Merge pull request #59 from plantbreeding/Isabelle-inrae-patch-2-1

[ci skip]

This build is based on
01f97e7.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/01f97e786525879db23a1d72a3716051fe743bd3/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/9811436575

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/f87c4197b7cb26dfecb51960773f70097e1bdfd5/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/01f97e786525879db23a1d72a3716051fe743bd3/>.
 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
-[`f87c4197b7cb26dfecb51960773f70097e1bdfd5`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/f87c4197b7cb26dfecb51960773f70097e1bdfd5).
+[`01f97e786525879db23a1d72a3716051fe743bd3`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/01f97e786525879db23a1d72a3716051fe743bd3).

index.html

@@ -123,8 +123,8 @@
   <meta name="dc.date" content="2024-07-05" />
   <meta name="citation_publication_date" content="2024-07-05" />
   <meta property="article:published_time" content="2024-07-05" />
-  <meta name="dc.modified" content="2024-07-05T16:54:59+00:00" />
-  <meta property="article:modified_time" content="2024-07-05T16:54:59+00:00" />
+  <meta name="dc.modified" content="2024-07-05T16:57:53+00:00" />
+  <meta property="article:modified_time" content="2024-07-05T16:57:53+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -340,9 +340,9 @@
   <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/f87c4197b7cb26dfecb51960773f70097e1bdfd5/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f87c4197b7cb26dfecb51960773f70097e1bdfd5/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f87c4197b7cb26dfecb51960773f70097e1bdfd5/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01f97e786525879db23a1d72a3716051fe743bd3/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01f97e786525879db23a1d72a3716051fe743bd3/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01f97e786525879db23a1d72a3716051fe743bd3/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" />
@@ -359,9 +359,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f87c4197b7cb26dfecb51960773f70097e1bdfd5/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01f97e786525879db23a1d72a3716051fe743bd3/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/f87c4197b7cb26dfecb51960773f70097e1bdfd5">plantbreeding/BrAPI-Manuscript2@f87c419</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/01f97e786525879db23a1d72a3716051fe743bd3">plantbreeding/BrAPI-Manuscript2@01f97e7</a>
 on July 5, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -1046,8 +1046,8 @@ <h4 id="imagebreed">ImageBreed</h4>
 <h4 id="phis">PHIS</h4>
 <!-- Isabelle -->
 <p>The Hybrid Phenotyping Information System (<a href="http://www.phis.inrae.fr/">PHIS</a><span class="citation" data-cites="3TbA7PwE"><sup><a href="#ref-3TbA7PwE" role="doc-biblioref">6</a></sup></span>), based on the <a href="https://github.com/OpenSILEX/">OpenSILEX</a> framework, is an ontology-driven information system based on semantic web technologies. PHIS is deployed in several field and greenhouse platforms of the French national <a href="https://www.phenome-emphasis.fr/">PHENOME</a> and European <a href="https://emphasis.plant-phenotyping.eu/">EMPHASIS</a> infrastructures. It manages and collects data from basic phenotyping and high throughput phenotyping experiments on a day to day basis. PHIS unambiguously identifies all the objects and traits in an experiment, and establishes their types and relationships via ontologies and semantics.</p>
-<p>PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment (<a href="https://www.miappe.org/">MIAPPE</a><span class="citation" data-cites="kWLsm7g6"><sup><a href="#ref-kWLsm7g6" role="doc-biblioref">7</a></sup></span>). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields. The fact that data within a PHIS instance can be queried through BrAPI services makes the indexing of PHIS in <a href="https://urgi.versailles.inrae.fr/faidare/">FAIDARE</a><span class="citation" data-cites="9aM2mdF4"><sup><a href="#ref-9aM2mdF4" role="doc-biblioref">8</a></sup></span> very easy to implement.</p>
-<p>Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adherence to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community.</p>
+<p>PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms, such as OLGA, a genebank accessions management system, to retrieve accession information. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment (<a href="https://www.miappe.org/">MIAPPE</a><span class="citation" data-cites="kWLsm7g6"><sup><a href="#ref-kWLsm7g6" role="doc-biblioref">7</a></sup></span>). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields. The fact that data within a PHIS instance can be queried through BrAPI services enables indexing of PHIS in <a href="https://urgi.versailles.inrae.fr/faidare/">FAIDARE</a><span class="citation" data-cites="9aM2mdF4"><sup><a href="#ref-9aM2mdF4" role="doc-biblioref">8</a></sup></span>.</p>
+<p>Furthermore, as PHIS offers BrAPI-compliant Web Services, it simplifies the integration and data exchange with other European information systems that handle phenotyping data. The adhesion to BrAPI standards ensures a common interface and compatibility, facilitating communication and collaboration between PHIS and other systems in the European context. This interoperability not only eases data sharing, but also promotes a more coherent and efficient approach to the management and use of phenotyping data on various platforms and research initiatives within the European scientific community.</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">9</a></sup></span> is a data management system used for collecting data from the <a href="https://www.wiwam.be/">WIWAM</a><span class="citation" data-cites="r84WbX0P"><sup><a href="#ref-r84WbX0P" role="doc-biblioref">10</a></sup></span> range of automated high throughput phenotyping platforms. These platforms have been deployed at different research institutes and commercial breeders across Europe. They can be setup 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 to pots (genotype, growth media, manual treatments), importing data, exporting data, and visualizing data. It also supports the integration of image analysis scripts and connections to a compute cluster for job submission.</p>