general edits

content/02.introduction.md

@@ -33,10 +33,10 @@ Over its lifetime, the BrAPI project has grown and changed substantially. The la
 
 ![A simplified domain map of the whole BrAPI data model, divided into organizational modules. A more detailed Entity Relationship Diagram (ERD) is available on brapi.org.](images/BrAPI_Domains_v2-1_vertical.png){#fig:domains width="100%"}
 
-As the specification has matured, so have the tools, services, and libraries available to the community to work with the specification. Every version of the specification is now released with a change log to guide developers upgrading from a previous version, an Entity Relationship Diagram (ERD) to describe the whole data model visually, and a JSON Schema data model to be used in some automated development efforts. For groups who are using Java, Java Script, Python, R, or Drupal, there are community maintained libraries available that contain full BrAPI implementations ready to be added to some existing code. The BrAPI Test Server and the BRAVA validation tool are both still available to the community for testing purposes, and they have been maintained to support every version of the specification. Finally, the three new resources list pages on brapi.org advertise the other BrAPI compatible software available in the community. The BrAPPs list page, servers list page, and compatible software list page showcase many of the BrAPI compatible applications and data resources available in the community.
+As the specification has matured, so have the tools, services, and libraries available to the community to work with the specification. Every version of the specification is now released with a change log to guide developers upgrading from a previous version, an Entity Relationship Diagram (ERD) to describe the whole data model visually, and a JSON Schema data model to be used in some automated development efforts. For groups who are using Java, Java Script, Python, R, or Drupal, there are community maintained libraries available that contain full BrAPI implementations ready to be added to some existing code. The BrAPI Test Server and the BRAVA validation tool are both still available to the community for testing purposes, and they have been maintained to support every version of the specification. Finally, there are three new resource list pages on brapi.org to advertise the BrAPI compatible software available in the community. The BrAPPs list page, servers list page, and compatible software list page showcase many of the BrAPI compatible applications and data resources available in the community.
 
 ### Community Growth
 
 The international BrAPI Community consists of software developers, breeders, and other scientists working on BrAPI related projects and data sources. This community is what sustains the BrAPI project, builds implementations, maintains development tools, and provides input to enhance the specification. As the project has grown, so has the community. The BrAPI project started in June 2014 with less than ten people coming together to discuss the idea. Over the next ten years, the community has grown to between 200 and 250 members. 
 
-The BrAPI Hackathons are a major staple of the BrAPI community. Twice a year, the community gathers to discuss the specification and collaborate on BrAPI related projects. This time is very valuable to the community; for some organizations, the hackathon is the only time during the year when they have time to work on anything related to BrAPI. During the COVID-19 pandemic, virtual hackathons took the place of in person events. While the virtual hackathons do not provide the same level of face-to-face time that is crucial to collaborative work, they did allow for more attendees to gather and share their opinions. Going forward, the community leadership has decided to have one in-person hackathon and one virtual hackathon each year, to balance the advantages of both. 
+The BrAPI Hackathons are a major staple of the BrAPI community. Twice a year, the community gathers to discuss the specification and collaborate on BrAPI related projects. This time is very valuable to the community; for some organizations, the hackathon is the only time during the year when they have time to work on anything related to BrAPI. During the COVID-19 pandemic, virtual hackathons took the place of in-person events. While the virtual hackathons do not provide the same level of face-to-face time that is crucial to collaborative work, they did allow for more attendees to gather and share their opinions. Going forward, the community leadership has decided to have one in-person hackathon and one virtual hackathon each year, to balance the advantages of both. 

content/03.01.01.Field_Book.md

@@ -1,8 +1,8 @@
 #### Field Book
 
 <!-- Trevor and Chaney -->
-Phenotypic data collection underpins scientific crop research and plant breeding. Knowledge gained from collected data and its analysis alongside data visualizations inform further phenotypic trials and ideally support research hypotheses. The importance of accuracy and efficiency in the collection of this data as well as the infrastructure to facilitate the flow of data from the field to a knowledge base cannot be underestimated. 
+Phenotypic data collection underpins scientific crop research and plant breeding. Knowledge gained from collected data and its analysis, alongside data visualizations, inform further phenotypic trials and ideally support research hypotheses. The importance of accuracy and efficiency in the collection of this data as well as the infrastructure to facilitate the flow of data from the field to a knowledge base cannot be underestimated. 
 
 Historically, gathering data in the field was done with pen and paper, or perhaps some version of a digital spreadsheet. The abundance and prevalence of smart phones has allowed the Field Book mobile app [@doi:10.2135/cropsci2013.08.0579] to enhance data collection. Field Book can create well-formed digital observation records from the moment they are taken. This can improve the efficiency of data collection and reduce human error. 
 
-In 2018, BrAPI was introduced into Field Book; specifically, the Core and Phenotyping modules. BrAPI was able to take things a step further by automating the flow of data from the Field Book mobile app to a central database server. This workflow allows data collection and storage to be expedited, removing the need of the user to transfer export files manually. Since Field Book’s adoption of BrAPI, many community servers have been integrated to simplify data storage. In this work flow, data is collected and stored completely digitally with little-to-no human involvement.
+In 2018, BrAPI was introduced into Field Book, allowing for the automated the flow of data from the mobile app into a central, BrAPI compatible, database server. This workflow allows data collection and storage to be expedited, removing the need of the user to export and transfer data files manually. Since Field Book’s adoption of BrAPI, many community servers have been integrated to simplify data storage. In this work flow, data is collected and stored completely digitally with little-to-no human involvement.

content/03.01.02.GridScore.md

@@ -4,6 +4,6 @@
 <!-- Make distinct from Field Book, highlight what makes GridScore different -->
 <!-- Better flow is needed between Field Book and GridScore -->
 
-[GridScore](https://ics.hutton.ac.uk/get-gridscore/) [@doi:10.1186/s12859-022-04755-2] is a modern mobile application for phenotypic observations that harnesses technological advancements in the area of mobile devices to enrich the data collection process. GridScore focuses on user experience by closely mirroring the look and feel of printed field plans but enriching the experience with a wide range of functionalities including data validation, a huge range of visualizations, georeferencing, cross-platform support, and BrAPI-independent data synchronization across multiple devices. GridScore is a multi-platform tool which works on any reasonably modern device with a web browser including laptops, PCs, tablets and phones. Once created, trials can be transferred to collection devices using a Quick Response (QR) code. Its approach towards data collection uses a top-down view onto the trial but also offers field navigation mechanisms using barcodes or QR codes or guided walks which take the data collector through the field in one of 16 pre-defined orders.
+[GridScore](https://ics.hutton.ac.uk/get-gridscore/) [@doi:10.1186/s12859-022-04755-2] is a modern mobile application for phenotypic observations that harnesses technological advancements in the area of mobile devices to enrich the data collection process. GridScore focuses on user experience by closely mirroring the look and feel of printed field plans. It also enriches the experience with a wide range of functionalities including data validation, data visualizations, georeferencing, cross-platform support, and data synchronization across multiple devices. GridScore is a multi-platform tool which works on any reasonably modern device with a web browser including laptops, PCs, tablets and phones. Once created, trials can be transferred to collection devices using a Quick Response (QR) code. Its approach towards data collection uses a top-down view onto the trial and offers field navigation mechanisms using barcodes, QR codes, or guided walks which take the data collector through the field in one of 16 pre-defined orders.
 
-BrAPI has further increased the value of GridScore by integrating it into the overarching workflow from trial creation, data collection, and its ultimate data storage for further processing. Specifically, trial designs as well as trait definitions can be imported into GridScore using BrAPI and a finalized trial can ultimately be exported via BrAPI to any compatible database.
+BrAPI has further increased the value of GridScore by integrating it into the overarching workflow, from trial creation, through data collection, and to its ultimate data storage for further processing. Specifically, trial designs as well as trait definitions can be imported into GridScore using BrAPI and a finalized trial can be exported via BrAPI to any compatible database.

content/03.01.03.ClimMob.md

@@ -2,6 +2,6 @@
 
 <!-- Marie-Angelique -->
 
-ClimMob [@doi:10.1016/j.compag.2023.108539] is a software suite for a different research paradigm in experimental agriculture. In traditional breeding, researchers designing complicated trials in search of the best solutions for a target environment. ClimMob enables many participants to carry out reasonably simple experiments across many environments. Taken together, this data can be very informative. It applies the principles of citizen science and choice experiments to scale the data collection process, mostly in the format of rankings. Although this data may not be as detailed as from a centralized experiment, it can be very useful to inform decisions to a wide range of locations and environments with increased external validity. ClimMob applications include testing crop varieties, evaluating agronomic practices, and investigating climate resilience strategies. The platform supports experiment design, data collection through mobile apps, and data analysis to provide actionable insights.
+ClimMob [@doi:10.1016/j.compag.2023.108539] is a software suite for a different research paradigm in experimental agriculture. In traditional breeding, a few researchers design complicated trials in search of the best solutions for a few target environments. ClimMob enables many participants to carry out reasonably simple experiments across many environments. Taken together, this data across many environments can be very informative. It applies the principles of citizen science and choice experiments to scale the data collection process, mostly in the format of rankings. Although this data may not be as detailed as from a centralized experiment, it can be very useful to inform decisions to a wide range of locations and environments with increased external validity. ClimMob applications include testing crop varieties, evaluating agronomic practices, and investigating climate resilience strategies. The platform supports experiment design, data collection through mobile apps, and data analysis to provide actionable insights.
 
-During a crop varieties trial, all farmer-collected data is stored in ClimMob. Upon data collection completion, the raw data is automatically uploaded via BrAPI to a central breeding database for long-term storage. To facilitate this synchronization, ClimMob uses BrAPI to retrieve curated germplasm information from breeding databases when designing a trial, significantly enhancing data quality. Additionally, a process has been developed to push analyzed data from ClimMob to the breeding databases, providing breeders with insights into the potential adoption of the tested crop varieties.
+During a crop trial, all farmer-collected data is stored in ClimMob. When data collection is complete, the raw data is automatically uploaded via BrAPI to a central breeding database for long-term storage and analysis. To facilitate this synchronization, ClimMob uses BrAPI to retrieve curated germplasm information from breeding databases when designing a trial, significantly enhancing data quality. Additionally, a process has been developed to push analyzed data from ClimMob to the breeding databases, providing breeders with insights into the potential adoption of the tested crop varieties.

content/03.01.05.PHIS.md

@@ -1,7 +1,7 @@
 #### PHIS 
 
 <!-- Isabelle -->
-The Hybrid Phenotyping Information System ([PHIS](http://www.phis.inrae.fr/) [@doi:10.1111/nph.15385]), based on the [OpenSILEX](https://github.com/OpenSILEX/) framework, is an ontology-driven information system based on semantic web technologies. PHIS is deployed in several field and greenhouse platforms of the French national [PHENOME](https://www.phenome-emphasis.fr/) and European [EMPHASIS](https://emphasis.plant-phenotyping.eu/) infrastructures. It manages and collects data from Phenotyping and High Throughput Phenotyping experiments on a day to day basis. PHIS unambiguously identifies all the objects and traits in an experiment, and establishes their types and relationships via ontologies and semantics.
+The Hybrid Phenotyping Information System ([PHIS](http://www.phis.inrae.fr/) [@doi:10.1111/nph.15385]), based on the [OpenSILEX](https://github.com/OpenSILEX/) framework, is an ontology-driven information system based on semantic web technologies. PHIS is deployed in several field and greenhouse platforms of the French national [PHENOME](https://www.phenome-emphasis.fr/) and European [EMPHASIS](https://emphasis.plant-phenotyping.eu/) infrastructures. It manages and collects data from basic phenotyping and high throughput phenotyping experiments on a day to day basis. PHIS unambiguously identifies all the objects and traits in an experiment, and establishes their types and relationships via ontologies and semantics.
 
 PHIS has been designed to be BrAPI-compliant. PHIS adheres to the standards and protocols specified by BrAPI and implements various services aligning with the BrAPI standards, encompassing the Core, Phenotyping, and Germplasm modules. This enables integration and compatibility with BrAPI-compliant systems and platforms. This prerequisite served as the basis for formalizing the data model, while also facilitating compatibility with other standards, such as the Minimal Information About a Plant Phenotyping Experiment ([MIAPPE](https://www.miappe.org/) [@doi:10.1111/nph.16544]). By integrating BrAPI requirements into its structure, PHIS not only meets the standards of the phenotyping field, but also strengthens its capacity for interoperability and effective collaboration in the wider context of plant breeding and related fields. The fact that data within a PHIS instance can be queried through BrAPI services makes the indexing of PHIS in [FAIDARE](https://urgi.versailles.inrae.fr/faidare/) [@https://urgi.versailles.inrae.fr/faidare] very easy to implement.
 

content/03.01.06.PIPPA.md

@@ -1,7 +1,7 @@
 #### PIPPA
 
 <!-- Rafael -->
-[PIPPA](https://pippa.psb.ugent.be) [@https://pippa.psb.ugent.be] is a data management system used for collecting data from the [WIWAM](https://www.wiwam.be/) [@https://www.wiwam.be/] range of automated high throughput phenotyping platforms. These platforms have been deployed at different research institutes and commercial breeders across Europe. They can be setup in a variety of configurations with different types of equipment including weighing scales, cameras, and environment sensors. The software features a web interface with functionality for setting up new experiments, planning imaging and irrigation treatments, linking metadata to pots (genotype, growth media, manual treatments), importing data, exporting data, and visualizing data. It also supports the integration of image analysis scripts and connections to a compute cluster for job submission.
+[PIPPA](https://pippa.psb.ugent.be) [@https://pippa.psb.ugent.be] is a data management system used for collecting data from the [WIWAM](https://www.wiwam.be/) [@https://www.wiwam.be] range of automated high throughput phenotyping platforms. These platforms have been deployed at different research institutes and commercial breeders across Europe. They can be setup in a variety of configurations with different types of equipment including weighing scales, cameras, and environment sensors. The software features a web interface with functionality for setting up new experiments, planning imaging and irrigation treatments, linking metadata to pots (genotype, growth media, manual treatments), importing data, exporting data, and visualizing data. It also supports the integration of image analysis scripts and connections to a compute cluster for job submission.
 
 To share the phenotype data of the experiments linked to publications, an implementation of BrAPI v1.3 was developed which allowed read only access to the data in the BrAPI standardized format. This server was registered on [FAIDARE](https://urgi.versailles.inrae.fr/faidare/) [@https://urgi.versailles.inrae.fr/faidare] which allows the data to be found alongside data from other BrAPI compatible repositories.