formatting updates

[ci skip]

This build is based on
3770f00.

This commit was created by the following CI build and job:
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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/e33a6b428a7d405e1adcc6fe73fb637ed5347b63/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/3770f007443891a5137dd0de958483f0222ec098/>.
 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
-[`e33a6b428a7d405e1adcc6fe73fb637ed5347b63`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/e33a6b428a7d405e1adcc6fe73fb637ed5347b63).
+[`3770f007443891a5137dd0de958483f0222ec098`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/3770f007443891a5137dd0de958483f0222ec098).

index.html

@@ -81,8 +81,8 @@
   <meta name="dc.date" content="2024-04-16" />
   <meta name="citation_publication_date" content="2024-04-16" />
   <meta property="article:published_time" content="2024-04-16" />
-  <meta name="dc.modified" content="2024-04-16T13:42:05+00:00" />
-  <meta property="article:modified_time" content="2024-04-16T13:42:05+00:00" />
+  <meta name="dc.modified" content="2024-04-16T13:52:32+00:00" />
+  <meta property="article:modified_time" content="2024-04-16T13:52:32+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -171,9 +171,9 @@
   <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/e33a6b428a7d405e1adcc6fe73fb637ed5347b63/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/e33a6b428a7d405e1adcc6fe73fb637ed5347b63/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/e33a6b428a7d405e1adcc6fe73fb637ed5347b63/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3770f007443891a5137dd0de958483f0222ec098/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3770f007443891a5137dd0de958483f0222ec098/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3770f007443891a5137dd0de958483f0222ec098/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" />
@@ -190,9 +190,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/e33a6b428a7d405e1adcc6fe73fb637ed5347b63/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/3770f007443891a5137dd0de958483f0222ec098/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/e33a6b428a7d405e1adcc6fe73fb637ed5347b63">plantbreeding/BrAPI-Manuscript2@e33a6b4</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/3770f007443891a5137dd0de958483f0222ec098">plantbreeding/BrAPI-Manuscript2@3770f00</a>
 on April 16, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -560,23 +560,22 @@ <h3 id="federated-data-management-infrastructures">Federated Data Management Inf
 <!-- Contribution BrAPI 2.0 paper
 Suggested Authors: Matthias Lange, Patrick König, Stephan Weise, Gouripriya Davuluri, Suman Kumar, Joseph Ruff, Paul Kersey, Cyril Pommier, Michael Alaux, Erwan Le-Floch -->
 <h4 id="agent-portal">AGENT Portal</h4>
-<p>{#sec:AGENT_BrAPI_Backend}</p>
-<p>In the global system for ex situ conservation of plant genetic resources (PGR) <span class="citation" data-cites="S1uQPBPG">[<a href="#ref-S1uQPBPG" role="doc-biblioref">9</a>]</span>, a total of ~5.8 million accessions are conserved in 1750 ex situ genebanks <span class="citation" data-cites="USun3Z8l">[<a href="#ref-USun3Z8l" role="doc-biblioref">10</a>]</span>. Unique and permanent identifiers in the form of DOIs are available for more than 1.7 million accessions <span class="citation" data-cites="doi:Food">[<a href="#ref-doi:Food" role="doc-biblioref"><strong>doi:Food?</strong></a> and Agriculture Organization (FAO) The Global Information System for PGRFA]</span>. Each DOI is linked to some basic descriptive data that facilitates the use of these resources. Many DOIs are also linked to additional data from different domains or will be in the future. In order to answer questions on the global biological diversity of a plant species, on duplicate detection, on provenance tracking for the identification of genetic integrity, on the selection of the most suitable material for various purposes, including breeding and research, and to support further applications in data mining or AI, a data space beyond the most basic information is needed that includes genotypic and phenotypic data. In this context, the aim of the AGENT project (https://www.agent-project.eu/) funded by the European Commission is to develop a concept for the digital exploitation and activation of this GenRes data space via European ex situ genebanks according to the FAIR criteria <span class="citation" data-cites="6DjakjNS">[<a href="#ref-6DjakjNS" role="doc-biblioref">11</a>]</span> and to test it in practice using two important crops, barley and wheat. In two work packages, standards and technology for data interoperability will be developed to establish a genetic resources infrastructure, which regulates data acquisition of genotypic and phenotypic data, integrates and archives them and makes them accessible according to FAIR principles. To this end, 13 European genebanks and 5 bioinformatics centers are cooperating and have agreed on standards and protocols for (i) the data flow (see figure <a href="#fig:AGENT_Genotyping_Data_Flow">3</a>) and data formats <span class="citation" data-cites="31NWAHsO">[<a href="#ref-31NWAHsO" role="doc-biblioref">12</a>]</span> for central archiving of genotypic and phenotypic data.</p>
+<p>In the global system for ex situ conservation of plant genetic resources (PGR) <span class="citation" data-cites="S1uQPBPG">[<a href="#ref-S1uQPBPG" role="doc-biblioref">9</a>]</span>, a total of ~5.8 million accessions are conserved in 1750 ex situ genebanks <span class="citation" data-cites="USun3Z8l">[<a href="#ref-USun3Z8l" role="doc-biblioref">10</a>]</span>. Unique and permanent identifiers in the form of DOIs are available for more than 1.7 million accessions <span class="citation" data-cites="doi:Food">[<a href="#ref-doi:Food" role="doc-biblioref"><strong>doi:Food?</strong></a> and Agriculture Organization (FAO) The Global Information System for PGRFA]</span>. Each DOI is linked to some basic descriptive data that facilitates the use of these resources. Many DOIs are also linked to additional data from different domains or will be in the future. In order to answer questions on the global biological diversity of a plant species, on duplicate detection, on provenance tracking for the identification of genetic integrity, on the selection of the most suitable material for various purposes, including breeding and research, and to support further applications in data mining or AI, a data space beyond the most basic information is needed that includes genotypic and phenotypic data. In this context, the aim of the AGENT project (<a href="https://www.agent-project.eu/" class="uri">https://www.agent-project.eu/</a>) funded by the European Commission is to develop a concept for the digital exploitation and activation of this GenRes data space via European ex situ genebanks according to the FAIR criteria <span class="citation" data-cites="6DjakjNS">[<a href="#ref-6DjakjNS" role="doc-biblioref">11</a>]</span> and to test it in practice using two important crops, barley and wheat. In two work packages, standards and technology for data interoperability will be developed to establish a genetic resources infrastructure, which regulates data acquisition of genotypic and phenotypic data, integrates and archives them and makes them accessible according to FAIR principles. To this end, 13 European genebanks and 5 bioinformatics centers are cooperating and have agreed on standards and protocols for (i) the data flow (see figure <a href="#fig:AGENT_Genotyping_Data_Flow">3</a>) and data formats <span class="citation" data-cites="31NWAHsO">[<a href="#ref-31NWAHsO" role="doc-biblioref">12</a>]</span> for central archiving of genotypic and phenotypic data.</p>
 <div id="fig:AGENT_Genotyping_Data_Flow" class="fignos">
 <figure>
 <img src="images/AGENT_Genotyping_Data_Flow.png" style="width:100.0%" alt="Figure 3: Figure Data flow of genotypic data from AGENT partner databases" />
 <figcaption aria-hidden="true"><span>Figure 3:</span> Figure Data flow of genotypic data from AGENT partner databases</figcaption>
 </figure>
 </div>
-<p>The AGENT portal as described in more detail in section {<span class="citation" data-cites="sec:Success_Story_AGENT">[<a href="#ref-sec:Success_Story_AGENT" role="doc-biblioref"><strong>sec:Success_Story_AGENT?</strong></a>]</span>} unlock the full potential of the biological material stored in genebanks around the globe by using FAIR international data standards and an open digital infrastructure for the management of plant genetic resources. The implemented BrAPI interface enables to mine current and historic genotypic and phenotypic information to drive the discovery of genes, traits and knowledge for future missions, complement existing information for wheat and barley and the new data standards and infrastructure to foster an improved management of PGR for other crop species across European genebanks.</p>
+<p>The AGENT portal as described in more detail in section unlock the full potential of the biological material stored in genebanks around the globe by using FAIR international data standards and an open digital infrastructure for the management of plant genetic resources. The implemented BrAPI interface enables to mine current and historic genotypic and phenotypic information to drive the discovery of genes, traits and knowledge for future missions, complement existing information for wheat and barley and the new data standards and infrastructure to foster an improved management of PGR for other crop species across European genebanks.</p>
 <p>For the joint research data infrastructure for the federation of collections of genotypic and phenotypic data from European gene banks and bioinformatics institutes, a AGENT portal (<a href="#fig:AGENT_WebFrontend">4</a>) as database infrastructure for integrated plant genetic resources on ex-situ genebanks is being created. It provides, manual data exploration, machine-readable access via BrAPI and provide data to the cored data deposition resources at the European Bioinformatics Institute (EBI).</p>
 <div id="fig:AGENT_WebFrontend" class="fignos">
 <figure>
 <img src="images/AGENT_WebFrontend.png" style="width:100.0%" alt="Figure 4: Figure AGENT Portal" />
 <figcaption aria-hidden="true"><span>Figure 4:</span> Figure AGENT Portal</figcaption>
 </figure>
 </div>
-<p>The AGENT database backend aggregates curated and integrated passport data, phenotypic and genotypic data about wheat and barley accessions of 18 project partners are harmonized and integrated via BrAPI endpoints (https://github.com/AGENTproject/BrAPI) and explorable in a web portal (https://agent.ipk-gatersleben.de). The BrAPI endpoints were made available by scattered implementation. Genotyping data use DivBrowse <span class="citation" data-cites="9fRbvOj2">[<a href="#ref-9fRbvOj2" role="doc-biblioref">13</a>]</span> storage engine and BrAPI interface. Endpoints for sample data are implemented using AGENT database SQL to BrAPI broker service.
+<p>The AGENT database backend aggregates curated and integrated passport data, phenotypic and genotypic data about wheat and barley accessions of 18 project partners are harmonized and integrated via BrAPI endpoints (<a href="https://github.com/AGENTproject/BrAPI" class="uri">https://github.com/AGENTproject/BrAPI</a>) and explorable in a web portal (<a href="https://agent.ipk-gatersleben.de" class="uri">https://agent.ipk-gatersleben.de</a>). The BrAPI endpoints were made available by scattered implementation. Genotyping data use DivBrowse <span class="citation" data-cites="9fRbvOj2">[<a href="#ref-9fRbvOj2" role="doc-biblioref">13</a>]</span> storage engine and BrAPI interface. Endpoints for sample data are implemented using AGENT database SQL to BrAPI broker service.
 To integrate those BrAPI endpoint provider into a single service and URL scheme, we work on their integration in a BrAPI proxy service. As next steps, we will expand BrAPI implementation to enable the integration of analysis pipelines in the AGENT portal, e.g. for genebank mining tools such as the FIGS+ pipeline developed by AGENT partner ICARDA <span class="citation" data-cites="6VGwG9za">[<a href="#ref-6VGwG9za" role="doc-biblioref">14</a>]</span>. Another perspective is to integrate the data collected in the AGENT project into the European Search Catalogue for Plant Genetic Resources (EURISCO) <span class="citation" data-cites="pk5OwSG6">[<a href="#ref-pk5OwSG6" role="doc-biblioref">15</a>]</span> and to implement BrAPI endpoints to make data on PGR collections in European genebanks programmatically accessible.</p>
 <h4 id="ipk-genebank">IPK-Genebank</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->