formatting updates

content/02.introduction.md

@@ -30,7 +30,7 @@ Data repositories and service providers can choose to represent their data as a
 
 Over its lifetime, the BrAPI project has grown and changed substantially. The latest stable version of the specification (v2.1) looks vastly different from the original version (v1.0) released in 2017. The total size of the specification has almost quadrupled in that time, going from 51 endpoints documented in v1.0 to 201 endpoints documented in v2.1. Because of this growth, the specification documents were reorganized into four modules: BrAPI-Core, BrAPI-Germplasm, BrAPI-Genotyping, and BrAPI-Phenotyping. Figure {@fig:domains} shows a simplified domain map of the whole BrAPI v2.1 data model, divided into the organizational modules. The early versions of the specification focused on read-only phenotype data, with a small consideration to the other domains. Now the specification has a full representation of most of the major concepts applicable to the breeding process. The new specification is also internally consistent, easier to navigate, and allows for read, write, and update capabilities. None of those qualities were a guarantee for the earlier versions. 
 
-![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}
+![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 version of the 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 displays the 10 standalone, plug-and-play, applications available to the community. The servers list displays the 27 registered public data servers, their current status, and a form for registering additional servers. The compatible software list shows the 31 software applications that are BrAPI compliant, and again, a form for registering additional applications. The process for registering new items for these lists is completely voluntary, so the totals represent a lower bound for the number of BrAPPs, data repositories, and applications available in the the community. 
 
@@ -42,4 +42,4 @@ The BrAPI Hackathons are a major staple of the BrAPI community. Twice a year, th
 
 As the project has matured, a formal project leadership structure became increasingly important. As described in Figure {@fig:org-chart}, the project governance is divided into two groups. The Project Management team is responsible for the day to day operations of the project. The PI and Co-PI are responsible for the project funds, and responsible for hiring the BrAPI Project Coordinator who is paid by the project funds. The Advisory Board is a group of elected officials representing the community. The board is responsible for long term planning of the project, as well as quick decision making on behalf of the community. The two groups meet quarterly to report on progress and stay synchronized. 
 
-![The formal governance structure of the BrAPI Project Community](images/BrAPI_org_structure.jpg){#fig:org-chart}
+![The formal governance structure of the BrAPI Project Community](images/BrAPI_org_structure.jpg){#fig:org-chart width="100%"}

content/03.03.federation-infrastructure.md

@@ -20,7 +20,7 @@ In the global system for ex situ conservation of plant genetic resources (PGR) [
 The AGENT portal as described in more detail in section {@sec:Success_Story_AGENT} unlock the full potential of the biological material stored in genebanks around the globe by using FAIR international data standards and an open digital infrastructure for the management of plant genetic resources. The implemented BrAPI interface enables to mine current and historic genotypic and phenotypic information to drive the discovery of genes, traits and knowledge for future missions, complement existing information for wheat and barley and the new data standards and infrastructure to foster an improved management of PGR for other crop species across European genebanks.
 
 For the joint research data infrastructure for the federation of collections of genotypic and phenotypic data from European gene banks and bioinformatics institutes, a AGENT portal ({@fig:AGENT_WebFrontend}) as database infrastructure for integrated plant genetic resources on ex-situ genebanks is being created. It provides, manual data exploration, machine-readable access via BrAPI and provide data to the cored data deposition resources at the European Bioinformatics Institute (EBI).
-![Figure AGENT Portal](images/AGENT_WebFrontend.png){#fig:AGENT_WebFrontend}
+![Figure AGENT Portal](images/AGENT_WebFrontend.png){#fig:AGENT_WebFrontend width="100%"}
 
 The AGENT database backend aggregates curated and integrated passport data, phenotypic and genotypic data about wheat and barley accessions of 18 project partners are harmonized and integrated via BrAPI endpoints (https://github.com/AGENTproject/BrAPI) and explorable in a web portal (https://agent.ipk-gatersleben.de). The BrAPI endpoints were made available by scattered implementation. Genotyping data use DivBrowse [@doi:10.1093/gigascience/giad025] storage engine and BrAPI interface. Endpoints for sample data are implemented using AGENT database SQL to BrAPI broker service.
 To integrate those BrAPI endpoint provider into a single service and URL scheme, we work on their integration in a BrAPI proxy service. As next steps, we will expand BrAPI implementation to enable the integration of analysis pipelines in the AGENT portal, e.g. for genebank mining tools such as the FIGS+ pipeline developed by AGENT partner ICARDA [@doi:10.22004/AG.ECON.266624]. Another perspective is to integrate the data collected in the AGENT project into the European Search Catalogue for Plant Genetic Resources (EURISCO) [@doi:10.1093/nar/gkac852] and to implement BrAPI endpoints to make data on PGR collections in European genebanks programmatically accessible.