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content/03.03.02.AGENT_Portal.md

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 <!-- Contribution BrAPI 2.0 paper
 Suggested Authors: Matthias Lange, Patrick König, Stephan Weise, Gouripriya Davuluri, Suman Kumar, Joseph Ruff, Paul Kersey, Cyril Pommier, Michael Alaux, Erwan Le-Floch -->
-#### AGENT Portal
+#### AGENT
 
 <!-- Matthias Lange -->
-In the global system for ex situ conservation of plant genetic resources (PGR) [@doi:10.3390/plants10081557], a total of ~5.8 million accessions are conserved in 1750 ex situ genebanks [@doi:10.2135/cropsci2017.01.0014]. Unique and permanent identifiers in the form of DOIs are available for more than 1.7 million accessions [@{https://glis.fao.org/glis/}]. Each DOI is linked to some basic descriptive data that facilitates the use of these resources. Many DOIs are also linked to additional data from different domains or will be in the future. However, a data space beyond the most basic information is needed that includes genotypic and phenotypic data. This space will help answer questions on the global biological diversity of a plant species, on duplicate detection, on provenance tracking for the identification of genetic integrity, on the selection of the most suitable material for various purposes, and to support further applications in data mining or AI. In this context, the aim of the [AGENT project](https://www.agent-project.eu/), funded by the European Commission, is to develop a concept for the digital exploitation and activation of this PGR data space, [@doi:10.1038/sdata.2016.18] and to test it in practice using two important crops, barley and wheat. Thirteen European genebanks and five bioinformatics centers are cooperating and have agreed on standards and protocols for the data flow and data formats [@doi:10.12688/f1000research.109080.2] for central archiving of genotypic and phenotypic data.
-
-The BrAPI specification is one of the agreed standards, that are detailed in the AGENT guidelines for dataflow [@doi:10.5281/zenodo.12625360]. The implemented BrAPI interface enables AGENT to mine current and historic genotypic and phenotypic information. This will drive the discovery of genes, traits, and knowledge for future missions. The AGENT database backend aggregates curated passport data, phenotypic data, and genotypic data about wheat and barley accessions from the 18 project partners. This data is integrated via [BrAPI endpoints](https://github.com/AGENTproject/BrAPI) and explorable in a [web portal](https://agent.ipk-gatersleben.de). Genotyping data uses the DivBrowse [@doi:10.1093/gigascience/giad025] storage engine and its BrAPI interface. Soon, the BrAPI implementation will be expanded to enable the integration of analysis pipelines in the AGENT portal, such as the FIGS+ pipeline developed by ICARDA [@doi:10.22004/AG.ECON.266624].
+In the global system for ex situ conservation of plant genetic resources (PGR) [@doi:10.3390/plants10081557], material is being conserved in about 1750 collections [@doi:10.2135/cropsci2017.01.0014] totalling ~5.8 million accessions. Unique and permanent identifiers in the form of DOIs are available for more than 1.7 million accessions via the Global Information System [@{https://glis.fao.org/glis/}] of the International Treaty on Plant Genetic Resources for Food and Agriculture. Each DOI is linked to some basic descriptive data that facilitates the use of these resources, mainly passport data. Many DOIs are also linked to additional data from different domains or will be in the future. However, a data space beyond the most basic information is needed that includes genotypic and phenotypic data. This space will help to answer questions about the global biological diversity of plant species, the detection of duplicates, the tracking of provenance for the identification of genetic integrity, the selection of the most suitable material for different purposes, and to support further applications in the field of data mining or AI. In this context, the aim of the [AGENT project](https://www.agent-project.eu/), funded by the European Commission, is to develop a concept for the digital exploitation and activation of this PGR via European ex situ genebanks according to the FAIR principles [@doi:10.1038/sdata.2016.18] and to test it in practice using two important crops, barley and wheat. Thirteen European genebanks and five bioinformatics centers are working together and have agreed on standards and protocols for data flow and data formats [@doi:10.12688/f1000research.109080.2] for the collection, integration, and archiving of genotypic and phenotypic data.
 
+The BrAPI specification is one of the agreed standards, that are detailed in the AGENT guidelines for dataflow [@doi:10.5281/zenodo.12625360]. The implemented BrAPI interface enables the analysis of current and historic genotypic and phenotypic information. This will drive the discovery of genes, traits, and knowledge for future missions, complement existing information for wheat and barley, and use the new data standards and infrastructure to promote better access and use of PGR for other crops in European genebanks. The AGENT database backend aggregates curated passport data, phenotypic data, and genotypic data on wheat and barley accessions of 18 project partners. This data is accessible via [BrAPI endpoints](https://github.com/AGENTproject/BrAPI) and explorable in a [web portal](https://agent.ipk-gatersleben.de). Genotyping data uses the DivBrowse [@doi:10.1093/gigascience/giad025] storage engine and its BrAPI interface. Soon, the BrAPI implementation will be expanded to enable the integration of analysis pipelines in the AGENT portal, such as the FIGS+ pipeline developed by ICARDA [@doi:10.22004/AG.ECON.266624]. There is also a plan to integrate the data collected by the AGENT project into the European Search Catalogue for Plant Genetic Resources (EURISCO) [@doi:10.1093/nar/gkac852].
 <!-- ![Figure Data flow of genotypic data from AGENT partner databases](images/AGENT_Genotyping_Data_Flow.png){#fig:AGENT_Genotyping_Data_Flow width="100%"} -->
 <!-- ![Figure AGENT Portal](images/AGENT_Web_Frontend.png){#fig:AGENT_Web_Frontend width="100%"} -->

content/03.04.04.BIMS.md

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 #### BIMS
 
 <!-- Sook -->
-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. 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 (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. 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 is also implemented in the public database [breedwithbims.org](https://wwww.breedwithbims.org) that any crop breeder can use.
 
 Right now, BIMS primarily utilizes BrAPI to connect with the Field Book Android App [@doi:10.2135/cropsci2013.08.0579], enabling seamless data transfer between BIMS and the app. Data transfer through BrAPI between BIMS and other resources such as BreedBase[@doi:10.1093/g3journal/jkac078], GIGWA[@doi:10.1093/gigascience/giz051], and Breeder Genomics Hub is on the way. Hopefully, the BIMS development team can easily reuse some of the solved use cases and workflows created by others in the BrAPI community.