Merge pull request #10 from plantbreeding/cpommier-patch-1

[ci skip] This build is based on 7bafa2d. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8102623737
plantbreeding · Feb 29, 2024 · 3a3f8c4 · 3a3f8c4
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diff --git a/manuscript.html b/manuscript.html
@@ -10,9 +10,10 @@
   <meta name="author" content="Isabelle Alic" />
   <meta name="author" content="Sebastian “Baz” Raubach" />
   <meta name="author" content="Iain Milne" />
+  <meta name="author" content="Cyril Pommier" />
   <meta name="author" content="Becky Smith" />
   <meta name="author" content="Chaney Courtney" />
-  <meta name="dcterms.date" content="2024-02-23" />
+  <meta name="dcterms.date" content="2024-02-29" />
   <meta name="keywords" content="brapi, breeding, api, standards, community" />
   <title>BrAPI Success Stories</title>
   <style>
@@ -57,11 +58,11 @@
   <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="2024-02-23" />
-  <meta name="citation_publication_date" content="2024-02-23" />
-  <meta property="article:published_time" content="2024-02-23" />
-  <meta name="dc.modified" content="2024-02-23T21:51:53+00:00" />
-  <meta property="article:modified_time" content="2024-02-23T21:51:53+00:00" />
+  <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.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -85,6 +86,10 @@
   <meta name="citation_author" content="Iain Milne" />
   <meta name="citation_author_institution" content="The James Hutton Institute" />
   <meta name="citation_author_orcid" content="0000-0002-4126-0859" />
+  <meta name="citation_author" content="Cyril Pommier" />
+  <meta name="citation_author_institution" content="Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France" />
+  <meta name="citation_author_institution" content="Université Paris-Saclay, INRAE, URGI, Versailles, France" />
+  <meta name="citation_author_orcid" content="0000-0002-9040-8733" />
   <meta name="citation_author" content="Becky Smith" />
   <meta name="citation_author_institution" content="The James Hutton Institute" />
   <meta name="citation_author_orcid" content="0000-0002-8968-3383" />
@@ -96,9 +101,9 @@
   <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/172704ccfbfbefb18f2d18059e1fbd2da92c557e/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/172704ccfbfbefb18f2d18059e1fbd2da92c557e/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/172704ccfbfbefb18f2d18059e1fbd2da92c557e/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" />
   <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" />
@@ -115,10 +120,10 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/172704ccfbfbefb18f2d18059e1fbd2da92c557e/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/172704ccfbfbefb18f2d18059e1fbd2da92c557e">plantbreeding/BrAPI-Manuscript2@172704c</a>
-on February 23, 2024.
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08">plantbreeding/BrAPI-Manuscript2@7bafa2d</a>
+on February 29, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
@@ -181,6 +186,17 @@ <h2 id="authors">Authors</h2>
 <small>
 The James Hutton Institute
 </small></p></li>
+<li><p><strong>Cyril Pommier</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0002-9040-8733">0000-0002-9040-8733</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/cpommier">cpommier</a>
+<br>
+<small>
+Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France; Université Paris-Saclay, INRAE, URGI, Versailles, France
+· Funded by French Infrastructure en Biologie Santé ‘Phenome-FPPN’ supported by the French National Research Agency (ANR-11-INBS-0012)
+</small></p></li>
 <li><p><strong>Becky Smith</strong>
 <br>
 <img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />

diff --git a/manuscript.md b/manuscript.md
@@ -7,14 +7,15 @@ keywords:
 - standards
 - community
 lang: en-US
-date-meta: '2024-02-23'
+date-meta: '2024-02-29'
 author-meta:
 - Peter "BrapMan" Selby
 - Trevor "Cool Kid" Rife
 - Khaled Al-Shamaa
 - Isabelle Alic
 - Sebastian "Baz" Raubach
 - Iain Milne
+- Cyril Pommier
 - Becky Smith
 - Chaney Courtney
 header-includes: |
@@ -28,11 +29,11 @@ header-includes: |
   <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="2024-02-23" />
-  <meta name="citation_publication_date" content="2024-02-23" />
-  <meta property="article:published_time" content="2024-02-23" />
-  <meta name="dc.modified" content="2024-02-23T21:51:53+00:00" />
-  <meta property="article:modified_time" content="2024-02-23T21:51:53+00:00" />
+  <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.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -56,6 +57,10 @@ header-includes: |
   <meta name="citation_author" content="Iain Milne" />
   <meta name="citation_author_institution" content="The James Hutton Institute" />
   <meta name="citation_author_orcid" content="0000-0002-4126-0859" />
+  <meta name="citation_author" content="Cyril Pommier" />
+  <meta name="citation_author_institution" content="Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France" />
+  <meta name="citation_author_institution" content="Université Paris-Saclay, INRAE, URGI, Versailles, France" />
+  <meta name="citation_author_orcid" content="0000-0002-9040-8733" />
   <meta name="citation_author" content="Becky Smith" />
   <meta name="citation_author_institution" content="The James Hutton Institute" />
   <meta name="citation_author_orcid" content="0000-0002-8968-3383" />
@@ -67,9 +72,9 @@ header-includes: |
   <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/172704ccfbfbefb18f2d18059e1fbd2da92c557e/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/172704ccfbfbefb18f2d18059e1fbd2da92c557e/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/172704ccfbfbefb18f2d18059e1fbd2da92c557e/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" />
   <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" />
@@ -91,10 +96,10 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/172704ccfbfbefb18f2d18059e1fbd2da92c557e/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@172704c](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/172704ccfbfbefb18f2d18059e1fbd2da92c557e)
-on February 23, 2024.
+from [plantbreeding/BrAPI-Manuscript2@7bafa2d](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/7bafa2d2c3a66e34f8cd7a087496339c08eb0f08)
+on February 29, 2024.
 </em></small>
 
 
@@ -168,6 +173,18 @@ on February 23, 2024.
      The James Hutton Institute
   </small>
 
++ **Cyril Pommier**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0002-9040-8733](https://orcid.org/0000-0002-9040-8733)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [cpommier](https://github.com/cpommier)
+    <br>
+  <small>
+     Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France; Université Paris-Saclay, INRAE, URGI, Versailles, France
+     · Funded by French Infrastructure en Biologie Santé ‘Phenome-FPPN’ supported by the French National Research Agency (ANR-11-INBS-0012)
+  </small>
+
 + **Becky Smith**
   <br>
     ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/spelling-error-locations.txt b/spelling-error-locations.txt
@@ -3,6 +3,7 @@ content/01.abstract.md:4:BrAPI
 content/01.abstract.md:6:BrAPI
 content/02.introduction.md:8:Hackathons
 content/02.introduction.md:17:datasets
+content/02.introduction.md:19:bioinformatics
 content/02.introduction.md:19:BrAPI
 content/02.introduction.md:19:BrAPI
 content/02.introduction.md:19:BrAPI
@@ -122,6 +123,7 @@ content/03.02.data-management.md:23:phenotyping
 content/03.02.data-management.md:25:BrAPI
 content/03.02.data-management.md:25:faidare
 content/03.02.data-management.md:25:FAIDARE
+content/03.02.data-management.md:25:urgi
 content/03.02.data-management.md:27:BrAPI
 content/03.02.data-management.md:27:BrAPI
 content/03.02.data-management.md:27:phenotyping

diff --git a/spelling-errors.txt b/spelling-errors.txt
@@ -3,6 +3,7 @@ agrosystems
 Alic
 alshamaa
 Analytics
+ANR
 APIs
 arial
 ARS
@@ -11,8 +12,11 @@ backend
 Batbaby
 Baz
 BIMS
+BioinfOmics
+Bioinformatics
+Biologie
 BMS
-BrAPI
+brapi
 BrapiCoordinatorSelby
 BrapMan
 BrAPP
@@ -23,6 +27,7 @@ chaneylc
 CLI
 ClimMob
 COVID
+cpommier
 CRAN
 DArTView
 datasets
@@ -34,26 +39,28 @@ DSFAS
 ERD
 FAIDARE
 focussing
+FPPN
 Genebank
 genebanks
 genomic
 genotype
 Genotypes
 genotypic
-Genotyping
-germplasm
-GIGWA
+genotyping
+Germplasm
+Gigwa
 GLIS
 hackathon
 Hackathons
-Haplotype
+haplotype
 haplotypes
 HortControl
 Iain
 ICARDA
 ImageBreed
 imbedded
 imilne
+INBS
 INRAE
 interoperable
 IPK
@@ -75,14 +82,17 @@ pangenome
 PHENOME
 Phenospex
 phenotypes
-phenotypic
+Phenotypic
 phenotyping
 PHG
 PHIS’s
+Pommier
 programmatically
 QBMS
-Raubach
+raubach
 rPHG
+Saclay
+Santé
 Selby
 Shamaa
 situ
@@ -92,5 +102,7 @@ transcriptomics
 trife
 UAVs
 UGVs
+Université
+URGI
 variantsets
 VCF