Merge pull request #63 from plantbreeding/24-07-08-raubach-jhi-updates

[ci skip] This build is based on 4dc279b. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/4dc279b8cc8829731e62fb3e3210ceaf8b16745d/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/9858676128
plantbreeding · Jul 9, 2024 · 07a820f · 07a820f
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diff --git a/citations.tsv b/citations.tsv
@@ -41,6 +41,7 @@ doi:10.5281/zenodo.10791627	doi:10.5281/zenodo.10791627	doi:10.5281/zenodo.10791
 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
+doi:10.2135/cropsci2016.09.0814	doi:10.2135/cropsci2016.09.0814	doi:10.2135/cropsci2016.09.0814	rPgDlCbt
 doi:10.3389/fpls.2023.1290078	doi:10.3389/fpls.2023.1290078	doi:10.3389/fpls.2023.1290078	7WXz7FUP
 doi:10.1038/ng.1054	doi:10.1038/ng.1054	doi:10.1038/ng.1054	KZc5ayvK
 https://datatracker.ietf.org/doc/html/rfc6749	https://datatracker.ietf.org/doc/html/rfc6749	url:https://datatracker.ietf.org/doc/html/rfc6749	KpTrsTH1
diff --git a/manuscript.html b/manuscript.html
diff --git a/manuscript.md b/manuscript.md
@@ -7,7 +7,7 @@ keywords:
 - standards
 - community
 lang: en-US
-date-meta: '2024-07-08'
+date-meta: '2024-07-09'
 author-meta:
 - Peter Selby
 - Rafael Abbeloos
@@ -93,11 +93,11 @@ 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="2024-07-08" />
-  <meta name="citation_publication_date" content="2024-07-08" />
-  <meta property="article:published_time" content="2024-07-08" />
-  <meta name="dc.modified" content="2024-07-08T21:53:26+00:00" />
-  <meta property="article:modified_time" content="2024-07-08T21:53:26+00:00" />
+  <meta name="dc.date" content="2024-07-09" />
+  <meta name="citation_publication_date" content="2024-07-09" />
+  <meta property="article:published_time" content="2024-07-09" />
+  <meta name="dc.modified" content="2024-07-09T14:12:52+00:00" />
+  <meta property="article:modified_time" content="2024-07-09T14:12:52+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -245,7 +245,7 @@ header-includes: |
   <meta name="citation_author_institution" content="Buckler Lab and Institute for Genomic Diversity, Cornell University" />
   <meta name="citation_author_orcid" content="0000-0002-5454-4527" />
   <meta name="citation_author" content="Iain Milne" />
-  <meta name="citation_author_institution" content="The James Hutton Institute" />
+  <meta name="citation_author_institution" content="Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland" />
   <meta name="citation_author_orcid" content="0000-0002-4126-0859" />
   <meta name="citation_author" content="Lukas A. Mueller" />
   <meta name="citation_author_institution" content="The Boyce Thompson Institute" />
@@ -270,7 +270,7 @@ header-includes: |
   <meta name="citation_author_institution" content="AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France." />
   <meta name="citation_author_orcid" content="0000-0002-5679-3877" />
   <meta name="citation_author" content="Sebastian Raubach" />
-  <meta name="citation_author_institution" content="The James Hutton Institute" />
+  <meta name="citation_author_institution" content="Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland" />
   <meta name="citation_author_orcid" content="0000-0001-5659-247X" />
   <meta name="citation_author" content="Trevor Rife" />
   <meta name="citation_author_institution" content="Clemson University" />
@@ -290,10 +290,10 @@ header-includes: |
   <meta name="citation_author" content="Romil Mayank Shah" />
   <meta name="citation_author_institution" content="North Carolina State University" />
   <meta name="citation_author" content="Paul Shaw" />
-  <meta name="citation_author_institution" content="The James Hutton Institute" />
+  <meta name="citation_author_institution" content="Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland" />
   <meta name="citation_author_orcid" content="0000-0002-0202-1150" />
   <meta name="citation_author" content="Becky Smith" />
-  <meta name="citation_author_institution" content="The James Hutton Institute" />
+  <meta name="citation_author_institution" content="Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland" />
   <meta name="citation_author_orcid" content="0000-0002-8968-3383" />
   <meta name="citation_author" content="Nahuel Soldevilla" />
   <meta name="citation_author_institution" content="Integrated Breeding Platform" />
@@ -321,9 +321,9 @@ 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/95a2c7211089fbaeb417557db05cf57e4844ae4b/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/95a2c7211089fbaeb417557db05cf57e4844ae4b/" />
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+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/4dc279b8cc8829731e62fb3e3210ceaf8b16745d/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/4dc279b8cc8829731e62fb3e3210ceaf8b16745d/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/4dc279b8cc8829731e62fb3e3210ceaf8b16745d/manuscript.pdf" />
   <meta property="og:type" content="article" />
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@@ -345,10 +345,10 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/95a2c7211089fbaeb417557db05cf57e4844ae4b/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/4dc279b8cc8829731e62fb3e3210ceaf8b16745d/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@95a2c72](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/95a2c7211089fbaeb417557db05cf57e4844ae4b)
-on July 8, 2024.
+from [plantbreeding/BrAPI-Manuscript2@4dc279b](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/4dc279b8cc8829731e62fb3e3210ceaf8b16745d)
+on July 9, 2024.
 </em></small>
 
 
@@ -834,7 +834,7 @@ on July 8, 2024.
     [imilne](https://github.com/imilne)
     <br>
   <small>
-     The James Hutton Institute
+     Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland
   </small>
 
 + **Lukas A. Mueller**
@@ -924,7 +924,7 @@ on July 8, 2024.
     [sebastian-raubach](https://github.com/sebastian-raubach)
     <br>
   <small>
-     The James Hutton Institute
+     Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland
   </small>
 
 + **Trevor Rife**
@@ -994,7 +994,7 @@ on July 8, 2024.
     [cardinalb](https://github.com/cardinalb)
     <br>
   <small>
-     The James Hutton Institute
+     Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland
   </small>
 
 + **Becky Smith**
@@ -1005,7 +1005,7 @@ on July 8, 2024.
     [Batbaby91](https://github.com/Batbaby91)
     <br>
   <small>
-     The James Hutton Institute
+     Information and Computational Sciences Department, The James Hutton Institute, Dundee, Scotland
   </small>
 
 + **Nahuel Soldevilla**
@@ -1391,7 +1391,7 @@ Right now, BIMS primarily utilizes BrAPI to connect with the Field Book Android
 #### Germinate
 
 <!-- Sebastian R -->
-[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](https://ics.hutton.ac.uk/get-germinate/) [@doi:10.1002/csc2.20248;@doi:10.2135/cropsci2016.09.0814] 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. Additionally, 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 data integrity.
 

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/references.json b/references.json
@@ -2963,6 +2963,69 @@
     "id": "MlqG0w6i",
     "note": "This CSL Item was generated by Manubot v0.5.6 from its persistent identifier (standard_id).\nstandard_id: doi:10.2135/cropsci2013.08.0579"
   },
+  {
+    "publisher": "Wiley",
+    "issue": "3",
+    "abstract": "<jats:p>Conservation and exploitation of crop wild relative species is an important component in ensuring food security and improving current agricultural output. By identifying agriculturally important characteristics that express favorable response to both biotic and abiotic stress currently unused by breeders, the incorporation of this new genetic material into genetic background stocks may help mitigate problems imposed by climate change, land degradation, and population pressure. This is particularly important in countries that will be more severely affected by the threat of reduced yields. The ability to effectively manage genetic resources collections and integrate unique and diverse data types is crucial in exploring, understanding, and exploiting the diversity contained within genebanks. Providing a common interface through which experimental and background data can be disseminated to both researchers and breeders will bring focus and facilitate community building into research communities. We have taken wild barley (<jats:italic>Hordeum</jats:italic> spp.) and potato (<jats:italic>Solanum</jats:italic> spp.) collections along with wheat (<jats:italic>Triticum</jats:italic> spp.) and maize (<jats:italic>Zea mays</jats:italic> subsp. <jats:italic>mays</jats:italic>) and their wild relatives and incorporated this data into web‐based information resources built using the Germinate platform (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://ics.hutton.ac.uk/get-germinate\">https://ics.hutton.ac.uk/get‐germinate</jats:ext-link>, accessed 4 Apr. 2017). We have tailored these to better meet the demands of researchers by developing both new data visualization tools and integration with current software such as Helium, Flapjack, and CurlyWhirly (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://ics.hutton.ac.uk/software\">https://ics.hutton.ac.uk/software</jats:ext-link>, accessed 4 Apr. 2017) and presented the data in a common platform. While the underlying species differ, the approach taken ensures that tools are compatible across all database instances. We will describe these database instances and show that Germinate offers a common platform that will aid in the exploration and wider use of these species.</jats:p>",
+    "DOI": "10.2135/cropsci2016.09.0814",
+    "type": "article-journal",
+    "page": "1259-1273",
+    "source": "Crossref",
+    "title": "Germinate 3: Development of a Common Platform to Support the Distribution of Experimental Data on Crop Wild Relatives",
+    "volume": "57",
+    "author": [
+      {
+        "given": "Paul D.",
+        "family": "Shaw"
+      },
+      {
+        "given": "Sebastian",
+        "family": "Raubach"
+      },
+      {
+        "given": "Sarah J.",
+        "family": "Hearne"
+      },
+      {
+        "given": "Kate",
+        "family": "Dreher"
+      },
+      {
+        "given": "Glenn",
+        "family": "Bryan"
+      },
+      {
+        "given": "Gaynor",
+        "family": "McKenzie"
+      },
+      {
+        "given": "Iain",
+        "family": "Milne"
+      },
+      {
+        "given": "Gordon",
+        "family": "Stephen"
+      },
+      {
+        "given": "David F.",
+        "family": "Marshall"
+      }
+    ],
+    "container-title": "Crop Science",
+    "language": "en",
+    "issued": {
+      "date-parts": [
+        [
+          2017,
+          5
+        ]
+      ]
+    },
+    "URL": "https://doi.org/gbmz5t",
+    "container-title-short": "Crop Science",
+    "id": "rPgDlCbt",
+    "note": "This CSL Item was generated by Manubot v0.5.6 from its persistent identifier (standard_id).\nstandard_id: doi:10.2135/cropsci2016.09.0814"
+  },
   {
     "publisher": "Wiley",
     "issue": "5",
@@ -3578,7 +3641,7 @@
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diff --git a/spelling-errors.txt b/spelling-errors.txt
@@ -82,10 +82,10 @@ OpenAPI
 Palladino
 pascalneveu
 Pérez
-Puthick
+puthick
 Rami
 Rica
-Romil
+romil
 RShiny
 SCT
 SCYarnes

diff --git a/variables.json b/variables.json
-Original file line number
+Diff line change
@@ Expand Up / @@ -82,10 +82,10 @@ OpenAPI @@
     Palladino
     pascalneveu
     Pérez
-    Puthick
+    puthick
     Rami
     Rica
-    Romil
+    romil
     RShiny
     SCT
     SCYarnes
@@ Expand Down @@