Merge pull request #15 from Isabelle-inrae/patch-3

[ci skip]

This build is based on
09f0067.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8269191912

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/7b11cbe59dcc9d84619310a19e224c06d972498b/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/>.
 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
-[`7b11cbe59dcc9d84619310a19e224c06d972498b`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/7b11cbe59dcc9d84619310a19e224c06d972498b).
+[`09f0067c036a09cb4b1d52af28fbf7db0cf025e6`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/09f0067c036a09cb4b1d52af28fbf7db0cf025e6).

index.html

@@ -21,7 +21,7 @@
   <meta name="author" content="Josh “Big Data” Lamos-Sweeney" />
   <meta name="author" content="Francisco López" />
   <meta name="author" content="Marco Marsella" />
-  <meta name="dcterms.date" content="2024-03-07" />
+  <meta name="dcterms.date" content="2024-03-13" />
   <meta name="keywords" content="brapi, breeding, api, standards, community" />
   <title>BrAPI Success Stories</title>
   <style>
@@ -66,11 +66,11 @@
   <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="2024-03-07" />
-  <meta name="citation_publication_date" content="2024-03-07" />
-  <meta property="article:published_time" content="2024-03-07" />
-  <meta name="dc.modified" content="2024-03-07T16:45:04+00:00" />
-  <meta property="article:modified_time" content="2024-03-07T16:45:04+00:00" />
+  <meta name="dc.date" content="2024-03-13" />
+  <meta name="citation_publication_date" content="2024-03-13" />
+  <meta property="article:published_time" content="2024-03-13" />
+  <meta name="dc.modified" content="2024-03-13T17:44:10+00:00" />
+  <meta property="article:modified_time" content="2024-03-13T17:44:10+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -131,9 +131,9 @@
   <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/7b11cbe59dcc9d84619310a19e224c06d972498b/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7b11cbe59dcc9d84619310a19e224c06d972498b/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7b11cbe59dcc9d84619310a19e224c06d972498b/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/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" />
@@ -150,10 +150,10 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/7b11cbe59dcc9d84619310a19e224c06d972498b/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/7b11cbe59dcc9d84619310a19e224c06d972498b">plantbreeding/BrAPI-Manuscript2@7b11cbe</a>
-on March 7, 2024.
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/09f0067c036a09cb4b1d52af28fbf7db0cf025e6">plantbreeding/BrAPI-Manuscript2@09f0067</a>
+on March 13, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
@@ -395,9 +395,9 @@ <h3 id="data-management">Data Management</h3>
 * Alternate solutions/ why is it better with BrAPI
 * future related use cases, areas to improve -->
 <h4 id="phis">PHIS</h4>
-<p>The Hybrid Phenotyping Information System (<a href="https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.15385">PHIS</a>), based on the <a href="https://github.com/OpenSILEX/">OpenSILEX</a> framework, assumes responsibility for the systematic collection and management of data from phenotyping and high-throughput phenotyping experiments on a day-to-day basis. PHIS has the ability to efficiently store, organize and manage a wide range of data sets, including images, spectra and growth curves. This functionality extends to data at multiple spatial and temporal scales, from leaf to canopy, from a variety of sources such as field and greenhouse environments.</p>
+<p>The Hybrid Phenotyping Information System (<a href="http://www.phis.inrae.fr/">PHIS</a>[doi:https://doi.org/10.1111/nph.15385]), based on the <a href="https://github.com/OpenSILEX/">OpenSILEX</a> framework, assumes responsibility for the systematic collection and management of data from phenotyping and high-throughput phenotyping experiments on a day-to-day basis. PHIS has the ability to efficiently store, organize and manage a wide range of data sets, including images, spectra and growth curves. This functionality extends to data at multiple spatial and temporal scales, from leaf to canopy, from a variety of sources such as field and greenhouse environments.</p>
 <p>A key feature of PHIS is the unambiguous identification of all objects and traits within an experiment, establishing consistent relationships between them through the application of ontologies and semantics. This approach is designed to adapt to variations in experimental conditions, whether in the field or in controlled environments. PHIS’s ontology-driven architecture emerges as a robust tool for integrating and managing data derived from diverse experiments and platforms, facilitating the creation of meaningful relationships between objects and augmenting datasets with relevant knowledge and metadata.</p>
-<p>Furthermore, PHIS adheres to the Minimal Information About a Plant Phenotyping Experiment (<a href="https://doi.org/10.1111/nph.16544">MIAPPE</a>) and the Breeding API (BrAPI) standards.</p>
+<p>Furthermore, PHIS adheres to the Minimal Information About a Plant Phenotyping Experiment (<a href="https://www.miappe.org/">MIAPPE</a>[doi:https://doi.org/10.1111/nph.16544]) and the Breeding API (BrAPI) standards.</p>
 <p>The system recommends specific naming conventions, fostering a standardized approach for users to declare their resources. Notably, PHIS is widely adopted by various experimental platforms of the national <a href="https://www.phenome-emphasis.fr/">PHENOME</a> and European <a href="https://emphasis.plant-phenotyping.eu/">EMPHASIS</a> infrastructure, serving as a hub for data management.
 Moreover, dedicated instances of PHIS have been established for the explicit purpose of resource sharing, encompassing projects, genetic resources, and variables, thereby fostering collaborative engagement and the dissemination of knowledge pertaining to studied concepts.</p>
 <h5 id="phis-brapi">PHIS &amp; BrAPI</h5>