Merge pull request #12 from plantbreeding/cpommier-patch-3

[ci skip] This build is based on 34cb3cc. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8113650616
plantbreeding · Mar 1, 2024 · ea881b8 · ea881b8
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diff --git a/citations.tsv b/citations.tsv
@@ -1,5 +1,7 @@
 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: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
+doi:10.1002/csc2.20248	doi:10.1002/csc2.20248	doi:10.1002/csc2.20248	sW9euzzP
diff --git a/manuscript.html b/manuscript.html
diff --git a/manuscript.md b/manuscript.md
@@ -7,13 +7,14 @@ keywords:
 - standards
 - community
 lang: en-US
-date-meta: '2024-02-29'
+date-meta: '2024-03-01'
 author-meta:
 - Peter "BrapMan" Selby
 - Trevor "Cool Kid" Rife
 - Khaled Al-Shamaa
 - Isabelle Alic
 - Sebastian "Baz" Raubach
+- Paul Shaw
 - Iain Milne
 - Cyril Pommier
 - Becky Smith
@@ -33,11 +34,11 @@ 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="2024-02-29" />
-  <meta name="citation_publication_date" content="2024-02-29" />
-  <meta property="article:published_time" content="2024-02-29" />
-  <meta name="dc.modified" content="2024-02-29T22:27:49+00:00" />
-  <meta property="article:modified_time" content="2024-02-29T22:27:49+00:00" />
+  <meta name="dc.date" content="2024-03-01" />
+  <meta name="citation_publication_date" content="2024-03-01" />
+  <meta property="article:published_time" content="2024-03-01" />
+  <meta name="dc.modified" content="2024-03-01T15:49:02+00:00" />
+  <meta property="article:modified_time" content="2024-03-01T15:49:02+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -58,6 +59,9 @@ header-includes: |
   <meta name="citation_author" content="Sebastian &#34;Baz&#34; Raubach" />
   <meta name="citation_author_institution" content="The James Hutton Institute" />
   <meta name="citation_author_orcid" content="0000-0001-5659-247X" />
+  <meta name="citation_author" content="Paul Shaw" />
+  <meta name="citation_author_institution" content="The James Hutton Institute" />
+  <meta name="citation_author_orcid" content="0000-0002-0202-1150" />
   <meta name="citation_author" content="Iain Milne" />
   <meta name="citation_author_institution" content="The James Hutton Institute" />
   <meta name="citation_author_orcid" content="0000-0002-4126-0859" />
@@ -88,9 +92,9 @@ 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/bbbe0c0843123d36f9b7701e83725d4f9c401dc7/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/bbbe0c0843123d36f9b7701e83725d4f9c401dc7/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/bbbe0c0843123d36f9b7701e83725d4f9c401dc7/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/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" />
@@ -112,10 +116,10 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/bbbe0c0843123d36f9b7701e83725d4f9c401dc7/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@bbbe0c0](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/bbbe0c0843123d36f9b7701e83725d4f9c401dc7)
-on February 29, 2024.
+from [plantbreeding/BrAPI-Manuscript2@34cb3cc](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e)
+on March 1, 2024.
 </em></small>
 
 
@@ -165,6 +169,7 @@ on February 29, 2024.
     <br>
   <small>
      INRAE
+     · Funded by {'Short version': 'This work was supported by the project Phenome-ANR-11-INBS-0012'}; {'OR Long version': "This work was supported by the Agence Nationale de la Recherche, programme Investissements d'avenir, ANR-11-INBS-0012 (Phenome)"}
   </small>
 
 + **Sebastian "Baz" Raubach**
@@ -178,6 +183,17 @@ on February 29, 2024.
      The James Hutton Institute
   </small>
 
++ **Paul Shaw**
+  <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
+    [0000-0002-0202-1150](https://orcid.org/0000-0002-0202-1150)
+    · ![GitHub icon](images/github.svg){.inline_icon width=16 height=16}
+    [cardinalb](https://github.com/cardinalb)
+    <br>
+  <small>
+     The James Hutton Institute
+  </small>
+
 + **Iain Milne**
   <br>
     ![ORCID icon](images/orcid.svg){.inline_icon width=16 height=16}
@@ -198,7 +214,7 @@ on February 29, 2024.
     <br>
   <small>
      Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France; Université Paris-Saclay, INRAE, URGI, Versailles, France
-     · Funded by French Infrastructure en Biologie Santé ‘Phenome-FPPN’ supported by the French National Research Agency (ANR-11-INBS-0012)
+     · Funded by {'Short version': 'This work was supported by the project Phenome-ANR-11-INBS-0012'}; {'OR Long version': "This work was supported by the Agence Nationale de la Recherche, programme Investissements d'avenir, ANR-11-INBS-0012 (Phenome)"}
   </small>
 
 + **Becky Smith**
@@ -364,6 +380,11 @@ High-throughput phenotyping has been gaining significant traction lately as a wa
 
 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 also has the option to use BrAPI to upload the raw images to the central breeding database, or any other BrAPI compatible long term storage service. The BrAPI models in the current version of the standard (V2.1) are rudimentary, but effective. The ImageBreed team has put in some work to enhance the BrAPI image data standards. 
 
+#### GridScore
+
+Phenotypic data collection underpins scientific crop research and plant breeding. Knowledge gained from collected data and its analysis alongside data visualizations inform further phenotypic trials and ideally support research hypotheses. The importance of accuracy and efficiency in the collection of this data as well as the infrastructure to facilitate the flow of data from the field to a knowledge base cannot be underestimated. [GridScore](https://ics.hutton.ac.uk/get-gridscore/) [@doi:10.1186/s12859-022-04755-2] is a modern mobile application for phenotypic observations that harnesses technological advancements in the area of mobile devices to enrich the data collection process.
+
+BrAPI has further increased the value of GridScore by integrating it into the overarching workflow from trial creation, data collection, and its ultimate data storage for further processing. Specifically, trial designs as well as trait definitions can be imported into GridScore using BrAPI and a finalized trial can ultimately be exported via BrAPI to any compatible database.
 
 ### Data Management 
 
@@ -430,7 +451,10 @@ BIMS (Breeding Information Management System) [@doi:10.1093/database/baab054] is
 #### Germinate
 
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
-Germinate is a combination breeding database and germplasm management database. 
+
+[Germinate](https://ics.hutton.ac.uk/get-germinate/) [@doi:10.1002/csc2.20248] 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.
+
+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.
 
 
 ### Federated Data Management Infrastructures

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/references.json b/references.json
@@ -1,4 +1,169 @@
 [
+  {
+    "publisher": "Wiley",
+    "issue": "3",
+    "abstract": "<jats:title>Abstract</jats:title><jats:p>Management and distribution of experimental data from prebreeding projects is important to ensure uptake of germplasm into breeding and research programs. Being able to access and share this data in standard formats is essential. The adoption of a common informatics platform for crops that may have limited resources brings economies of scale, allowing common informatics components to be used across multiple species. The close integration of such a platform with commonly used breeding software, visualization, and analysis tools reduces the barrier for entry to researchers and provides a common framework to facilitate collaborations and data sharing. This work presents significant updates to the Germinate platform and highlights its value in distributing prebreeding data for 14 crops as part of the project ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ (hereafter Crop Trust Crop Wild Relatives project) led by the Crop Trust (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://www.cwrdiversity.org\">https://www.cwrdiversity.org</jats:ext-link>). The addition of data on these species compliments data already publicly available in Germinate. We present a suite of updated Germinate features using examples from these crop species and their wild relatives. The use of Germinate within the Crop Trust Crop Wild Relatives project demonstrates the usefulness of the system and the benefits a shared informatics platform provides. These data resources provide a foundation on which breeding and research communities can develop additional online resources for their crops, harness new data as it becomes available, and benefit collectively from future developments of the Germinate platform.</jats:p>",
+    "DOI": "10.1002/csc2.20248",
+    "type": "article-journal",
+    "page": "1538-1566",
+    "source": "Crossref",
+    "title": "From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives",
+    "volume": "61",
+    "author": [
+      {
+        "given": "Sebastian",
+        "family": "Raubach"
+      },
+      {
+        "given": "Benjamin",
+        "family": "Kilian"
+      },
+      {
+        "given": "Kate",
+        "family": "Dreher"
+      },
+      {
+        "given": "Ahmed",
+        "family": "Amri"
+      },
+      {
+        "given": "Filippo M.",
+        "family": "Bassi"
+      },
+      {
+        "given": "Ousmane",
+        "family": "Boukar"
+      },
+      {
+        "given": "Douglas",
+        "family": "Cook"
+      },
+      {
+        "given": "Alan",
+        "family": "Cruickshank"
+      },
+      {
+        "given": "Christian",
+        "family": "Fatokun"
+      },
+      {
+        "given": "Noureddine",
+        "family": "El Haddad"
+      },
+      {
+        "given": "Alan",
+        "family": "Humphries"
+      },
+      {
+        "given": "David",
+        "family": "Jordan"
+      },
+      {
+        "given": "Zakaria",
+        "family": "Kehel"
+      },
+      {
+        "given": "Shiv",
+        "family": "Kumar"
+      },
+      {
+        "given": "Sandy Jan",
+        "family": "Labarosa"
+      },
+      {
+        "given": "Loi Huu",
+        "family": "Nguyen"
+      },
+      {
+        "given": "Emma",
+        "family": "Mace"
+      },
+      {
+        "given": "Susan",
+        "family": "McCouch"
+      },
+      {
+        "given": "Ken",
+        "family": "McNally"
+      },
+      {
+        "given": "David F.",
+        "family": "Marshall"
+      },
+      {
+        "given": "Erick Owuor",
+        "family": "Mikwa"
+      },
+      {
+        "given": "Iain",
+        "family": "Milne"
+      },
+      {
+        "given": "Damaris Achieng",
+        "family": "Odeny"
+      },
+      {
+        "given": "Mariola",
+        "family": "Plazas"
+      },
+      {
+        "given": "Jaime",
+        "family": "Prohens"
+      },
+      {
+        "given": "Loren H.",
+        "family": "Rieseberg"
+      },
+      {
+        "given": "Roland",
+        "family": "Schafleitner"
+      },
+      {
+        "given": "Shivali",
+        "family": "Sharma"
+      },
+      {
+        "given": "Gordon",
+        "family": "Stephen"
+      },
+      {
+        "given": "Huynh Quang",
+        "family": "Tin"
+      },
+      {
+        "given": "Abou",
+        "family": "Togola"
+      },
+      {
+        "given": "Emily",
+        "family": "Warschefsky"
+      },
+      {
+        "given": "Peter",
+        "family": "Werner"
+      },
+      {
+        "given": "Paul D.",
+        "family": "Shaw"
+      },
+      {}
+    ],
+    "container-title": "Crop Science",
+    "language": "en",
+    "issued": {
+      "date-parts": [
+        [
+          2020,
+          8,
+          20
+        ]
+      ]
+    },
+    "URL": "https://doi.org/gm66th",
+    "container-title-short": "Crop Science",
+    "id": "sW9euzzP",
+    "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1002/csc2.20248"
+  },
   {
     "publisher": "Oxford University Press (OUP)",
     "issue": "20",
@@ -442,6 +607,47 @@
     "id": "eaDrNpsp",
     "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1093/nar/gky1000"
   },
+  {
+    "publisher": "Springer Science and Business Media LLC",
+    "issue": "1",
+    "abstract": "<jats:title>Abstract</jats:title><jats:sec>\n                <jats:title>Background</jats:title>\n                <jats:p>Plant breeding and crop research rely on experimental phenotyping trials. These trials generate data for large numbers of traits and plant varieties that needs to be captured efficiently and accurately to support further research and downstream analysis. Traditionally scored by hand, phenotypic data is nowadays collected using spreadsheets or specialized apps. While many solutions exist, which increase efficiency and reduce errors, none offer the same familiarity as printed field plans which have been used for decades and offer an intuitive overview over the trial setup, previously recorded data and plots still requiring scoring.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Results</jats:title>\n                <jats:p>We introduce GridScore which utilizes cutting-edge web technologies to reproduce the familiarity of printed field plans while enhancing the phenotypic data collection process by adding advanced features like georeferencing, image tagging and speech recognition. GridScore is a cross-platform open-source plant phenotyping app that combines barcode-based systems with a guided data collection approach while offering a top-down view onto the data collected in a field layout. GridScore is compared to existing tools across a wide spectrum of criteria including support for barcodes, multiple platforms, and visualizations.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Conclusion</jats:title>\n                <jats:p>Compared to its competition, GridScore shows strong performance across the board offering a complete manual phenotyping experience.</jats:p>\n              </jats:sec>",
+    "DOI": "10.1186/s12859-022-04755-2",
+    "type": "article-journal",
+    "source": "Crossref",
+    "title": "GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization",
+    "volume": "23",
+    "author": [
+      {
+        "given": "Sebastian",
+        "family": "Raubach"
+      },
+      {
+        "given": "Miriam",
+        "family": "Schreiber"
+      },
+      {
+        "given": "Paul D.",
+        "family": "Shaw"
+      }
+    ],
+    "container-title": "BMC Bioinformatics",
+    "language": "en",
+    "issued": {
+      "date-parts": [
+        [
+          2022,
+          6,
+          6
+        ]
+      ]
+    },
+    "URL": "https://doi.org/gtkcsv",
+    "container-title-short": "BMC Bioinformatics",
+    "PMCID": "PMC9169276",
+    "PMID": "35668357",
+    "id": "Ne0E9HbC",
+    "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1186/s12859-022-04755-2"
+  },
   {
     "publisher": "MDPI AG",
     "issue": "12",

diff --git a/spelling-error-locations.txt b/spelling-error-locations.txt
@@ -94,6 +94,17 @@ content/03.01.data-collection.md:28:ImageBreed
 content/03.01.data-collection.md:28:ImageBreed
 content/03.01.data-collection.md:28:phenotypes
 content/03.01.data-collection.md:28:phenotypes
+content/03.01.data-collection.md:30:GridScore
+content/03.01.data-collection.md:32:gridscore
+content/03.01.data-collection.md:32:GridScore
+content/03.01.data-collection.md:32:phenotypic
+content/03.01.data-collection.md:32:phenotypic
+content/03.01.data-collection.md:32:Phenotypic
+content/03.01.data-collection.md:34:BrAPI
+content/03.01.data-collection.md:34:BrAPI
+content/03.01.data-collection.md:34:BrAPI
+content/03.01.data-collection.md:34:GridScore
+content/03.01.data-collection.md:34:GridScore
 content/03.02.data-management.md:5:BrAPI
 content/03.02.data-management.md:10:OpenSILEX
 content/03.02.data-management.md:10:OpenSILEX
@@ -184,7 +195,17 @@ content/03.02.data-management.md:61:germplasm
 content/03.02.data-management.md:61:GIGWA
 content/03.02.data-management.md:61:Rosaceae
 content/03.02.data-management.md:61:Vaccinium
-content/03.02.data-management.md:66:germplasm
+content/03.02.data-management.md:67:BrAPI
+content/03.02.data-management.md:67:BrAPI
+content/03.02.data-management.md:67:genotypic
+content/03.02.data-management.md:67:phenotypic
+content/03.02.data-management.md:69:BrAPI
+content/03.02.data-management.md:69:BrAPI
+content/03.02.data-management.md:69:BrAPI
+content/03.02.data-management.md:69:BrAPI
+content/03.02.data-management.md:69:genotypic
+content/03.02.data-management.md:69:GridScore
+content/03.02.data-management.md:69:phenotypic
 content/03.03.federation-infrastructure.md:5:agrosystems
 content/03.03.federation-infrastructure.md:5:genebanks
 content/03.03.federation-infrastructure.md:5:germplasm