, and online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data. BIMS enables individual breeders to have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving for their germplasm, phenotype, genotype, and image data. BIMS is currently implemented in five community databases, the Genome Database for Rosaceae <span class="citation" data-cites="eaDrNpsp">[<a href="#ref-eaDrNpsp" role="doc-biblioref">3</a>]</span>, CottonGEN <span class="citation" data-cites="dcg0274X">[<a href="#ref-dcg0274X" role="doc-biblioref">4</a>]</span>, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, <a href="https://breedwithbims.org" class="uri">https://breedwithbims.org</a>. BIMS in these five community databases enables individual breeders to import publicly available data so that they can utilize public data in their breeding program. BIMS utilizes the Android App Field Book, enabling seamless data transfer between BIMS and the Field Book App through either files or BrAPI. Data transfer through BrAPI between BIMS and other resources such as BreedBase, GIGWA, and Breeder Genomics Hub is also on the way.</p>
 <h4 id="germinate">Germinate</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p>Germinate is a combination breeding database and germplasm management database.</p>
@@ -501,6 +501,15 @@ <h2 class="page_break_before" id="references">References</h2>
 <div id="ref-QfGEJ6km" class="csl-entry" role="doc-biblioentry">
 <div class="csl-left-margin">1. </div><div class="csl-right-inline"><strong>BrAPI—an application programming interface for plant breeding applications</strong> <div class="csl-block">Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar E Benites-Alfaro, Clay Birkett, Viana C Calaminos, Pierre Carceller, Guillaume Cornut, … </div> <em>Bioinformatics</em> (2019-03-23) <a href="https://doi.org/gjgxxr">https://doi.org/gjgxxr</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/bioinformatics/btz190">10.1093/bioinformatics/btz190</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30903186">30903186</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6792114">PMC6792114</a></div></div>
 </div>
+<div id="ref-ArPSsaJQ" class="csl-entry" role="doc-biblioentry">
+<div class="csl-left-margin">2. </div><div class="csl-right-inline"><strong>The Breeding Information Management System (BIMS): an online resource for crop breeding</strong> <div class="csl-block">Sook Jung, Taein Lee, Ksenija Gasic, BTodd Campbell, Jing Yu, Jodi Humann, Sushan Ru, Daniel Edge-Garza, Heidi Hough, Dorrie Main</div> <em>Database</em> (2021-01-01) <a href="https://doi.org/gtj95x">https://doi.org/gtj95x</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/database/baab054">10.1093/database/baab054</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34415997">34415997</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8378516">PMC8378516</a></div></div>
+</div>
+<div id="ref-eaDrNpsp" class="csl-entry" role="doc-biblioentry">
+<div class="csl-left-margin">3. </div><div class="csl-right-inline"><strong>15 years of GDR: New data and functionality in the Genome Database for Rosaceae</strong> <div class="csl-block">Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P Ficklin, Ksenija Gasic, Kristin Scott, … Dorrie Main</div> <em>Nucleic Acids Research</em> (2018-10-24) <a href="https://doi.org/gjqq8v">https://doi.org/gjqq8v</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/nar/gky1000">10.1093/nar/gky1000</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30357347">30357347</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324069">PMC6324069</a></div></div>
+</div>
+<div id="ref-dcg0274X" class="csl-entry" role="doc-biblioentry">
+<div class="csl-left-margin">4. </div><div class="csl-right-inline"><strong>CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research</strong> <div class="csl-block">Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, … Dorrie Main</div> <em>Plants</em> (2021-12-18) <a href="https://doi.org/gqqwfm">https://doi.org/gqqwfm</a> <div class="csl-block">DOI: <a href="https://doi.org/10.3390/plants10122805">10.3390/plants10122805</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34961276">34961276</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8705096">PMC8705096</a></div></div>
+</div>
 </div>
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