Kelly Robbins feedback/edits

[ci skip]

This build is based on
982057e.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/982057ee7978b2e4e83a9452e1bdb9cd6a851231/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/9944913548

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/d00841fc47e8764c25a9c65e15c4d72427b78a96/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/982057ee7978b2e4e83a9452e1bdb9cd6a851231/>.
 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
-[`d00841fc47e8764c25a9c65e15c4d72427b78a96`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/d00841fc47e8764c25a9c65e15c4d72427b78a96).
+[`982057ee7978b2e4e83a9452e1bdb9cd6a851231`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/982057ee7978b2e4e83a9452e1bdb9cd6a851231).

index.html

@@ -126,8 +126,8 @@
   <meta name="dc.date" content="2024-07-15" />
   <meta name="citation_publication_date" content="2024-07-15" />
   <meta property="article:published_time" content="2024-07-15" />
-  <meta name="dc.modified" content="2024-07-15T18:31:39+00:00" />
-  <meta property="article:modified_time" content="2024-07-15T18:31:39+00:00" />
+  <meta name="dc.modified" content="2024-07-15T18:47:53+00:00" />
+  <meta property="article:modified_time" content="2024-07-15T18:47:53+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -357,9 +357,9 @@
   <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/d00841fc47e8764c25a9c65e15c4d72427b78a96/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/d00841fc47e8764c25a9c65e15c4d72427b78a96/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/d00841fc47e8764c25a9c65e15c4d72427b78a96/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/982057ee7978b2e4e83a9452e1bdb9cd6a851231/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/982057ee7978b2e4e83a9452e1bdb9cd6a851231/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/982057ee7978b2e4e83a9452e1bdb9cd6a851231/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" />
@@ -376,9 +376,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/d00841fc47e8764c25a9c65e15c4d72427b78a96/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/982057ee7978b2e4e83a9452e1bdb9cd6a851231/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/d00841fc47e8764c25a9c65e15c4d72427b78a96">plantbreeding/BrAPI-Manuscript2@d00841f</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/982057ee7978b2e4e83a9452e1bdb9cd6a851231">plantbreeding/BrAPI-Manuscript2@982057e</a>
 on July 15, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -929,7 +929,7 @@ <h2 id="authors">Authors</h2>
 <br>
 <small>
 Cornell University
-· Funded by The Bill and Malinda Gates Foundation in cooperation with the Excellence in Breeding Platform of the CGIAR
+· Funded by The BrAPI Project is funded by the USDA grant NIFA-DSFAS 2022-67021-37024.
 </small></p></li>
 <li><p><strong>Mathieu Rouard</strong>
 <br>
@@ -1125,7 +1125,7 @@ <h4 id="climmob">ClimMob</h4>
 <p><a href="https://climmob.net/">ClimMob</a><span class="citation" data-cites="LCpCba21"><sup><a href="#ref-LCpCba21" role="doc-biblioref">4</a></sup></span> is a software suite for a different research paradigm in experimental agriculture. In traditional breeding, a few researchers design complicated trials in search of the best solutions for a few target environments. ClimMob enables many participants to carry out reasonably simple experiments across many environments. Taken together, this data across many environments can be very informative. It applies the principles of citizen science and choice experiments to scale the data collection process, mostly in the format of rankings. Although this data may not be as detailed as from a centralized experiment, it can be very useful to inform decisions to a wide range of locations and environments with increased external validity. ClimMob applications include testing crop varieties, evaluating agronomic practices, and investigating climate resilience strategies. The platform supports experiment design, data collection through mobile apps, and data analysis to provide actionable insights.</p>
 <p>During a crop trial, all farmer-collected data is stored in ClimMob. When data collection is complete, the raw data is automatically uploaded via BrAPI to a central breeding database for long-term storage and analysis. To facilitate this synchronization, ClimMob uses BrAPI to retrieve curated germplasm information from breeding databases when designing a trial, significantly enhancing data quality. Additionally, a process has been developed to push analyzed data from ClimMob to the breeding databases, providing breeders with insights into the potential adoption of the tested crop varieties.</p>
 <h4 id="imagebreed">ImageBreed</h4>
-<p><a href="https://imagebreed.org/">ImageBreed</a><span class="citation" data-cites="Dhlmsxng"><sup><a href="#ref-Dhlmsxng" role="doc-biblioref">5</a></sup></span> is an image collection pipeline tool to support regular use of UAVs and UGVs. High-throughput phenotyping has been gaining significant traction lately as a way to collect lots of data very quickly. Image collection from unmanned aerial and ground vehicles (UAVs and UGVs) are a great way to collect a lot of raw data all at once, then analyze it later.</p>
+<p><a href="https://imagebreed.org/">ImageBreed</a><span class="citation" data-cites="Dhlmsxng"><sup><a href="#ref-Dhlmsxng" role="doc-biblioref">5</a></sup></span> is an image collection pipeline tool to support regular use of UAVs and UGVs. High-throughput phenotyping has been gaining significant traction lately as a way to collect large amounts of data very quickly. Image collection from unmanned aerial and ground vehicles (UAVs and UGVs) are a great way to collect a lot of raw data all at once, then analyze it later.</p>
 <p>When the raw images have been processed through the standardization pipelines in ImageBreed, useful phenotypes can be extracted from the images. The BrAPI standard is used to push these phenotypes back to a central breeding database where they can be analyzed with other data. In addition to this, ImageBreed has the ability to use BrAPI to upload the raw images to the central breeding database, or any other BrAPI compatible long term storage service. In the current version of the standard (V2.1), the BrAPI data models for images are rudimentary, but effective. The ImageBreed team has put in some work into enhancing the BrAPI image data standards, collaborating with others in the community.</p>
 <h4 id="phis">PHIS</h4>
 <!-- Isabelle -->
@@ -1240,7 +1240,7 @@ <h3 id="analytics">Analytics</h3>
 <p>The tools developed by the BrAPI community can pull in data from multiple BrAPI compatible data sources and provide enhanced analytical functionality. In many cases, there is no longer a need to import and export large data files to a local computational environment just to run standard analytical models. These tools are able to extract the data they need from a data source without much human intervention or human error.</p>
 <h4 id="g-crunch">G-Crunch</h4>
 <!-- Josh -->
-<p>G-Crunch is an upcoming user-facing analysis tool that attempts to fill the space of simple, user driven analytics requests, with a generic user interface and the ability to swap out data sources and analysis tools. G-Crunch hopes to streamline repeatable, debuggable, simple analytic requests and results.</p>
+<p>G-Crunch is an upcoming user-facing analysis tool that integrates genomic and phenotypic data to fulfill the need for simple, user driven analytics requests. It includes a generic user interface and the ability to swap out data sources and analysis tools. The G-Crunch team hopes to streamline repeatable, debuggable, simple analytic requests and results.</p>
 <p>G-Crunch, as a tool, couldn’t feasibly exist without BrAPI. The support of BrAPI interfaces allows G-Crunch to use one unified request method, and adapt to the user’s (BrAPI-compliant) existing network of tools. This lowers the barrier to entry for adoption, and makes analysis pipelines easily repeatable.</p>
 <h4 id="qbms">QBMS</h4>
 <!-- Khaled -->
@@ -1288,7 +1288,7 @@ <h2 id="discussion">Discussion</h2>
 <h3 id="brapi-for-breeders-and-scientists">BrAPI for Breeders and Scientists</h3>
 <p>The BrAPI technical specification document is meant to be read and used by software developers. However, the purpose of the specification, and the community around it, is to make things faster, easier, and cheaper for the breeders and scientists working on breeding, genetics, phenomics and other agricultural projects. BrAPI offers a convenient path to automation, interoperability, and data integration for software tools in those domains. All of the software described above could be made interoperable with manual effort, moving and editing data files by hand from tool to tool. However, when the basic structure and flow of data becomes automated, breeders and scientists can spend less time on data management and more time focusing on the science. For many, the ultimate goal is the development of a digital ecosystem: a collection of software tools and applications that can all work together seamlessly. In this ideal digital ecosystem, data is collected digitally from the beginning, reducing as much human error as possible. The data is checked by quality control and stored automatically, then it can be sent to any internal tool or external lab for further analysis with just the click of a button. This idea might sound too good to be true, but as more tools start sharing a universal data standard, automating data flow becomes easier, and the community gets closer to total interoperability.</p>
 <h3 id="looking-ahead">Looking Ahead</h3>
-<p>The BrAPI specification will continue a controlled and necessary growth. It will enable more use cases and new types of data that might include newer scientific techniques and technologies. There will be careful evaluation the relevance of using REST web service approaches, and in particular BrAPI, for things like drone imaging data, spectroscopy, LIDAR, metabolomics, transcriptomics, high-throughput phenotyping, pan genomes, and machine learning analysis. All of these technologies can open new avenues for research and development of new crop varieties. All of these technologies also generate more data, and require data sharing between different software applications and data repositories. The BrAPI project leadership and community is committed to building the standards to support these new use cases as they arrive and become accepted by the scientific community. In fact, small groups within the BrAPI community have already start building generic data models and proposed communication standards for many of the technologies listed above. These community efforts will eventually become part of the BrAPI standard in a future version of the specification document.</p>
+<p>The BrAPI specification will continue a controlled and necessary growth. It will enable more use cases and new types of data that might include newer scientific techniques and technologies. There will be careful evaluation of the relevance of using REST web service approaches, and in particular BrAPI, for things like drone imaging data, spectroscopy, LIDAR, metabolomics, transcriptomics, high-throughput phenotyping, pan genomes, and machine learning analysis. All of these technologies can open new avenues for research and development of new crop varieties. However, they will also generate more data, more types of data, and require data sharing between different software applications and data repositories. The BrAPI project leadership and community is committed to building the standards to support these new use cases as they arrive and become accepted by the scientific community. In fact, small groups within the BrAPI community have already start building generic data models and proposed communication standards for many of the technologies listed above. These community efforts will eventually become part of the BrAPI standard in a future version of the specification document.</p>
 <p>Expanding the BrAPI specification is important for the community, however it is just as important not to reinvent or compete with existing functional standards. Additions to the BrAPI specification are reviewed thoroughly by the community to make sure BrAPI is compliant with existing standards and data structures. For example, the community has requested compliance with the GFF3 standard for genomic data and the GeoTIFF standard for aerial image data. Pieces of these existing popular data structures might be integrated into the overall BrAPI standard documentation. In some cases, BrAPI will only reference other standards instead of including them in the specification. For example, there have been community discussions around developing connections with the NOAA CDO standard for weather data, or the Galaxy Analytics API for analytics pipeline controls and information. These standards are perfectly adequate on their own, recreating them in the BrAPI standard would be redundant and outside the main scope of the project.</p>
 <h3 id="conclusion">Conclusion</h3>
 <p>The BrAPI project only exists because of the community of software engineers, biologists, and other scientists who support and use it. While there were many tools and use cases presented here, it is not an exhaustive list of all BrAPI compliant systems. As long as the standard continues to be supported, there is potential for exponential growth of the community. As more groups make their tools BrAPI compliant, these tools can be shared with the community. As more BrAPI compliant tools are shared with the community, more groups can see the value in implementing BrAPI in their own tools. This feedback loop will allow the community to strengthen and grow.</p>
@@ -1308,7 +1308,7 @@ <h2 id="acknowledgements">Acknowledgements</h2>
 <p>The authors would like to acknowledge the following funding sources:</p>
 <ul>
 <li>The BrAPI Project is funded by the USDA grant NIFA-DSFAS 2022-67021-37024.</li>
-<li>Innovation Lab for Crop Improvement Cornell, FFAR</li>
+<li>Innovation Lab for Crop Improvement Cornell, ILCI: 7200AA19LE00005, FFAR: CA20-SS-0000000103</li>
 <li>The AGENT project is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 862613.</li>
 <li>USDA National Institute of Food and Agriculture National Research Support Project 10</li>
 <li>USDA NIFA: 2022-51181-38449</li>