Since the inception of BrAPI in 2014, the Breedbase group has been a heavy contributor to the BrAPI community.
BIMS
-
BIMS (Breeding Information Management System) [https://doi.org/10.1093/database/baab054] 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 [https://doi.org/10.1093/nar/gky1000], CottonGEN [https://doi.org/10.3390/plants10122805], the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, https://breedwithbims.org. 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.
+
BIMS (Breeding Information Management System) [2] 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 [3], CottonGEN [4], the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, https://breedwithbims.org. 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.
Germinate
Germinate is a combination breeding database and germplasm management database.
@@ -501,6 +501,15 @@
References
1.
BrAPI—an application programming interface for plant breeding applications
Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar E Benites-Alfaro, Clay Birkett, Viana C Calaminos, Pierre Carceller, Guillaume Cornut, …
diff --git a/manuscript.md b/manuscript.md
index aabc518..55c3f3a 100644
--- a/manuscript.md
+++ b/manuscript.md
@@ -36,8 +36,8 @@ header-includes: |
-
-
+
+
@@ -88,9 +88,9 @@ header-includes: |
-
-
-
+
+
+
@@ -112,9 +112,9 @@ manubot-clear-requests-cache: false
This manuscript
-([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/))
+([permalink](https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/))
was automatically generated
-from [plantbreeding/BrAPI-Manuscript2@838c21c](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/838c21cfb2bae42f8511dd75468c931bea0ed267)
+from [plantbreeding/BrAPI-Manuscript2@33af47f](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/33af47f71b3fba2a27bd70b3a00e45cf68190776)
on February 29, 2024.
@@ -425,7 +425,7 @@ Since the inception of BrAPI in 2014, the Breedbase group has been a heavy contr
#### BIMS
-BIMS (Breeding Information Management System) [https://doi.org/10.1093/database/baab054] 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 [https://doi.org/10.1093/nar/gky1000], CottonGEN [https://doi.org/10.3390/plants10122805], the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, . 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.
+BIMS (Breeding Information Management System) [@doi:10.1093/database/baab054] 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 [@doi:10.1093/nar/gky1000], CottonGEN [@doi:10.3390/plants10122805], the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, as well as a crop-independent website, . 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.
#### Germinate
diff --git a/manuscript.pdf b/manuscript.pdf
index 54ae149..2a9fe12 100644
Binary files a/manuscript.pdf and b/manuscript.pdf differ
diff --git a/references.json b/references.json
index 65e9d7e..7657ec5 100644
--- a/references.json
+++ b/references.json
@@ -254,5 +254,274 @@
"PMID": "30903186",
"id": "QfGEJ6km",
"note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1093/bioinformatics/btz190"
+ },
+ {
+ "publisher": "Oxford University Press (OUP)",
+ "abstract": "Abstract\n In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium.\n Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/)",
+ "DOI": "10.1093/database/baab054",
+ "type": "article-journal",
+ "source": "Crossref",
+ "title": "The Breeding Information Management System (BIMS): an online resource for crop breeding",
+ "volume": "2021",
+ "author": [
+ {
+ "given": "Sook",
+ "family": "Jung"
+ },
+ {
+ "given": "Taein",
+ "family": "Lee"
+ },
+ {
+ "given": "Ksenija",
+ "family": "Gasic"
+ },
+ {
+ "given": "B. Todd",
+ "family": "Campbell"
+ },
+ {
+ "given": "Jing",
+ "family": "Yu"
+ },
+ {
+ "given": "Jodi",
+ "family": "Humann"
+ },
+ {
+ "given": "Sushan",
+ "family": "Ru"
+ },
+ {
+ "given": "Daniel",
+ "family": "Edge-Garza"
+ },
+ {
+ "given": "Heidi",
+ "family": "Hough"
+ },
+ {
+ "given": "Dorrie",
+ "family": "Main"
+ }
+ ],
+ "container-title": "Database",
+ "language": "en",
+ "issued": {
+ "date-parts": [
+ [
+ 2021,
+ 1,
+ 1
+ ]
+ ]
+ },
+ "URL": "https://doi.org/gtj95x",
+ "PMCID": "PMC8378516",
+ "PMID": "34415997",
+ "id": "ArPSsaJQ",
+ "note": "This CSL Item was generated by Manubot v0.5.5 from its persistent identifier (standard_id).\nstandard_id: doi:10.1093/database/baab054"
+ },
+ {
+ "publisher": "Oxford University Press (OUP)",
+ "issue": "D1",
+ "DOI": "10.1093/nar/gky1000",
+ "type": "article-journal",
+ "page": "D1137-D1145",
+ "source": "Crossref",
+ "title": "15 years of GDR: New data and functionality in the Genome Database for Rosaceae",
+ "volume": "47",
+ "author": [
+ {
+ "given": "Sook",
+ "family": "Jung"
+ },
+ {
+ "given": "Taein",
+ "family": "Lee"
+ },
+ {
+ "given": "Chun-Huai",
+ "family": "Cheng"
+ },
+ {
+ "given": "Katheryn",
+ "family": "Buble"
+ },
+ {
+ "given": "Ping",
+ "family": "Zheng"
+ },
+ {
+ "given": "Jing",
+ "family": "Yu"
+ },
+ {
+ "given": "Jodi",
+ "family": "Humann"
+ },
+ {
+ "given": "Stephen P",
+ "family": "Ficklin"
+ },
+ {
+ "given": "Ksenija",
+ "family": "Gasic"
+ },
+ {
+ "given": "Kristin",
+ "family": "Scott"
+ },
+ {
+ "given": "Morgan",
+ "family": "Frank"
+ },
+ {
+ "given": "Sushan",
+ "family": "Ru"
+ },
+ {
+ "given": "Heidi",
+ "family": "Hough"
+ },
+ {
+ "given": "Kate",
+ "family": "Evans"
+ },
+ {
+ "given": "Cameron",
+ "family": "Peace"
+ },
+ {
+ "given": "Mercy",
+ "family": "Olmstead"
+ },
+ {
+ "given": "Lisa W",
+ "family": "DeVetter"
+ },
+ {
+ "given": "James",
+ "family": "McFerson"
+ },
+ {
+ "given": "Michael",
+ "family": "Coe"
+ },
+ {
+ "given": "Jill L",
+ "family": "Wegrzyn"
+ },
+ {
+ "given": "Margaret E",
+ "family": "Staton"
+ },
+ {
+ "given": "Albert G",
+ "family": "Abbott"
+ },
+ {
+ "given": "Dorrie",
+ "family": "Main"
+ }
+ ],
+ "container-title": "Nucleic Acids Research",
+ "language": "en",
+ "issued": {
+ "date-parts": [
+ [
+ 2018,
+ 10,
+ 24
+ ]
+ ]
+ },
+ "URL": "https://doi.org/gjqq8v",
+ "PMCID": "PMC6324069",
+ "PMID": "30357347",
+ "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": "MDPI AG",
+ "issue": "12",
+ "abstract": "Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.",
+ "DOI": "10.3390/plants10122805",
+ "type": "article-journal",
+ "page": "2805",
+ "source": "Crossref",
+ "title": "CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research",
+ "volume": "10",
+ "author": [
+ {
+ "given": "Jing",
+ "family": "Yu"
+ },
+ {
+ "given": "Sook",
+ "family": "Jung"
+ },
+ {
+ "given": "Chun-Huai",
+ "family": "Cheng"
+ },
+ {
+ "given": "Taein",
+ "family": "Lee"
+ },
+ {
+ "given": "Ping",
+ "family": "Zheng"
+ },
+ {
+ "given": "Katheryn",
+ "family": "Buble"
+ },
+ {
+ "given": "James",
+ "family": "Crabb"
+ },
+ {
+ "given": "Jodi",
+ "family": "Humann"
+ },
+ {
+ "given": "Heidi",
+ "family": "Hough"
+ },
+ {
+ "given": "Don",
+ "family": "Jones"
+ },
+ {
+ "given": "J. Todd",
+ "family": "Campbell"
+ },
+ {
+ "given": "Josh",
+ "family": "Udall"
+ },
+ {
+ "given": "Dorrie",
+ "family": "Main"
+ }
+ ],
+ "container-title": "Plants",
+ "language": "en",
+ "issued": {
+ "date-parts": [
+ [
+ 2021,
+ 12,
+ 18
+ ]
+ ]
+ },
+ "URL": "https://doi.org/gqqwfm",
+ "container-title-short": "Plants",
+ "PMCID": "PMC8705096",
+ "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"
}
]
diff --git a/spelling-errors.txt b/spelling-errors.txt
index 3744ce4..4bea329 100644
--- a/spelling-errors.txt
+++ b/spelling-errors.txt
@@ -2,7 +2,7 @@ Agrosystem
agrosystems
Alic
alshamaa
-analytics
+Analytics
ANR
APIs
arial
@@ -22,7 +22,7 @@ BrapMan
BrAPP
BrAPPs
BRAVA
-BreedBase
+Breedbase
Casstevens
chaneylc
CLI
@@ -50,10 +50,10 @@ Genotypes
genotypic
genotyping
Germplasm
-Gigwa
+GIGWA
GLIS
hackathon
-hackathons
+Hackathons
haplotype
haplotypes
HortControl
@@ -68,7 +68,7 @@ interoperable
IPK
ISA
JSON
-khaled
+Khaled
leetaei
LIDAR
metabolomics
@@ -82,17 +82,17 @@ NIFA
ontologies
OpenSILEX
pangenome
-Phenome
+PHENOME
Phenospex
phenotypes
Phenotypic
-phenotyping
+Phenotyping
PHG
PHIS’s
Pommier
programmatically
QBMS
-Raubach
+raubach
Rosaceae
rPHG
Saclay
diff --git a/variables.json b/variables.json
index c4f8243..2eb100f 100644
--- a/variables.json
+++ b/variables.json
@@ -25,7 +25,7 @@
"Sook Jung",
"Taein Lee"
],
- "header-includes": "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n",
+ "header-includes": "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n",
"bibliography": [
"content/manual-references.json"
],
@@ -37,7 +37,7 @@
"manubot": {
"date": "2024-02-29",
"date_long": "February 29, 2024",
- "generated": "2024-02-29T21:21:31+00:00",
+ "generated": "2024-02-29T22:00:04+00:00",
"generated_date_long": "February 29, 2024",
"randomize_author_order": false,
"authors": [
@@ -279,15 +279,15 @@
"repo_slug": "plantbreeding/BrAPI-Manuscript2",
"repo_owner": "plantbreeding",
"repo_name": "BrAPI-Manuscript2",
- "commit": "838c21cfb2bae42f8511dd75468c931bea0ed267",
- "triggering_commit": "838c21cfb2bae42f8511dd75468c931bea0ed267",
- "build_url": "https://github.com/plantbreeding/BrAPI-Manuscript2/commit/838c21cfb2bae42f8511dd75468c931bea0ed267/checks",
- "job_url": "https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8102754236"
+ "commit": "33af47f71b3fba2a27bd70b3a00e45cf68190776",
+ "triggering_commit": "33af47f71b3fba2a27bd70b3a00e45cf68190776",
+ "build_url": "https://github.com/plantbreeding/BrAPI-Manuscript2/commit/33af47f71b3fba2a27bd70b3a00e45cf68190776/checks",
+ "job_url": "https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8103147174"
},
"html_url": "https://plantbreeding.github.io/BrAPI-Manuscript2/",
"pdf_url": "https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf",
- "html_url_versioned": "https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/",
- "pdf_url_versioned": "https://plantbreeding.github.io/BrAPI-Manuscript2/v/838c21cfb2bae42f8511dd75468c931bea0ed267/manuscript.pdf",
+ "html_url_versioned": "https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/",
+ "pdf_url_versioned": "https://plantbreeding.github.io/BrAPI-Manuscript2/v/33af47f71b3fba2a27bd70b3a00e45cf68190776/manuscript.pdf",
"manubot_version": "0.5.5",
"rootstock_commit": "f3e0520060162f71f0950ea88d44de526d241ad1",
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