updates

[ci skip] This build is based on 838c21c. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/838c21cfb2bae42f8511dd75468c931bea0ed267/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8102754236
plantbreeding · Feb 29, 2024 · 208c847 · 208c847
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diff --git a/manuscript.html b/manuscript.html
@@ -13,6 +13,10 @@
   <meta name="author" content="Cyril Pommier" />
   <meta name="author" content="Becky Smith" />
   <meta name="author" content="Chaney Courtney" />
+  <meta name="author" content="Zachary Miller" />
+  <meta name="author" content="Terry Casstevens" />
+  <meta name="author" content="Sook Jung" />
+  <meta name="author" content="Taein Lee" />
   <meta name="dcterms.date" content="2024-02-29" />
   <meta name="keywords" content="brapi, breeding, api, standards, community" />
   <title>BrAPI Success Stories</title>
@@ -61,8 +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="2024-02-29T21:09:23+00:00" />
-  <meta property="article:modified_time" content="2024-02-29T21:09:23+00:00" />
+  <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.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -95,15 +99,27 @@
   <meta name="citation_author_orcid" content="0000-0002-8968-3383" />
   <meta name="citation_author" content="Chaney Courtney" />
   <meta name="citation_author_institution" content="Clemson University" />
+  <meta name="citation_author" content="Zachary Miller" />
+  <meta name="citation_author_institution" content="Cornell University" />
+  <meta name="citation_author_orcid" content="0000-0002-5454-4527" />
+  <meta name="citation_author" content="Terry Casstevens" />
+  <meta name="citation_author_institution" content="Cornell University" />
+  <meta name="citation_author_orcid" content="0000-0001-7602-0487" />
+  <meta name="citation_author" content="Sook Jung" />
+  <meta name="citation_author_institution" content="Department of Horticulture, Washington State University" />
+  <meta name="citation_author_orcid" content="0000-0003-3968-2769" />
+  <meta name="citation_author" content="Taein Lee" />
+  <meta name="citation_author_institution" content="Department of Horticulture, Washington State University" />
+  <meta name="citation_author_orcid" content="0000-0002-2000-2586" />
   <link rel="canonical" href="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta property="og:url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta property="twitter:url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <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/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/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" />
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@@ -120,9 +136,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08">plantbreeding/BrAPI-Manuscript2@7bafa2d</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/838c21cfb2bae42f8511dd75468c931bea0ed267">plantbreeding/BrAPI-Manuscript2@838c21c</a>
 on February 29, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -215,6 +231,44 @@ <h2 id="authors">Authors</h2>
 <small>
 Clemson University
 </small></p></li>
+<li><p><strong>Zachary Miller</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0002-5454-4527">0000-0002-5454-4527</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/zrm22">zrm22</a>
+<br>
+<small>
+Cornell University
+</small></p></li>
+<li><p><strong>Terry Casstevens</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0001-7602-0487">0000-0001-7602-0487</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/tcasstevens">tcasstevens</a>
+<br>
+<small>
+Cornell University
+</small></p></li>
+<li><p><strong>Sook Jung</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0003-3968-2769">0000-0003-3968-2769</a>
+<br>
+<small>
+Department of Horticulture, Washington State University
+</small></p></li>
+<li><p><strong>Taein Lee</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0002-2000-2586">0000-0002-2000-2586</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/leetaei">leetaei</a>
+<br>
+<small>
+Department of Horticulture, Washington State University
+</small></p></li>
 </ul>
 <div id="correspondence">
 <p>✉ — Correspondence possible via <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/issues">GitHub Issues</a>
@@ -326,8 +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>
-<!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
-<p>BIMS is relatively new to the BrAPI community, with their primary focus being a link to the Field Book mobile data collection app.</p>
+<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>
 <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>

diff --git a/manuscript.md b/manuscript.md
@@ -18,6 +18,10 @@ author-meta:
 - Cyril Pommier
 - Becky Smith
 - Chaney Courtney
+- Zachary Miller
+- Terry Casstevens
+- Sook Jung
+- Taein Lee
 header-includes: |
   <!--
   Manubot generated metadata rendered from header-includes-template.html.
@@ -32,8 +36,8 @@ header-includes: |
   <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="2024-02-29T21:09:23+00:00" />
-  <meta property="article:modified_time" content="2024-02-29T21:09:23+00:00" />
+  <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.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -66,15 +70,27 @@ header-includes: |
   <meta name="citation_author_orcid" content="0000-0002-8968-3383" />
   <meta name="citation_author" content="Chaney Courtney" />
   <meta name="citation_author_institution" content="Clemson University" />
+  <meta name="citation_author" content="Zachary Miller" />
+  <meta name="citation_author_institution" content="Cornell University" />
+  <meta name="citation_author_orcid" content="0000-0002-5454-4527" />
+  <meta name="citation_author" content="Terry Casstevens" />
+  <meta name="citation_author_institution" content="Cornell University" />
+  <meta name="citation_author_orcid" content="0000-0001-7602-0487" />
+  <meta name="citation_author" content="Sook Jung" />
+  <meta name="citation_author_institution" content="Department of Horticulture, Washington State University" />
+  <meta name="citation_author_orcid" content="0000-0003-3968-2769" />
+  <meta name="citation_author" content="Taein Lee" />
+  <meta name="citation_author_institution" content="Department of Horticulture, Washington State University" />
+  <meta name="citation_author_orcid" content="0000-0002-2000-2586" />
   <link rel="canonical" href="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta property="og:url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta property="twitter:url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
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   <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/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/" />
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+  <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" />
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@@ -96,9 +112,9 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@7bafa2d](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08)
+from [plantbreeding/BrAPI-Manuscript2@838c21c](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/838c21cfb2bae42f8511dd75468c931bea0ed267)
 on February 29, 2024.
 </em></small>
 
@@ -205,6 +221,48 @@ on February 29, 2024.
      Clemson University
   </small>
 
++ **Zachary Miller**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0002-5454-4527](https://orcid.org/0000-0002-5454-4527)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [zrm22](https://github.com/zrm22)
+    <br>
+  <small>
+     Cornell University
+  </small>
+
++ **Terry Casstevens**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0001-7602-0487](https://orcid.org/0000-0001-7602-0487)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [tcasstevens](https://github.com/tcasstevens)
+    <br>
+  <small>
+     Cornell University
+  </small>
+
++ **Sook Jung**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0003-3968-2769](https://orcid.org/0000-0003-3968-2769)
+    <br>
+  <small>
+     Department of Horticulture, Washington State University
+  </small>
+
++ **Taein Lee**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0002-2000-2586](https://orcid.org/0000-0002-2000-2586)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [leetaei](https://github.com/leetaei)
+    <br>
+  <small>
+     Department of Horticulture, Washington State University
+  </small>
+
 
 ::: {#correspondence}
 ✉ — Correspondence possible via [GitHub Issues](https://github.com/plantbreeding/BrAPI-Manuscript2/issues)
@@ -367,8 +425,7 @@ Since the inception of BrAPI in 2014, the Breedbase group has been a heavy contr
 
 #### BIMS
 
-<!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
-BIMS is relatively new to the BrAPI community, with their primary focus being a link to the Field Book mobile data collection app.
+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, <https://breedwithbims.org>. 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. 
 
 #### Germinate
 

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/spelling-error-locations.txt b/spelling-error-locations.txt
@@ -168,9 +168,23 @@ content/03.02.data-management.md:57:BrAPI
 content/03.02.data-management.md:57:BrAPI
 content/03.02.data-management.md:57:Breedbase
 content/03.02.data-management.md:59:BIMS
-content/03.02.data-management.md:62:BIMS
-content/03.02.data-management.md:62:BrAPI
-content/03.02.data-management.md:67:germplasm
+content/03.02.data-management.md:61:BIMS
+content/03.02.data-management.md:61:BIMS
+content/03.02.data-management.md:61:BIMS
+content/03.02.data-management.md:61:BIMS
+content/03.02.data-management.md:61:BIMS
+content/03.02.data-management.md:61:BIMS
+content/03.02.data-management.md:61:BIMS
+content/03.02.data-management.md:61:BrAPI
+content/03.02.data-management.md:61:BrAPI
+content/03.02.data-management.md:61:BreedBase
+content/03.02.data-management.md:61:CottonGEN
+content/03.02.data-management.md:61:genotype
+content/03.02.data-management.md:61:germplasm
+content/03.02.data-management.md:61:GIGWA
+content/03.02.data-management.md:61:Rosaceae
+content/03.02.data-management.md:61:Vaccinium
+content/03.02.data-management.md:66:germplasm
 content/03.03.federation-infrastructure.md:5:agrosystems
 content/03.03.federation-infrastructure.md:5:genebanks
 content/03.03.federation-infrastructure.md:5:germplasm

diff --git a/spelling-errors.txt b/spelling-errors.txt
@@ -2,7 +2,7 @@ Agrosystem
 agrosystems
 Alic
 alshamaa
-Analytics
+analytics
 ANR
 APIs
 arial
@@ -16,16 +16,18 @@ BioinfOmics
 Bioinformatics
 Biologie
 BMS
-brapi
+BrAPI
 BrapiCoordinatorSelby
 BrapMan
 BrAPP
 BrAPPs
 BRAVA
-Breedbase
+BreedBase
+Casstevens
 chaneylc
 CLI
 ClimMob
+CottonGEN
 COVID
 cpommier
 CRAN
@@ -51,7 +53,7 @@ Germplasm
 Gigwa
 GLIS
 hackathon
-Hackathons
+hackathons
 haplotype
 haplotypes
 HortControl
@@ -66,7 +68,8 @@ interoperable
 IPK
 ISA
 JSON
-Khaled
+khaled
+leetaei
 LIDAR
 metabolomics
 MGIS
@@ -79,7 +82,7 @@ NIFA
 ontologies
 OpenSILEX
 pangenome
-PHENOME
+Phenome
 Phenospex
 phenotypes
 Phenotypic
@@ -89,20 +92,25 @@ PHIS’s
 Pommier
 programmatically
 QBMS
-raubach
+Raubach
+Rosaceae
 rPHG
 Saclay
 Santé
 Selby
 Shamaa
 situ
 stateful
+Taein
+tcasstevens
 TCP
 transcriptomics
 trife
 UAVs
 UGVs
 Université
 URGI
+Vaccinium
 variantsets
 VCF
+zrm