Merge pull request #36 from plantbreeding/pippa

[ci skip]

This build is based on
56ffcc7.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/56ffcc7177cbbf6f1220253aba8378c4fb10f783/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8990362266

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/3671c33f310460b0e09706adc07ef2f98204ccb2/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/56ffcc7177cbbf6f1220253aba8378c4fb10f783/>.
 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
-[`3671c33f310460b0e09706adc07ef2f98204ccb2`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/3671c33f310460b0e09706adc07ef2f98204ccb2).
+[`56ffcc7177cbbf6f1220253aba8378c4fb10f783`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/56ffcc7177cbbf6f1220253aba8378c4fb10f783).

index.html

@@ -48,6 +48,7 @@
   <meta name="author" content="Valentin Guignon" />
   <meta name="author" content="Mathieu Rouard" />
   <meta name="author" content="Asis Hallab" />
+  <meta name="author" content="Rafael Abbeloos" />
   <meta name="author" content="Laszlo Lang" />
   <meta name="author" content="Vivian Bass Vega" />
   <meta name="author" content="Mirella Flores-Gonzalez" />
@@ -99,8 +100,8 @@
   <meta name="dc.date" content="2024-05-07" />
   <meta name="citation_publication_date" content="2024-05-07" />
   <meta property="article:published_time" content="2024-05-07" />
-  <meta name="dc.modified" content="2024-05-07T18:13:56+00:00" />
-  <meta property="article:modified_time" content="2024-05-07T18:13:56+00:00" />
+  <meta name="dc.modified" content="2024-05-07T18:20:50+00:00" />
+  <meta property="article:modified_time" content="2024-05-07T18:20:50+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -235,6 +236,9 @@
   <meta name="citation_author" content="Asis Hallab" />
   <meta name="citation_author_institution" content="Jülich research center, Institute of Bio- and Geosciences (IBG), Bioinformatics (IBG-4) and Bingen Technical University of Applied Sciences, Germany" />
   <meta name="citation_author_orcid" content="0000-0002-2421-5431" />
+  <meta name="citation_author" content="Rafael Abbeloos" />
+  <meta name="citation_author_institution" content="VIB AgroIncubator" />
+  <meta name="citation_author_orcid" content="0000-0002-0177-3887" />
   <meta name="citation_author" content="Laszlo Lang" />
   <meta name="citation_author_institution" content="Bingen Technical University of Applied Sciences, Berlinstraße 109, 55411 Bingen am Rhein, Germany" />
   <meta name="citation_author_orcid" content="0009-0009-8936-4532" />
@@ -250,9 +254,9 @@
   <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/3671c33f310460b0e09706adc07ef2f98204ccb2/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3671c33f310460b0e09706adc07ef2f98204ccb2/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3671c33f310460b0e09706adc07ef2f98204ccb2/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/56ffcc7177cbbf6f1220253aba8378c4fb10f783/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/56ffcc7177cbbf6f1220253aba8378c4fb10f783/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/56ffcc7177cbbf6f1220253aba8378c4fb10f783/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" />
@@ -269,9 +273,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3671c33f310460b0e09706adc07ef2f98204ccb2/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/56ffcc7177cbbf6f1220253aba8378c4fb10f783/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/3671c33f310460b0e09706adc07ef2f98204ccb2">plantbreeding/BrAPI-Manuscript2@3671c33</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/56ffcc7177cbbf6f1220253aba8378c4fb10f783">plantbreeding/BrAPI-Manuscript2@56ffcc7</a>
 on May 7, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -628,6 +632,16 @@ <h2 id="authors">Authors</h2>
 <small>
 Jülich research center, Institute of Bio- and Geosciences (IBG), Bioinformatics (IBG-4) and Bingen Technical University of Applied Sciences, Germany
 </small></p></li>
+<li><p><strong>Rafael Abbeloos</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0002-0177-3887">0000-0002-0177-3887</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/raabb">raabb</a>
+<br>
+<small>
+VIB AgroIncubator
+</small></p></li>
 <li><p><strong>Laszlo Lang</strong>
 <br>
 <img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
@@ -772,6 +786,16 @@ <h4 id="germinate">Germinate</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p><a href="https://ics.hutton.ac.uk/get-germinate/">Germinate</a> <span class="citation" data-cites="sW9euzzP">[<a href="#ref-sW9euzzP" role="doc-biblioref">13</a>]</span> is an open-source plant genetic resources database that combines and integrates various kinds of plant breeding data including genotypic data, phenotypic trials data, passport data, images, geographic information and climate data into a single repository. Germinate is tightly linked to the BrAPI specification and supports a majority of BrAPI endpoints for querying, filtering and submission.</p>
 <p>Germinate integrates and connects with other BrAPI-enabled tools such as GridScore for phenotypic data collection, Flapjack for genotypic data visualization and Helium for pedigree visualization, but, due to the nature of BrAPI, Germinate can act as a data repository for any BrAPI-compatible tool. Thanks to the interoperability provided by BrAPI the need for manual data handling becomes a rarity with the direct benefit of faster data processing, fewer to no human errors, data security and integrity.</p>
+<h4 id="pippa">PIPPA</h4>
+<p><a href="https://pippa.psb.ugent.be">PIPPA</a> is a data management system used for collecting data from the <a href="https://www.wiwam.be/">WIWAM</a> range of automated high throughput phenotyping platforms. These platforms have been deployed at different research institutes and commercial breeders across Europe in a variety of configurations with different types of equipment such as weighing scales, cameras and environment sensors. Examples are:</p>
+<ul>
+<li><a href="https://www.upsc.se/plant-growth-facilities-at-upsc-and-slu-umea/325-upsc-tree-phenotyping-platform.html">Umea Plant Science Centre</a></li>
+<li><a href="https://cri.fmach.it/en/Facilities/Technological-Facilities/Plant-Phenotyping#application_fields">Fondazione Edmund Mach</a></li>
+<li><a href="https://www.psb.ugent.be/phenotyping/phenovision">Phenovision</a></li>
+</ul>
+<p>Developed from 2016 onwards, the software features a web interface with functionality for setting up new experiments for the platform(s), planning imaging and irrigation treatments, linking metadata to pots (genotype, growth media, manual treatments), exporting data, importing data and visualizing data as charts. It also supports the integration of image analysis scripts and connections to a compute cluster for job submission.</p>
+<p>To share the phenotype data of the experiments linked to publications, an implementation of BrAPI 1.3 was developed on a separate public PIPPA server open to the public, which allowed read only access to the data in a standardized format. This endpoint was registered on <a href="https://urgi.versailles.inra.fr/faidare/">FAIDARE</a> and allows the data to be found alongside data from other BrAPI endpoints.</p>
+<p>As the BrAPI ecosystem has matured, it created a clear path for the development of PIPPA as to how to share data in a manner according to the FAIR principles which are becoming standard in plant research data management best practices. In combination with the support for <a href="https://www.miappe.org/">MIAPPE</a>, these have served as guidelines in the current development, which is focussed on delivering a public BraPI 2.1 endpoint and making more high throughput datasets publicly available via BrAPI.</p>
 <h4 id="mgis">MGIS</h4>
 <!-- authors: Mathieu Rouard, Valentin Guignon -->
 <p>The Musa Germplasm information system, <a href="https://www.crop-diversity.org/mgis/">MGIS</a>, serves as a comprehensive community portal dedicated to banana diversity, a crop critical to global food security <span class="citation" data-cites="84Yn3FWj">[<a href="#ref-84Yn3FWj" role="doc-biblioref">14</a>]</span>. MGIS offers detailed information on banana germplasm, focusing on the collections held by the CGIAR International Banana Genebank (ITC) <span class="citation" data-cites="JWi7AKhJ">[<a href="#ref-JWi7AKhJ" role="doc-biblioref">15</a>]</span>. It is built on the Build on the Drupal/Tripal technology, like BIMS and Florilège. Since its inception, MGIS developers have actively participated in the Breeding API (BrAPI) community, pushing for the integration of Multicrop Passport Data (MCPD) into Germplasm module call of the API. MGIS thus provides passport data information on ITC banana genebank accessions (with GLIS DOI), synchronized with <a href="https://www.genesys-pgr.org/a/overview/v2YdWZGrZjD">Genesys</a>, but also enriches it by incorporating additional data from other germplasm collections worldwide. All those germplasm data are available through BrAPI germplasm module calls implementations. For genotyping data, MGIS incorporates GIGWA <span class="citation" data-cites="AVjkjraw">[<a href="#ref-AVjkjraw" role="doc-biblioref">16</a>]</span>, which provides tailored implementations for BrAPI genotyping module calls. Furthermore, MGIS supports the implementation of a set of BrAPI phenotyping module calls, facilitating the exposing of morphological descriptors and trait information supported by ontologies like the Crop Ontology <span class="citation" data-cites="VndIxnl3">[<a href="#ref-VndIxnl3" role="doc-biblioref">17</a>]</span>. It is integrated with the Trait Selector BrAPP, developed as part of a project involving Breedbase <span class="citation" data-cites="al3Hd9Ml">[<a href="#ref-al3Hd9Ml" role="doc-biblioref">5</a>]</span>. Uses cases between the Musa implementation of Breedbase, MusaBase, and MGIS to interlink genebank and breeding data.</p>