Merge pull request #76 from plantbreeding/raabb-pippa-patch-1

[ci skip]

This build is based on
5752688.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/5752688cf89414affb18f937e85e6a16c85ac6e6/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/10391105690

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/13118e2cf2a2d455e44529e79097f9ba591501cb/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/5752688cf89414affb18f937e85e6a16c85ac6e6/>.
 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
-[`13118e2cf2a2d455e44529e79097f9ba591501cb`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/13118e2cf2a2d455e44529e79097f9ba591501cb).
+[`5752688cf89414affb18f937e85e6a16c85ac6e6`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/5752688cf89414affb18f937e85e6a16c85ac6e6).

index.html

@@ -129,8 +129,8 @@
   <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="2024-08-14T15:58:11+00:00" />
-  <meta property="article:modified_time" content="2024-08-14T15:58:11+00:00" />
+  <meta name="dc.modified" content="2024-08-14T16:09:58+00:00" />
+  <meta property="article:modified_time" content="2024-08-14T16:09:58+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/13118e2cf2a2d455e44529e79097f9ba591501cb/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/13118e2cf2a2d455e44529e79097f9ba591501cb/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/13118e2cf2a2d455e44529e79097f9ba591501cb/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/5752688cf89414affb18f937e85e6a16c85ac6e6/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/5752688cf89414affb18f937e85e6a16c85ac6e6/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/5752688cf89414affb18f937e85e6a16c85ac6e6/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" />
@@ -387,9 +387,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/13118e2cf2a2d455e44529e79097f9ba591501cb/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/5752688cf89414affb18f937e85e6a16c85ac6e6/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/13118e2cf2a2d455e44529e79097f9ba591501cb">plantbreeding/BrAPI-Manuscript2@13118e2</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/5752688cf89414affb18f937e85e6a16c85ac6e6">plantbreeding/BrAPI-Manuscript2@5752688</a>
 on August 14, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -1179,7 +1179,7 @@ <h4 id="phis">PHIS</h4>
 By integrating BrAPI requirements into its structure, PHIS strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields.</p>
 <h4 id="pippa">PIPPA</h4>
 <!-- Rafael -->
-<p><a href="https://pippa.psb.ugent.be">PIPPA</a><span class="citation" data-cites="okf3YI9z"><sup><a href="#ref-okf3YI9z" role="doc-biblioref">11</a></sup></span> is a data management system used for collecting data from the Weighing, Imaging and Watering Machines (<a href="https://www.wiwam.be/">WIWAM</a>)<span class="citation" data-cites="r84WbX0P"><sup><a href="#ref-r84WbX0P" role="doc-biblioref">12</a></sup></span>, whcih are a range of automated high-throughput phenotyping platforms.
+<p><a href="https://pippa.psb.ugent.be">PIPPA</a><span class="citation" data-cites="okf3YI9z"><sup><a href="#ref-okf3YI9z" role="doc-biblioref">11</a></sup></span> is a data management system used for collecting data from the Weighing, Imaging and Watering Machines (<a href="https://www.wiwam.be/">WIWAM</a>)<span class="citation" data-cites="r84WbX0P"><sup><a href="#ref-r84WbX0P" role="doc-biblioref">12</a></sup></span>, which are a range of automated high-throughput phenotyping platforms.
 These platforms have been deployed by research institutes and commercial breeders across Europe.
 They can be set up in a variety of configurations with different types of equipment including weighing scales, cameras, and environment sensors.
 The software features a web interface with functionality for setting up new experiments, planning imaging and irrigation treatments, linking metadata (genotype, growth media, manual treatments) to pots, and importing, exporting, and visualizing data.
@@ -1524,7 +1524,7 @@ <h2 class="page_break_before" id="references">References</h2>
 <div class="csl-left-margin">15. </div><div class="csl-right-inline">Danecek, P. <em>et al.</em> <a href="https://doi.org/10.1093/bioinformatics/btr330">The variant call format and VCFtools</a>. <em>Bioinformatics</em> <strong>27</strong>, 2156–2158 (2011).</div>
 </div>
 <div id="ref-186zclKvK" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">16. </div><div class="csl-right-inline">GitHub - ga4gh-metadata/SchemaBlocks: Building Blocks and Schemas for GA4GH Implementations. <em>GitHub</em> <a href="https://github.com/ga4gh-metadata/SchemaBlocks">https://github.com/ga4gh-metadata/SchemaBlocks</a>.</div>
+<div class="csl-left-margin">16. </div><div class="csl-right-inline"><a href="https://github.com/ga4gh-metadata/SchemaBlocks">ga4gh-metadata/SchemaBlocks</a>. GA4GH Metadata Schema Development Team (2023).</div>
 </div>
 <div id="ref-9fRbvOj2" class="csl-entry" role="doc-biblioentry">
 <div class="csl-left-margin">17. </div><div class="csl-right-inline">König, P. <em>et al.</em> <a href="https://doi.org/10.1093/gigascience/giad025">DivBrowse—interactive visualization and exploratory data analysis of variant call matrices</a>. <em>GigaScience</em> <strong>12</strong>, (2022).</div>
@@ -1614,7 +1614,7 @@ <h2 class="page_break_before" id="references">References</h2>
 <div class="csl-left-margin">45. </div><div class="csl-right-inline">Pommier, C. <a href="https://hal.science/hal-04425516">FAIR Plant Phenomics Data Management Tools and Guidelines.</a> in (2024).</div>
 </div>
 <div id="ref-smRihyhY" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">46. </div><div class="csl-right-inline">GitHub - elixir-europe/plant-brapi-etl-faidare: Harvest and index meta data from BrAPI endpoints for data access through the plant-faidare data lookup portal (https://github.com/elixir-europe/plant-faidare). <em>GitHub</em> <a href="https://github.com/elixir-europe/plant-brapi-etl-faidare">https://github.com/elixir-europe/plant-brapi-etl-faidare</a>.</div>
+<div class="csl-left-margin">46. </div><div class="csl-right-inline"><a href="https://github.com/elixir-europe/plant-brapi-etl-faidare">elixir-europe/plant-brapi-etl-faidare</a>. ELIXIR Europe (2024).</div>
 </div>
 <div id="ref-sW9euzzP" class="csl-entry" role="doc-biblioentry">
 <div class="csl-left-margin">47. </div><div class="csl-right-inline">Raubach, S. <em>et al.</em> <a href="https://doi.org/10.1002/csc2.20248">From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives</a>. <em>Crop Science</em> <strong>61</strong>, 1538–1566 (2020).</div>