diff --git a/citations.tsv b/citations.tsv
index 2d6bd1c..19473a3 100644
--- a/citations.tsv
+++ b/citations.tsv
@@ -1,6 +1,8 @@
 input_id	dealiased_id	standard_id	short_id
 doi:10.1093/bioinformatics/btz190	doi:10.1093/bioinformatics/btz190	doi:10.1093/bioinformatics/btz190	QfGEJ6km
 doi:10.1186/s12859-022-04755-2	doi:10.1186/s12859-022-04755-2	doi:10.1186/s12859-022-04755-2	Ne0E9HbC
+doi:https://doi.org/10.1111/nph.15385	doi:https://doi.org/10.1111/nph.15385	doi:https://doi.org/10.1111/nph.15385	OodVqG7n
+doi:https://doi.org/10.1111/nph.16544	doi:https://doi.org/10.1111/nph.16544	doi:https://doi.org/10.1111/nph.16544	TVXmHLRk
 doi:10.1093/database/baab054	doi:10.1093/database/baab054	doi:10.1093/database/baab054	ArPSsaJQ
 doi:10.1093/nar/gky1000	doi:10.1093/nar/gky1000	doi:10.1093/nar/gky1000	eaDrNpsp
 doi:10.3390/plants10122805	doi:10.3390/plants10122805	doi:10.3390/plants10122805	dcg0274X
diff --git a/manuscript.html b/manuscript.html
index 7d55845..b80c2d2 100644
--- a/manuscript.html
+++ b/manuscript.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="2024-03-13" />
+  <meta name="dcterms.date" content="2024-03-14" />
   <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="2024-03-13" />
-  <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.date" content="2024-03-14" />
+  <meta name="citation_publication_date" content="2024-03-14" />
+  <meta property="article:published_time" content="2024-03-14" />
+  <meta name="dc.modified" content="2024-03-14T17:38:48+00:00" />
+  <meta property="article:modified_time" content="2024-03-14T17:38:48+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/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/" />
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+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/manuscript.pdf" />
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@@ -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/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/09f0067c036a09cb4b1d52af28fbf7db0cf025e6">plantbreeding/BrAPI-Manuscript2@09f0067</a>
-on March 13, 2024.
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162">plantbreeding/BrAPI-Manuscript2@0b749b9</a>
+on March 14, 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="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>The Hybrid Phenotyping Information System (<a href="http://www.phis.inrae.fr/">PHIS</a><span class="citation" data-cites="OodVqG7n">[<a href="#ref-OodVqG7n" role="doc-biblioref">3</a>]</span>), 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://www.miappe.org/">MIAPPE</a>[doi:https://doi.org/10.1111/nph.16544]) 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><span class="citation" data-cites="TVXmHLRk">[<a href="#ref-TVXmHLRk" role="doc-biblioref">4</a>]</span>) 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>
@@ -429,10 +429,10 @@ <h4 id="breedbase">Breedbase</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p>Since the inception of BrAPI in 2014, the Breedbase group has been a heavy contributor to the BrAPI community.</p>
 <h4 id="bims">BIMS</h4>
-<p>BIMS (Breeding Information Management System) <span class="citation" data-cites="ArPSsaJQ">[<a href="#ref-ArPSsaJQ" role="doc-biblioref">3</a>]</span> is a free, secure, and online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data. BIMS enables individual breeders to have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving for their germplasm, phenotype, genotype, and image data. BIMS is currently implemented in five community databases, the Genome Database for Rosaceae <span class="citation" data-cites="eaDrNpsp">[<a href="#ref-eaDrNpsp" role="doc-biblioref">4</a>]</span>, CottonGEN <span class="citation" data-cites="dcg0274X">[<a href="#ref-dcg0274X" role="doc-biblioref">5</a>]</span>, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, <a href="https://breedwithbims.org" class="uri">https://breedwithbims.org</a>. BIMS in these five community databases enables individual breeders to import publicly available data so that they can utilize public data in their breeding program. BIMS utilizes the Android App Field Book, enabling seamless data transfer between BIMS and the Field Book App through either files or BrAPI. Data transfer through BrAPI between BIMS and other resources such as BreedBase, GIGWA, and Breeder Genomics Hub is also on the way.</p>
+<p>BIMS (Breeding Information Management System) <span class="citation" data-cites="ArPSsaJQ">[<a href="#ref-ArPSsaJQ" role="doc-biblioref">5</a>]</span> is a free, secure, and online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data. BIMS enables individual breeders to have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving for their germplasm, phenotype, genotype, and image data. BIMS is currently implemented in five community databases, the Genome Database for Rosaceae <span class="citation" data-cites="eaDrNpsp">[<a href="#ref-eaDrNpsp" role="doc-biblioref">6</a>]</span>, CottonGEN <span class="citation" data-cites="dcg0274X">[<a href="#ref-dcg0274X" role="doc-biblioref">7</a>]</span>, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, <a href="https://breedwithbims.org" class="uri">https://breedwithbims.org</a>. BIMS in these five community databases enables individual breeders to import publicly available data so that they can utilize public data in their breeding program. BIMS utilizes the Android App Field Book, enabling seamless data transfer between BIMS and the Field Book App through either files or BrAPI. Data transfer through BrAPI between BIMS and other resources such as BreedBase, GIGWA, and Breeder Genomics Hub is also on the way.</p>
 <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">6</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><a href="https://ics.hutton.ac.uk/get-germinate/">Germinate</a> <span class="citation" data-cites="sW9euzzP">[<a href="#ref-sW9euzzP" role="doc-biblioref">8</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>
 <h3 id="federated-data-management-infrastructures">Federated Data Management Infrastructures</h3>
 <!-- 
@@ -459,7 +459,7 @@ <h3 id="data-visualization">Data visualization</h3>
 * future related use cases, areas to improve -->
 <h4 id="flapjack">Flapjack</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/flapjack">Flapjack</a> <span class="citation" data-cites="Wz8l0HlN">[<a href="#ref-Wz8l0HlN" role="doc-biblioref">7</a>]</span> is a multiplatform desktop application for data visualization and breeding analysis (eg, pedigree verification, marker-assisted backcrossing and forward breeding) using high-throughput genotype data. Data can be easily imported into Flapjack from any BrAPI compatible data source with genotype data available. <a href="https://github.com/cropgeeks/flapjack-bytes">Flapjack Bytes</a> is a smaller, lightweight and fully web-based counterpart to Flapjack, which can be easily embedded into a database website to provide similiar visualizations online. Traditionally supporting its own text-based data formats, Flapjack’s use of BrAPI has streamlined the end-user experience for data import and work is underway to determine the best methods to exchange analysis results using future versions of the API.</p>
+<p><a href="https://ics.hutton.ac.uk/flapjack">Flapjack</a> <span class="citation" data-cites="Wz8l0HlN">[<a href="#ref-Wz8l0HlN" role="doc-biblioref">9</a>]</span> is a multiplatform desktop application for data visualization and breeding analysis (eg, pedigree verification, marker-assisted backcrossing and forward breeding) using high-throughput genotype data. Data can be easily imported into Flapjack from any BrAPI compatible data source with genotype data available. <a href="https://github.com/cropgeeks/flapjack-bytes">Flapjack Bytes</a> is a smaller, lightweight and fully web-based counterpart to Flapjack, which can be easily embedded into a database website to provide similiar visualizations online. Traditionally supporting its own text-based data formats, Flapjack’s use of BrAPI has streamlined the end-user experience for data import and work is underway to determine the best methods to exchange analysis results using future versions of the API.</p>
 <h4 id="helium">Helium</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p>Helium is a platform for reviewing and managing pedigree data. It is BrAPI enabled, so pedigree data can be viewed straight from a database.</p>
@@ -557,20 +557,26 @@ <h2 class="page_break_before" id="references">References</h2>
 <div id="ref-Ne0E9HbC" class="csl-entry" role="doc-biblioentry">
 <div class="csl-left-margin">2. </div><div class="csl-right-inline"><strong>GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization</strong> <div class="csl-block">Sebastian Raubach, Miriam Schreiber, Paul D Shaw</div> <em>BMC Bioinformatics</em> (2022-06-06) <a href="https://doi.org/gtkcsv">https://doi.org/gtkcsv</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1186/s12859-022-04755-2">10.1186/s12859-022-04755-2</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35668357">35668357</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9169276">PMC9169276</a></div></div>
 </div>
+<div id="ref-OodVqG7n" class="csl-entry" role="doc-biblioentry">
+<div class="csl-left-margin">3. </div><div class="csl-right-inline"><strong>Dealing with multi‐source and multi‐scale information in plant phenomics: the ontology‐driven Phenotyping Hybrid Information System</strong> <div class="csl-block">Pascal Neveu, Anne Tireau, Nadine Hilgert, Vincent Nègre, Jonathan Mineau‐Cesari, Nicolas Brichet, Romain Chapuis, Isabelle Sanchez, Cyril Pommier, Brigitte Charnomordic, … Llorenç Cabrera‐Bosquet</div> <em>New Phytologist</em> (2019-01) <a href="https://doi.org/gm9b9j">https://doi.org/gm9b9j</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1111/nph.15385">https://doi.org/10.1111/nph.15385</a></div></div>
+</div>
+<div id="ref-TVXmHLRk" class="csl-entry" role="doc-biblioentry">
+<div class="csl-left-margin">4. </div><div class="csl-right-inline"><strong>Enabling reusability of plant phenomic datasets with MIAPPE 1.1</strong> <div class="csl-block">Evangelia A Papoutsoglou, Daniel Faria, Daniel Arend, Elizabeth Arnaud, Ioannis N Athanasiadis, Inês Chaves, Frederik Coppens, Guillaume Cornut, Bruno V Costa, Hanna Ćwiek‐Kupczyńska, … Cyril Pommier</div> <em>New Phytologist</em> (2020-07) <a href="https://doi.org/gjqcmb">https://doi.org/gjqcmb</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1111/nph.16544">https://doi.org/10.1111/nph.16544</a></div></div>
+</div>
 <div id="ref-ArPSsaJQ" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">3. </div><div class="csl-right-inline"><strong>The Breeding Information Management System (BIMS): an online resource for crop breeding</strong> <div class="csl-block">Sook Jung, Taein Lee, Ksenija Gasic, BTodd Campbell, Jing Yu, Jodi Humann, Sushan Ru, Daniel Edge-Garza, Heidi Hough, Dorrie Main</div> <em>Database</em> (2021-01-01) <a href="https://doi.org/gtj95x">https://doi.org/gtj95x</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/database/baab054">10.1093/database/baab054</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34415997">34415997</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8378516">PMC8378516</a></div></div>
+<div class="csl-left-margin">5. </div><div class="csl-right-inline"><strong>The Breeding Information Management System (BIMS): an online resource for crop breeding</strong> <div class="csl-block">Sook Jung, Taein Lee, Ksenija Gasic, BTodd Campbell, Jing Yu, Jodi Humann, Sushan Ru, Daniel Edge-Garza, Heidi Hough, Dorrie Main</div> <em>Database</em> (2021-01-01) <a href="https://doi.org/gtj95x">https://doi.org/gtj95x</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/database/baab054">10.1093/database/baab054</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34415997">34415997</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8378516">PMC8378516</a></div></div>
 </div>
 <div id="ref-eaDrNpsp" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">4. </div><div class="csl-right-inline"><strong>15 years of GDR: New data and functionality in the Genome Database for Rosaceae</strong> <div class="csl-block">Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P Ficklin, Ksenija Gasic, Kristin Scott, … Dorrie Main</div> <em>Nucleic Acids Research</em> (2018-10-24) <a href="https://doi.org/gjqq8v">https://doi.org/gjqq8v</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/nar/gky1000">10.1093/nar/gky1000</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30357347">30357347</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324069">PMC6324069</a></div></div>
+<div class="csl-left-margin">6. </div><div class="csl-right-inline"><strong>15 years of GDR: New data and functionality in the Genome Database for Rosaceae</strong> <div class="csl-block">Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P Ficklin, Ksenija Gasic, Kristin Scott, … Dorrie Main</div> <em>Nucleic Acids Research</em> (2018-10-24) <a href="https://doi.org/gjqq8v">https://doi.org/gjqq8v</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/nar/gky1000">10.1093/nar/gky1000</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30357347">30357347</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324069">PMC6324069</a></div></div>
 </div>
 <div id="ref-dcg0274X" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">5. </div><div class="csl-right-inline"><strong>CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research</strong> <div class="csl-block">Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, … Dorrie Main</div> <em>Plants</em> (2021-12-18) <a href="https://doi.org/gqqwfm">https://doi.org/gqqwfm</a> <div class="csl-block">DOI: <a href="https://doi.org/10.3390/plants10122805">10.3390/plants10122805</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34961276">34961276</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8705096">PMC8705096</a></div></div>
+<div class="csl-left-margin">7. </div><div class="csl-right-inline"><strong>CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research</strong> <div class="csl-block">Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, … Dorrie Main</div> <em>Plants</em> (2021-12-18) <a href="https://doi.org/gqqwfm">https://doi.org/gqqwfm</a> <div class="csl-block">DOI: <a href="https://doi.org/10.3390/plants10122805">10.3390/plants10122805</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/34961276">34961276</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8705096">PMC8705096</a></div></div>
 </div>
 <div id="ref-sW9euzzP" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">6. </div><div class="csl-right-inline"><strong>From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives</strong> <div class="csl-block">Sebastian Raubach, Benjamin Kilian, Kate Dreher, Ahmed Amri, Filippo M Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, … </div> <em>Crop Science</em> (2020-08-20) <a href="https://doi.org/gm66th">https://doi.org/gm66th</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1002/csc2.20248">10.1002/csc2.20248</a></div></div>
+<div class="csl-left-margin">8. </div><div class="csl-right-inline"><strong>From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives</strong> <div class="csl-block">Sebastian Raubach, Benjamin Kilian, Kate Dreher, Ahmed Amri, Filippo M Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, … </div> <em>Crop Science</em> (2020-08-20) <a href="https://doi.org/gm66th">https://doi.org/gm66th</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1002/csc2.20248">10.1002/csc2.20248</a></div></div>
 </div>
 <div id="ref-Wz8l0HlN" class="csl-entry" role="doc-biblioentry">
-<div class="csl-left-margin">7. </div><div class="csl-right-inline"><strong>Flapjack—graphical genotype visualization</strong> <div class="csl-block">Iain Milne, Paul Shaw, Gordon Stephen, Micha Bayer, Linda Cardle, William TB Thomas, Andrew J Flavell, David Marshall</div> <em>Bioinformatics</em> (2010-10-18) <a href="https://doi.org/cdvnt8">https://doi.org/cdvnt8</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/bioinformatics/btq580">10.1093/bioinformatics/btq580</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20956241">20956241</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995120">PMC2995120</a></div></div>
+<div class="csl-left-margin">9. </div><div class="csl-right-inline"><strong>Flapjack—graphical genotype visualization</strong> <div class="csl-block">Iain Milne, Paul Shaw, Gordon Stephen, Micha Bayer, Linda Cardle, William TB Thomas, Andrew J Flavell, David Marshall</div> <em>Bioinformatics</em> (2010-10-18) <a href="https://doi.org/cdvnt8">https://doi.org/cdvnt8</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/bioinformatics/btq580">10.1093/bioinformatics/btq580</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20956241">20956241</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995120">PMC2995120</a></div></div>
 </div>
 </div>
 <!-- default theme -->
diff --git a/manuscript.md b/manuscript.md
index fa53c74..557e3c5 100644
--- a/manuscript.md
+++ b/manuscript.md
@@ -7,7 +7,7 @@ keywords:
 - standards
 - community
 lang: en-US
-date-meta: '2024-03-13'
+date-meta: '2024-03-14'
 author-meta:
 - Peter "BrapMan" Selby
 - Trevor "Cool Kid" Rife
@@ -37,11 +37,11 @@ header-includes: |
   <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="2024-03-13" />
-  <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.date" content="2024-03-14" />
+  <meta name="citation_publication_date" content="2024-03-14" />
+  <meta property="article:published_time" content="2024-03-14" />
+  <meta name="dc.modified" content="2024-03-14T17:38:48+00:00" />
+  <meta property="article:modified_time" content="2024-03-14T17:38:48+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -102,9 +102,9 @@ header-includes: |
   <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/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/" />
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+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/manuscript.pdf" />
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   <meta property="twitter:card" content="summary_large_image" />
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@@ -126,10 +126,10 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/09f0067c036a09cb4b1d52af28fbf7db0cf025e6/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@09f0067](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/09f0067c036a09cb4b1d52af28fbf7db0cf025e6)
-on March 13, 2024.
+from [plantbreeding/BrAPI-Manuscript2@0b749b9](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/0b749b9c7850ae2c189e7eecf89b84e8c5f4c162)
+on March 14, 2024.
 </em></small>
 
 
@@ -429,11 +429,11 @@ BrAPI has further increased the value of GridScore by integrating it into the ov
 
 #### PHIS 
 
-The Hybrid Phenotyping Information System ([PHIS](http://www.phis.inrae.fr/)[doi:https://doi.org/10.1111/nph.15385]), based on the [OpenSILEX](https://github.com/OpenSILEX/) 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.
+The Hybrid Phenotyping Information System ([PHIS](http://www.phis.inrae.fr/)[@doi:https://doi.org/10.1111/nph.15385]), based on the [OpenSILEX](https://github.com/OpenSILEX/) 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.
 
 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.
 
-Furthermore, PHIS adheres to the Minimal Information About a Plant Phenotyping Experiment ([MIAPPE](https://www.miappe.org/)[doi:https://doi.org/10.1111/nph.16544]) and the Breeding API (BrAPI) standards. 
+Furthermore, PHIS adheres to the Minimal Information About a Plant Phenotyping Experiment ([MIAPPE](https://www.miappe.org/)[@doi:https://doi.org/10.1111/nph.16544]) and the Breeding API (BrAPI) standards. 
 
 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 [PHENOME](https://www.phenome-emphasis.fr/) and European [EMPHASIS](https://emphasis.plant-phenotyping.eu/) 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.
diff --git a/manuscript.pdf b/manuscript.pdf
index ad1e58b..d2a5e16 100644
Binary files a/manuscript.pdf and b/manuscript.pdf differ
diff --git a/references.json b/references.json
index d41af95..dac44aa 100644
--- a/references.json
+++ b/references.json
@@ -790,5 +790,274 @@
     "PMID": "34961276",
     "id": "dcg0274X",
     "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.3390/plants10122805"
+  },
+  {
+    "id": "OodVqG7n",
+    "type": "article-journal",
+    "abstract": "Summary\r\n            \r\n              \r\n                \r\n                  Phenomic datasets need to be accessible to the scientific community. Their reanalysis requires tracing relevant information on thousands of plants, sensors and events.\r\n                \r\n                \r\n                  \r\n                    The open‐source Phenotyping Hybrid Information System (\r\n                    PHIS\r\n                    ) is proposed for plant phenotyping experiments in various categories of installations (field, glasshouse). It unambiguously identifies all objects and traits in an experiment and establishes their relations via ontologies and semantics that apply to both field and controlled conditions. For instance, the genotype is declared for a plant or plot and is associated with all objects related to it. Events such as successive plant positions, anomalies and annotations are associated with objects so they can be easily retrieved.\r\n                  \r\n                \r\n                \r\n                  Its ontology‐driven architecture is a powerful tool for integrating and managing data from multiple experiments and platforms, for creating relationships between objects and enriching datasets with knowledge and metadata. It interoperates with external resources via web services, thereby allowing data integration into other systems; for example, modelling platforms or external databases.\r\n                \r\n                \r\n                  It has the potential for rapid diffusion because of its ability to integrate, manage and visualize multi‐source and multi‐scale data, but also because it is based on 10 yr of trial and error in our groups.",
+    "container-title": "New Phytologist",
+    "DOI": "https://doi.org/10.1111/nph.15385",
+    "ISSN": "0028-646X, 1469-8137",
+    "issue": "1",
+    "journalAbbreviation": "New Phytologist",
+    "language": "en",
+    "page": "588-601",
+    "source": "DOI.org (Crossref)",
+    "title": "Dealing with multi‐source and multi‐scale information in plant phenomics: the ontology‐driven Phenotyping Hybrid Information System",
+    "title-short": "Dealing with multi‐source and multi‐scale information in plant phenomics",
+    "URL": "https://doi.org/gm9b9j",
+    "volume": "221",
+    "author": [
+      {
+        "family": "Neveu",
+        "given": "Pascal"
+      },
+      {
+        "family": "Tireau",
+        "given": "Anne"
+      },
+      {
+        "family": "Hilgert",
+        "given": "Nadine"
+      },
+      {
+        "family": "Nègre",
+        "given": "Vincent"
+      },
+      {
+        "family": "Mineau‐Cesari",
+        "given": "Jonathan"
+      },
+      {
+        "family": "Brichet",
+        "given": "Nicolas"
+      },
+      {
+        "family": "Chapuis",
+        "given": "Romain"
+      },
+      {
+        "family": "Sanchez",
+        "given": "Isabelle"
+      },
+      {
+        "family": "Pommier",
+        "given": "Cyril"
+      },
+      {
+        "family": "Charnomordic",
+        "given": "Brigitte"
+      },
+      {
+        "family": "Tardieu",
+        "given": "François"
+      },
+      {
+        "family": "Cabrera‐Bosquet",
+        "given": "Llorenç"
+      }
+    ],
+    "accessed": {
+      "date-parts": [
+        [
+          "2024",
+          3,
+          14
+        ]
+      ]
+    },
+    "issued": {
+      "date-parts": [
+        [
+          "2019",
+          1
+        ]
+      ]
+    },
+    "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:https://doi.org/10.1111/nph.15385"
+  },
+  {
+    "id": "TVXmHLRk",
+    "type": "article-journal",
+    "abstract": "Summary\r\n            \r\n              \r\n                \r\n                  Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity.\r\n                \r\n                \r\n                  We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples.\r\n                \r\n                \r\n                  We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0.\r\n                \r\n                \r\n                  MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.",
+    "container-title": "New Phytologist",
+    "DOI": "https://doi.org/10.1111/nph.16544",
+    "ISSN": "0028-646X, 1469-8137",
+    "issue": "1",
+    "journalAbbreviation": "New Phytologist",
+    "language": "en",
+    "page": "260-273",
+    "source": "DOI.org (Crossref)",
+    "title": "Enabling reusability of plant phenomic datasets with MIAPPE 1.1",
+    "URL": "https://doi.org/gjqcmb",
+    "volume": "227",
+    "author": [
+      {
+        "family": "Papoutsoglou",
+        "given": "Evangelia A."
+      },
+      {
+        "family": "Faria",
+        "given": "Daniel"
+      },
+      {
+        "family": "Arend",
+        "given": "Daniel"
+      },
+      {
+        "family": "Arnaud",
+        "given": "Elizabeth"
+      },
+      {
+        "family": "Athanasiadis",
+        "given": "Ioannis N."
+      },
+      {
+        "family": "Chaves",
+        "given": "Inês"
+      },
+      {
+        "family": "Coppens",
+        "given": "Frederik"
+      },
+      {
+        "family": "Cornut",
+        "given": "Guillaume"
+      },
+      {
+        "family": "Costa",
+        "given": "Bruno V."
+      },
+      {
+        "family": "Ćwiek‐Kupczyńska",
+        "given": "Hanna"
+      },
+      {
+        "family": "Droesbeke",
+        "given": "Bert"
+      },
+      {
+        "family": "Finkers",
+        "given": "Richard"
+      },
+      {
+        "family": "Gruden",
+        "given": "Kristina"
+      },
+      {
+        "family": "Junker",
+        "given": "Astrid"
+      },
+      {
+        "family": "King",
+        "given": "Graham J."
+      },
+      {
+        "family": "Krajewski",
+        "given": "Paweł"
+      },
+      {
+        "family": "Lange",
+        "given": "Matthias"
+      },
+      {
+        "family": "Laporte",
+        "given": "Marie‐Angélique"
+      },
+      {
+        "family": "Michotey",
+        "given": "Célia"
+      },
+      {
+        "family": "Oppermann",
+        "given": "Markus"
+      },
+      {
+        "family": "Ostler",
+        "given": "Richard"
+      },
+      {
+        "family": "Poorter",
+        "given": "Hendrik"
+      },
+      {
+        "family": "Ramı́rez‐Gonzalez",
+        "given": "Ricardo"
+      },
+      {
+        "family": "Ramšak",
+        "given": "Živa"
+      },
+      {
+        "family": "Reif",
+        "given": "Jochen C."
+      },
+      {
+        "family": "Rocca‐Serra",
+        "given": "Philippe"
+      },
+      {
+        "family": "Sansone",
+        "given": "Susanna‐Assunta"
+      },
+      {
+        "family": "Scholz",
+        "given": "Uwe"
+      },
+      {
+        "family": "Tardieu",
+        "given": "François"
+      },
+      {
+        "family": "Uauy",
+        "given": "Cristobal"
+      },
+      {
+        "family": "Usadel",
+        "given": "Björn"
+      },
+      {
+        "family": "Visser",
+        "given": "Richard G. F."
+      },
+      {
+        "family": "Weise",
+        "given": "Stephan"
+      },
+      {
+        "family": "Kersey",
+        "given": "Paul J."
+      },
+      {
+        "family": "Miguel",
+        "given": "Célia M."
+      },
+      {
+        "family": "Adam‐Blondon",
+        "given": "Anne‐Françoise"
+      },
+      {
+        "family": "Pommier",
+        "given": "Cyril"
+      }
+    ],
+    "accessed": {
+      "date-parts": [
+        [
+          "2024",
+          3,
+          14
+        ]
+      ]
+    },
+    "issued": {
+      "date-parts": [
+        [
+          "2020",
+          7
+        ]
+      ]
+    },
+    "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:https://doi.org/10.1111/nph.16544"
   }
 ]
diff --git a/spelling-errors.txt b/spelling-errors.txt
index 15eb626..412e2b2 100644
--- a/spelling-errors.txt
+++ b/spelling-errors.txt
@@ -57,14 +57,14 @@ genotype
 Genotypes
 genotypic
 Genotyping
-germplasm
+Germplasm
 germplasms
 GIGWA
 GLIS
 GridScore
 hackathon
 hackathons
-haplotype
+Haplotype
 haplotypes
 HortControl
 Iain
@@ -72,7 +72,7 @@ ICARDA
 ImageBreed
 imilne
 INBS
-inrae
+INRAE
 interoperable
 intitated
 Investissements
@@ -80,8 +80,8 @@ IPK
 ISA
 ITPGRFA
 jlamossweeney
-JSON
-Khaled
+json
+khaled
 Lamos
 LD
 leetaei
@@ -104,11 +104,11 @@ OpenSILEX
 pangenome
 parralel
 PGRFA
-PHENOME
+Phenome
 phenomic
 Phenospex
 phenotypes
-phenotypic
+Phenotypic
 Phenotyping
 PHG
 PHIS’s
@@ -118,7 +118,7 @@ programmatically
 programme
 QBMS
 QTL
-Raubach
+raubach
 Rosaceae
 rPHG
 Saclay
diff --git a/variables.json b/variables.json
index c99e5da..e1a1f36 100644
--- a/variables.json
+++ b/variables.json
@@ -9,7 +9,7 @@
       "community"
     ],
     "lang": "en-US",
-    "date-meta": "2024-03-13",
+    "date-meta": "2024-03-14",
     "author-meta": [
       "Peter \"BrapMan\" Selby",
       "Trevor \"Cool Kid\" Rife",
@@ -29,7 +29,7 @@
       "Francisco López",
       "Marco Marsella"
     ],
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