reformat for database

Author: BrapiCoordinatorSelby

build/pandoc/defaults/common.yaml

@@ -11,5 +11,6 @@ wrap: preserve
 metadata:
   #csl: build/assets/style.csl
   # csl: https://www.zotero.org/styles/nature
-  csl: https://www.zotero.org/styles/plos-computational-biology
+  # csl: https://www.zotero.org/styles/plos-computational-biology
+  csl: https://www.zotero.org/styles/database
   link-citations: true

content/01.abstract.md

@@ -1,5 +1,6 @@
 ## Abstract {.page_break_before}
 
+Population growth and the impacts of climate change are placing increasing pressure on global agriculture and breeding programs. 
 Recent advancements in phenotyping techniques, genotyping technologies, and prediction approaches are facilitating increased genetic gains in breeding programs, helping researchers and breeders develop better crops at a faster rate. 
 However, these advancements have also led to an overwhelming torrent of disconnected data.
 The successful implementation of these methods depends on proper data management, which is particularly challenging due to the need to integrate datasets across various types, formats, and sources. 
@@ -9,14 +10,3 @@ This community driven standard is software agnostic, open-source, and can be use
 This manuscript presents an overview of the BrAPI project, the substantial growth of the data standard, and the wide variety of BrAPI-compatible, community-built tools for breeding and research.
 This manuscript provides an overview of the BrAPI project, highlighting the significant progress made in the development of the data standard and the expansion of its community. 
 It also presents a showcase of the wide variety of BrAPI-compatible tools that have been built to enhance breeding and research activities, demonstrating how the project is advancing agricultural innovation and data management practices.
-
-## Author Summary
-
-Population growth and the impacts of climate change are placing increasing pressure on global agriculture and breeding programs. 
-To meet the growing demand for food and resources while coping with the unpredictability of changing climates, extraordinary efforts are required to boost the efficiency of these systems.
-This increase in efficiency will in part come from better computer technology and better data management. 
-The ability to share data and software is crucial to get better technology with fewer resources, allowing scientists to build on each others work more easily. 
-Creating an international data standard, such as BrAPI, within the breeding and agricultural domain allows for easy data sharing and software interoperability. 
-The BrAPI community combines the expertise of breeders, computational biologists, software engineers, and data scientists to build this agreed upon data standard. 
-The community actively encourages collaboration between research groups, creating a network of shared technology and knowledge. 
-This spirit of collaboration not only accelerates progress but also helps to use resources more efficiently, reducing duplication of effort and enabling research groups to focus on new innovations.

content/04.discussion.md

@@ -9,7 +9,3 @@ While the BrAPI technical specification is designed to be read and used by softw
 The BrAPI project leadership and community are committed to building standards to support new use cases and technologies as they are adopted by breeders and other scientists, potentially including drone imaging data, spectroscopy, LIDAR, metabolomics, transcriptomics, agronomics, high-throughput phenotyping, pangenomics, and machine learning based analysis. Each of these technologies will have unique challenges, generate different types of data, and require substantial thought and discussion before being added to the BrAPI specification. This process has already begun for several data types, with small groups working to build generic data models and proposed communication standards. As these community efforts are completed, they will become part of a future version of the BrAPI standard, enabling further interoperability and simplifying data exchange.
 
 Expanding the BrAPI specification is important for the community, but this growth should not reinvent or compete with existing functional standards. Additions to the BrAPI specification are reviewed thoroughly by the community to make sure BrAPI is compliant with existing standards and data structures. For example, the community has requested compliance with the GFF3 standard for genomic data and the GeoTIFF standard for aerial image data. Pieces of these existing popular data structures might be integrated into the overall BrAPI standard documentation. In some cases, BrAPI will only reference other standards instead of including them in the specification. For example, there have been community discussions around developing connections with the NOAA CDO standard for weather data or the Galaxy Analytics API for analytics pipeline controls and information. These standards are perfectly adequate on their own and recreating them in the BrAPI standard would be redundant.
-
-### Conclusion
-
-The BrAPI project only exists because of the community of software engineers, biologists, and other scientists who support and use it. While there were many tools and use cases presented here, it is not an exhaustive list of all BrAPI-compliant systems. As long as the standard continues to be supported, the community will continue to expand. As more groups continue to make their tools BrAPI compliant, others will see the value in implementing BrAPI into their own tools, allowing the community to strengthen and grow. By providing an open standard for breeding data, and the infrastructure and community to support it, the BrAPI project is doing its part to support a productive agricultural system amidst the pressing challenges of climate change. If this manuscript is your first introduction to the BrAPI project, the authors invite you to join the community. More information is available at [brapi.org](https://brapi.org).

content/05.conclusion.md

@@ -0,0 +1,3 @@
+## Conclusion
+
+The BrAPI project only exists because of the community of software engineers, biologists, and other scientists who support and use it. While there were many tools and use cases presented here, it is not an exhaustive list of all BrAPI-compliant systems. As long as the standard continues to be supported, the community will continue to expand. As more groups continue to make their tools BrAPI compliant, others will see the value in implementing BrAPI into their own tools, allowing the community to strengthen and grow. By providing an open standard for breeding data, and the infrastructure and community to support it, the BrAPI project is doing its part to support a productive agricultural system amidst the pressing challenges of climate change. If this manuscript is your first introduction to the BrAPI project, the authors invite you to join the community. More information is available at [brapi.org](https://brapi.org).