Merge pull request #42 from plantbreeding/helium-text

[ci skip] This build is based on f8e5556. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/f8e55569f5cb11fe0ecc7954df3385314242aa77/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8990107251
plantbreeding · May 7, 2024 · 1a43c1d · 1a43c1d
1 parent e392c5f
commit 1a43c1d
Show file tree

Hide file tree

Showing 8 changed files with 327 additions and 93 deletions.
diff --git a/citations.tsv b/citations.tsv
@@ -18,5 +18,8 @@ doi:10.1093/nar/gkac852	doi:10.1093/nar/gkac852	doi:10.1093/nar/gkac852	pk5OwSG6
 doi:10.1111/nph.16544	doi:10.1111/nph.16544	doi:10.1111/nph.16544	kWLsm7g6
 doi:10.1038/ng.1054	doi:10.1038/ng.1054	doi:10.1038/ng.1054	KZc5ayvK
 doi:10.1093/bioinformatics/btq580	doi:10.1093/bioinformatics/btq580	doi:10.1093/bioinformatics/btq580	Wz8l0HlN
+doi:10.1186/1471-2105-15-259	doi:10.1186/1471-2105-15-259	doi:10.1186/1471-2105-15-259	X22hwO1v
+doi:10.3389/fpls.2024.1268847	doi:10.3389/fpls.2024.1268847	doi:10.3389/fpls.2024.1268847	1HmEHgW8h
+doi:10.1007/s10592-024-01611-z	doi:10.1007/s10592-024-01611-z	doi:10.1007/s10592-024-01611-z	x8DIc6zn
 doi:10.1093/gigascience/giz051	doi:10.1093/gigascience/giz051	doi:10.1093/gigascience/giz051	AVjkjraw
 doi:10.1002/ppp3.10187	doi:10.1002/ppp3.10187	doi:10.1002/ppp3.10187	bvSFyrtt
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: '2024-04-18'
+date-meta: '2024-05-07'
 author-meta:
 - Peter "BrapMan" Selby
 - Trevor "Cool Kid" Rife
@@ -60,11 +60,11 @@ 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="2024-04-18" />
-  <meta name="citation_publication_date" content="2024-04-18" />
-  <meta property="article:published_time" content="2024-04-18" />
-  <meta name="dc.modified" content="2024-04-18T07:25:46+00:00" />
-  <meta property="article:modified_time" content="2024-04-18T07:25:46+00:00" />
+  <meta name="dc.date" content="2024-05-07" />
+  <meta name="citation_publication_date" content="2024-05-07" />
+  <meta property="article:published_time" content="2024-05-07" />
+  <meta name="dc.modified" content="2024-05-07T18:01:38+00:00" />
+  <meta property="article:modified_time" content="2024-05-07T18:01:38+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -188,9 +188,9 @@ 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/50ad6b3fb0699c3ec10a6105bf51a4a3d16b81fb/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/50ad6b3fb0699c3ec10a6105bf51a4a3d16b81fb/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/50ad6b3fb0699c3ec10a6105bf51a4a3d16b81fb/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f8e55569f5cb11fe0ecc7954df3385314242aa77/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f8e55569f5cb11fe0ecc7954df3385314242aa77/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/f8e55569f5cb11fe0ecc7954df3385314242aa77/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" />
@@ -212,10 +212,10 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/50ad6b3fb0699c3ec10a6105bf51a4a3d16b81fb/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/f8e55569f5cb11fe0ecc7954df3385314242aa77/))
 was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@50ad6b3](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/50ad6b3fb0699c3ec10a6105bf51a4a3d16b81fb)
-on April 18, 2024.
+from [plantbreeding/BrAPI-Manuscript2@f8e5556](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/f8e55569f5cb11fe0ecc7954df3385314242aa77)
+on May 7, 2024.
 </em></small>
 
 
@@ -828,7 +828,12 @@ Since the release of BrAPI 1.3, efforts have been made to incorporate support fo
 #### Helium
 
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
-Helium is a platform for reviewing and managing pedigree data. It is BrAPI enabled, so pedigree data can be viewed straight from a database. 
+Helium (https://helium.hutton.ac.uk) [@doi:10.1186/1471-2105-15-259] is a plant pedigree visualization platform designed to account for the specific problems that are unique to plant pedigrees. A pedigree is a representation of how genetically discrete individuals are related to one another and is therefore a representation of the genetic relationship between individual plant lines, their parents and progeny. Plant pedigrees are often used to check for potential genotyping or phenotyping errors, since these errors, by the very nature of Mendelian inheritance, are constrained by the pedigree structure in which they exist (Paterson 2011). The accurate representation of pedigrees, and the ability to pull pedigree data from different data sources is therefore important in plant breeding and genetics and therefore ways to visualize and interact this complex data in meaningful ways is critical.
+
+From its original desktop interface (https://github.com/cardinalb/helium-docs/wiki), Helium has developed into a web-based visualization platform implementing BrAPI calls to allow users to import data from other BrAPI compliant databases (https://helium.hutton.ac.uk). The ability to pull data from BrAPI compliant data sources has significantly expanded Helium’s capability and utility within the community. Helium is used in projects ranging in size from tens to tens of thousands of lines and across a wide variety of crops and species. While originally designed for plant data [@doi:10.3389/fpls.2024.1268847] it has also found utility in other non-plant projects [@doi:10.1007/s10592-024-01611-z] highlighting its broad utility. This also allows Helium users to provide direct dataset links to collaborators allowing the original data to be held with the data provider and utilising Helium for its visualization functionality. Our current Helium deployment includes example BrAPI calls to a barley dataset at Hutton to allow users to test the system and features it offers. 
+
+
+
 
 #### Tassel
 

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/references.json b/references.json
@@ -223,6 +223,71 @@
     "id": "bvSFyrtt",
     "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1002/ppp3.10187"
   },
+  {
+    "publisher": "Springer Science and Business Media LLC",
+    "abstract": "<jats:title>Abstract</jats:title><jats:p>Small populations of endangered species risk losing already eroded genetic diversity, important for adaptive potential, through the effects of genetic drift. The magnitude of drift can be mitigated by maximising the effective population size, as is the goal of genetic management strategies. Different mating systems, specifically those leading to reproductive skew, exacerbate genetic drift by distorting contributions. In the absence of an active management strategy, reproductive skew will have long-term effects on the genetic composition of a population, particularly where admixture is present. Here we examine the contrasting effects of conservation management strategies in two ex situ populations of the Critically Endangered eastern black rhino <jats:italic>(Diceros bicornis michaeli)</jats:italic>, one managed as a semi-wild population in South Africa (SAx), and one managed under a mean-kinship breeding strategy in European zoos. We use molecular data to reconstruct pedigrees for both populations and validate the method using the zoo studbook. Using the reconstructed pedigree and studbook we show there is male sex-specific skew in both populations. However, the zoo’s mean-kinship breeding strategy effectively reduces reproductive skew in comparison to a semi-wild population with little genetic management. We also show that strong male reproductive skew in SAx has resulted in extensive admixture, which may require a re-evaluation of the population’s original intended role in the black rhino meta-population. With a high potential for admixture in many ex situ populations of endangered species, molecular and pedigree data remain vital tools for populations needing to balance drift and selection.</jats:p>",
+    "DOI": "10.1007/s10592-024-01611-z",
+    "type": "article-journal",
+    "source": "Crossref",
+    "title": "Admixture and reproductive skew shape the conservation value of ex situ populations of the Critically Endangered eastern black rhino",
+    "author": [
+      {
+        "given": "Franziska",
+        "family": "Elsner-Gearing"
+      },
+      {
+        "given": "Petra",
+        "family": "Kretzschmar"
+      },
+      {
+        "given": "Susanne",
+        "family": "Shultz"
+      },
+      {
+        "given": "Mark",
+        "family": "Pilgrim"
+      },
+      {
+        "given": "Deborah Ann",
+        "family": "Dawson"
+      },
+      {
+        "given": "Gavin John",
+        "family": "Horsburgh"
+      },
+      {
+        "given": "Jírí",
+        "family": "Hruby"
+      },
+      {
+        "given": "Jane",
+        "family": "Hopper"
+      },
+      {
+        "given": "Tony",
+        "family": "King"
+      },
+      {
+        "given": "Catherine",
+        "family": "Walton"
+      }
+    ],
+    "container-title": "Conservation Genetics",
+    "language": "en",
+    "issued": {
+      "date-parts": [
+        [
+          2024,
+          3,
+          22
+        ]
+      ]
+    },
+    "URL": "https://doi.org/gtstdm",
+    "container-title-short": "Conserv Genet",
+    "id": "x8DIc6zn",
+    "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1007/s10592-024-01611-z"
+  },
   {
     "publisher": "Springer Science and Business Media LLC",
     "issue": "2",
@@ -1530,6 +1595,54 @@
     "id": "kWLsm7g6",
     "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1111/nph.16544"
   },
+  {
+    "publisher": "Springer Science and Business Media LLC",
+    "issue": "1",
+    "DOI": "10.1186/1471-2105-15-259",
+    "type": "article-journal",
+    "source": "Crossref",
+    "title": "Helium: visualization of large scale plant pedigrees",
+    "volume": "15",
+    "author": [
+      {
+        "given": "Paul D",
+        "family": "Shaw"
+      },
+      {
+        "given": "Martin",
+        "family": "Graham"
+      },
+      {
+        "given": "Jessie",
+        "family": "Kennedy"
+      },
+      {
+        "given": "Iain",
+        "family": "Milne"
+      },
+      {
+        "given": "David F",
+        "family": "Marshall"
+      }
+    ],
+    "container-title": "BMC Bioinformatics",
+    "language": "en",
+    "issued": {
+      "date-parts": [
+        [
+          2014,
+          8,
+          1
+        ]
+      ]
+    },
+    "URL": "https://doi.org/f6gfzs",
+    "container-title-short": "BMC Bioinformatics",
+    "PMCID": "PMC4133633",
+    "PMID": "25085009",
+    "id": "X22hwO1v",
+    "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1186/1471-2105-15-259"
+  },
   {
     "publisher": "Springer Science and Business Media LLC",
     "issue": "1",
@@ -1725,6 +1838,101 @@
     "URL": "https://doi.org/gtq5n8",
     "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.22004/ag.econ.266624"
   },
+  {
+    "publisher": "Frontiers Media SA",
+    "abstract": "<jats:p>In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures.  ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession’s year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.</jats:p>",
+    "DOI": "10.3389/fpls.2024.1268847",
+    "type": "article-journal",
+    "source": "Crossref",
+    "title": "Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT)",
+    "volume": "15",
+    "author": [
+      {
+        "given": "Villő",
+        "family": "Bernád"
+      },
+      {
+        "given": "Nadia",
+        "family": "Al-Tamimi"
+      },
+      {
+        "given": "Patrick",
+        "family": "Langan"
+      },
+      {
+        "given": "Gary",
+        "family": "Gillespie"
+      },
+      {
+        "given": "Timothy",
+        "family": "Dempsey"
+      },
+      {
+        "given": "Joey",
+        "family": "Henchy"
+      },
+      {
+        "given": "Mary",
+        "family": "Harty"
+      },
+      {
+        "given": "Luke",
+        "family": "Ramsay"
+      },
+      {
+        "given": "Kelly",
+        "family": "Houston"
+      },
+      {
+        "given": "Malcolm",
+        "family": "Macaulay"
+      },
+      {
+        "given": "Paul D.",
+        "family": "Shaw"
+      },
+      {
+        "given": "Sebastian",
+        "family": "Raubach"
+      },
+      {
+        "given": "Kevin P.",
+        "family": "Mcdonnel"
+      },
+      {
+        "given": "Joanne",
+        "family": "Russell"
+      },
+      {
+        "given": "Robbie",
+        "family": "Waugh"
+      },
+      {
+        "given": "Mortaza",
+        "family": "Khodaeiaminjan"
+      },
+      {
+        "given": "Sónia",
+        "family": "Negrão"
+      }
+    ],
+    "container-title": "Frontiers in Plant Science",
+    "issued": {
+      "date-parts": [
+        [
+          2024,
+          3,
+          20
+        ]
+      ]
+    },
+    "URL": "https://doi.org/gtstdn",
+    "container-title-short": "Front. Plant Sci.",
+    "PMCID": "PMC10987740",
+    "PMID": "38571708",
+    "id": "1HmEHgW8h",
+    "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.3389/fpls.2024.1268847"
+  },
   {
     "publisher": "MDPI AG",
     "issue": "8",
@@ -1915,8 +2123,8 @@
       "date-parts": [
         [
           "2024",
-          4,
-          18
+          5,
+          7
         ]
       ]
     },
@@ -2099,8 +2307,8 @@
       "date-parts": [
         [
           "2024",
-          4,
-          18
+          5,
+          7
         ]
       ]
     },