Merge pull request #35 from plantbreeding/lukas_2024_04_17

Lukas 2024 04 17

content/01.abstract.md

@@ -1,6 +1,6 @@
 ## Abstract {.page_break_before}
 
-The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases.
-BrAPI is a standardized RESTful web service API specification for communicating plant breeding data.
-This community driven standard is free to be used by anyone interested in plant breeding data management.
-This manuscript describes updates and outlook for the current version of BrAPI.
+Population growth and climate change require extraordinary efforts to increase efficiency in breeding programs around the world. In the last few years, genomics technologies and genomic prediction approaches have provided a boost in genetic gain in breeding, but has also created a flood of data that needs careful management to be fully harnessed.
+The Breeding API (BrAPI) project is an international, grass-roots effort to enable more efficient data management by enabling interoperability among plant breeding databases and tools, using a standardized RESTful web service API specification for communicating plant breeding data.
+This community driven standard is free to be used by anyone interested in plant breeding data management, including trial data, phenotypic data and genotyping data management.
+This manuscript describes advances in implementations of BrAPI in different breeding tools, and outlook for the current version of BrAPI. 

content/02.introduction.md

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 * Standardization of endpoints across objects - said in a non-tech way
 -->
 
-<!-- Pete S: This opening paragraph is hot garbage and should be rewritten, but I needed to start somewhere to get the creative writing process flowing.  -->
-Plant and animal breeding is an incredibly important part of today's society. Almost every country in the world has some kind of breeding program supporting the agricultural community to produce bigger, better, healthier, and more sustainable crops. Modern breeding techniques require large amounts of high quality data to be effective. In the digital age, that breeding data is being collected, managed, and analyzed with computer software. Interoperability between breeding software tools, systems, and databases can substantially increase the efficiency of a breeding program. The ability to share tools gives each program a boost in computational power. The ability to share data allows the community to leverage access to larger, more complete, datasets; similarly, the community can build more accurate computational models and produce more accurate predictions.
+To address consequences of climate change and population growth, plant and animal breeding need to become more efficient and data driven to produce bigger, better, healthier, more sustainable crops. Modern breeding techniques require large amounts of high quality data to be effective, requiring digital methods for data collection, management, and analysis. Interoperability between breeding software tools, systems, and databases can substantially increase the efficiency of a breeding program. The ability to efficiently share data means access to larger and more complete datasets, enabling to build more accurate computational models and produce more accurate predictions and improved selections.
 
 The Breeding API (BrAPI) project is an effort to enable interoperability among breeding tools, systems, and databases. BrAPI is a standardized Representational State Transfer (REST), web service, Application Programming Interface (API), specification for breeding and related agricultural data. [@doi:10.1093/bioinformatics/btz190] By using the BrAPI standard, breeding software can more easily become interoperable, allowing groups to more easily share data and software tools.
 

content/03.02.data-management.md

@@ -48,8 +48,7 @@ Additionally, brapi-sync improves data management by utilizing the externalRefer
 
 #### Breedbase
 
-<!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
-Since the inception of BrAPI in 2014, the Breedbase group has been a heavy contributor to the BrAPI community.
+Breedbase is a comprehensive breeding data management system [@doi:10.1093/g3journal/jkac078][@doi:10.1371/journal.pone.0240059] that implements a digital ecosystem for all breeding data, including trial data, phenotypic data, and genotypic data. Data acquisition is through tabled-based apps such as Fieldbook [@doi:10.2135/cropsci2013.08.0579] and related apps, such as Coordinate and InterCross apps, through drone imagery, Near Infra-Red Spectroscopy (NIRS), and other technologies. Search functions such as the Search Wizard interface provide powerful query capabilities, and various breeding-centric analysis tools are available, including mixed models, heritability, stability, PCA, and various clustering algorithms. The original impetus for creating Breedbase was the advent of new breeding paradigms based on genomic information such as genomic prediction algorithms [@doi:10.1093/genetics/157.4.1819] and the accompanying data management challenges, and complete genomic prediction workflow is integrated in the system.  The first instance was created for the NextGen Cassava project in 2012 as the Cassavabase (https://cassavabase.org/) database. Databases for other CGIAR root, tuber and banana (RTB) crops followed with database for yam (https://yambase.org/), sweet potato (https://sweetpotatobase.org/), banana (https://musabase.org/) as well as instances in labs and companies. The BrAPI interface[@doi:10.1093/bioinformatics/btz190] is crucial for Breedbase: Breedbase communicates via BrAPI with the data collection tablets, connection to other projects such as CLIMMOB [@doi:10.1016/j.compag.2023.108539], and many native tools use the BrAPI interface for accessing data. Users also appreciate the ability to connect to Breedbase instances using packages such as QBMS <https://icarda-git.github.io/QBMS/> for data import into R for custom analyses. Breedbase has been an early and continuous adopter of, and contributor to, the BrAPI standard.
 
 #### BIMS