From 561dbbdb4440e81c5976844ed78611d5e89c9416 Mon Sep 17 00:00:00 2001
From: Peter Selby <ps664@cornell.edu>
Date: Wed, 8 May 2024 14:38:47 -0400
Subject: [PATCH] rearrange content, add header paragraphs

---
 content/03.01.--.HEADER.Data_Collection.md                | 7 -------
 content/03.01.--.HEADER.Phenotyping.md                    | 3 +++
 content/{03.02.01.PHIS.md => 03.01.05.PHIS.md}            | 0
 content/{03.02.07.PIPPA.md => 03.01.06.PIPPA.md}          | 0
 ...Selector_BrAPP.md => 03.01.07.Trait_Selector_BrAPP.md} | 0
 content/03.02.--.HEADER.Data_Management.md                | 6 ------
 content/03.02.--.HEADER.Genotyping.md                     | 3 +++
 content/{03.04.01.Flapjack.md => 03.02.01.Flapjack.md}    | 0
 content/{03.04.04.DArTView.md => 03.02.02.DArTView.md}    | 0
 content/{03.04.05.DivBrowse.md => 03.02.03.DivBrowse.md}  | 0
 content/{03.06.01.GIGWA.md => 03.02.04.GIGWA.md}          | 0
 content/{03.06.02.PHG.md => 03.02.05.PHG.md}              | 0
 content/03.03.--.HEADER.Federation_Infrastructure.md      | 8 --------
 content/03.03.--.HEADER.Germplasm_Management.md           | 3 +++
 content/{03.02.08.MGIS.md => 03.03.01.MGIS.md}            | 0
 ...{03.03.01.AGENT_Portal.md => 03.03.02.AGENT_Portal.md} | 0
 content/{03.04.02.Helium.md => 03.03.03.Helium.md}        | 0
 content/{03.07.02.GLIS.md => 03.03.04.GLIS.md}            | 0
 content/{03.07.03.FLORILEGE.md => 03.03.05.FLORILEGE.md}  | 0
 content/{03.07.01.FAIDARE.md => 03.03.06.FAIDARE.md}      | 0
 content/03.04.--.HEADER.Data_Management.md                | 3 +++
 content/03.04.--.HEADER.Data_Visualization.md             | 6 ------
 .../{03.02.02.DeltaBreed.md => 03.04.01.DeltaBreed.md}    | 0
 content/{03.02.03.BMS.md => 03.04.02.BMS.md}              | 0
 content/{03.02.04.Breedbase.md => 03.04.03.Breedbase.md}  | 0
 content/{03.02.05.BIMS.md => 03.04.04.BIMS.md}            | 0
 content/{03.02.06.Germinate.md => 03.04.05.Germinate.md}  | 0
 content/03.05.--.HEADER.Analytics.md                      | 7 ++-----
 content/03.06.--.HEADER.Infrastructure.md                 | 3 +++
 content/03.06.--.HEADER.Samples_and_Genotypes.md          | 6 ------
 .../{03.03.02.MIAPPE_MIRA.md => 03.06.01.MIAPPE_MIRA.md}  | 0
 ...3.MIAPPE_BrAPI2ISA.md => 03.06.02.MIAPPE_BrAPI2ISA.md} | 0
 .../{03.03.04.BrAPIMapper.md => 03.06.03.BrAPIMapper.md}  | 0
 content/{03.07.04.Zendro.md => 03.06.04.Zendro.md}        | 0
 content/03.07.00.HEADER.Data_Portals.md                   | 6 ------
 35 files changed, 17 insertions(+), 44 deletions(-)
 delete mode 100644 content/03.01.--.HEADER.Data_Collection.md
 create mode 100644 content/03.01.--.HEADER.Phenotyping.md
 rename content/{03.02.01.PHIS.md => 03.01.05.PHIS.md} (100%)
 rename content/{03.02.07.PIPPA.md => 03.01.06.PIPPA.md} (100%)
 rename content/{03.04.03.Trait_Selector_BrAPP.md => 03.01.07.Trait_Selector_BrAPP.md} (100%)
 delete mode 100644 content/03.02.--.HEADER.Data_Management.md
 create mode 100644 content/03.02.--.HEADER.Genotyping.md
 rename content/{03.04.01.Flapjack.md => 03.02.01.Flapjack.md} (100%)
 rename content/{03.04.04.DArTView.md => 03.02.02.DArTView.md} (100%)
 rename content/{03.04.05.DivBrowse.md => 03.02.03.DivBrowse.md} (100%)
 rename content/{03.06.01.GIGWA.md => 03.02.04.GIGWA.md} (100%)
 rename content/{03.06.02.PHG.md => 03.02.05.PHG.md} (100%)
 delete mode 100644 content/03.03.--.HEADER.Federation_Infrastructure.md
 create mode 100644 content/03.03.--.HEADER.Germplasm_Management.md
 rename content/{03.02.08.MGIS.md => 03.03.01.MGIS.md} (100%)
 rename content/{03.03.01.AGENT_Portal.md => 03.03.02.AGENT_Portal.md} (100%)
 rename content/{03.04.02.Helium.md => 03.03.03.Helium.md} (100%)
 rename content/{03.07.02.GLIS.md => 03.03.04.GLIS.md} (100%)
 rename content/{03.07.03.FLORILEGE.md => 03.03.05.FLORILEGE.md} (100%)
 rename content/{03.07.01.FAIDARE.md => 03.03.06.FAIDARE.md} (100%)
 create mode 100644 content/03.04.--.HEADER.Data_Management.md
 delete mode 100644 content/03.04.--.HEADER.Data_Visualization.md
 rename content/{03.02.02.DeltaBreed.md => 03.04.01.DeltaBreed.md} (100%)
 rename content/{03.02.03.BMS.md => 03.04.02.BMS.md} (100%)
 rename content/{03.02.04.Breedbase.md => 03.04.03.Breedbase.md} (100%)
 rename content/{03.02.05.BIMS.md => 03.04.04.BIMS.md} (100%)
 rename content/{03.02.06.Germinate.md => 03.04.05.Germinate.md} (100%)
 create mode 100644 content/03.06.--.HEADER.Infrastructure.md
 delete mode 100644 content/03.06.--.HEADER.Samples_and_Genotypes.md
 rename content/{03.03.02.MIAPPE_MIRA.md => 03.06.01.MIAPPE_MIRA.md} (100%)
 rename content/{03.03.03.MIAPPE_BrAPI2ISA.md => 03.06.02.MIAPPE_BrAPI2ISA.md} (100%)
 rename content/{03.03.04.BrAPIMapper.md => 03.06.03.BrAPIMapper.md} (100%)
 rename content/{03.07.04.Zendro.md => 03.06.04.Zendro.md} (100%)
 delete mode 100644 content/03.07.00.HEADER.Data_Portals.md

diff --git a/content/03.01.--.HEADER.Data_Collection.md b/content/03.01.--.HEADER.Data_Collection.md
deleted file mode 100644
index ab6db92..0000000
--- a/content/03.01.--.HEADER.Data_Collection.md
+++ /dev/null
@@ -1,7 +0,0 @@
-### Data Collection 
-<!-- (Field Book, Climmob, other Phenoapps, ImageBreed, etc) -->
-
-<!-- * General use case description(s)
-* Specific tool examples 
-* Alternate solutions/ why is it better with BrAPI
-* future related use cases, areas to improve -->
diff --git a/content/03.01.--.HEADER.Phenotyping.md b/content/03.01.--.HEADER.Phenotyping.md
new file mode 100644
index 0000000..fa9d5db
--- /dev/null
+++ b/content/03.01.--.HEADER.Phenotyping.md
@@ -0,0 +1,3 @@
+### Phenotyping
+
+Phenotyping is the basis for all breeding efforts. All the downstream analysis and decision making procedures rely on a foundation of accurate, high-quality, phenotypic data. The BrAPI specification supports phenotypic data as it passes through the entire breeding pipeline, as it is published, and as it is archived. The community has developed tools that use BrAPI during the data collection process, to get the data into a standard format as soon as possible. There are BrAPI compatible systems to store and curate phenotypic data, and tools to manage trait meta data. The community has also begun developing BrAPI compatible tools for managing images and other high throughput phenotyping techniques. 
diff --git a/content/03.02.01.PHIS.md b/content/03.01.05.PHIS.md
similarity index 100%
rename from content/03.02.01.PHIS.md
rename to content/03.01.05.PHIS.md
diff --git a/content/03.02.07.PIPPA.md b/content/03.01.06.PIPPA.md
similarity index 100%
rename from content/03.02.07.PIPPA.md
rename to content/03.01.06.PIPPA.md
diff --git a/content/03.04.03.Trait_Selector_BrAPP.md b/content/03.01.07.Trait_Selector_BrAPP.md
similarity index 100%
rename from content/03.04.03.Trait_Selector_BrAPP.md
rename to content/03.01.07.Trait_Selector_BrAPP.md
diff --git a/content/03.02.--.HEADER.Data_Management.md b/content/03.02.--.HEADER.Data_Management.md
deleted file mode 100644
index de65d87..0000000
--- a/content/03.02.--.HEADER.Data_Management.md
+++ /dev/null
@@ -1,6 +0,0 @@
-### Data Management 
-
-<!-- * General use case description(s)
-* Specific tool examples 
-* Alternate solutions/ why is it better with BrAPI
-* future related use cases, areas to improve -->
diff --git a/content/03.02.--.HEADER.Genotyping.md b/content/03.02.--.HEADER.Genotyping.md
new file mode 100644
index 0000000..5af99de
--- /dev/null
+++ b/content/03.02.--.HEADER.Genotyping.md
@@ -0,0 +1,3 @@
+### Genotyping
+
+Genotyping has become a cornerstone of most breeding processes, but the data can be difficult to manage. BrAPI supports genotypic data, relying on some existing standards including VCF and the GA4GH Variants standards. The BrAPI Community has built BrAPI compatible tools for storing, searching, visualizing, and analyzing genotypic data. 
diff --git a/content/03.04.01.Flapjack.md b/content/03.02.01.Flapjack.md
similarity index 100%
rename from content/03.04.01.Flapjack.md
rename to content/03.02.01.Flapjack.md
diff --git a/content/03.04.04.DArTView.md b/content/03.02.02.DArTView.md
similarity index 100%
rename from content/03.04.04.DArTView.md
rename to content/03.02.02.DArTView.md
diff --git a/content/03.04.05.DivBrowse.md b/content/03.02.03.DivBrowse.md
similarity index 100%
rename from content/03.04.05.DivBrowse.md
rename to content/03.02.03.DivBrowse.md
diff --git a/content/03.06.01.GIGWA.md b/content/03.02.04.GIGWA.md
similarity index 100%
rename from content/03.06.01.GIGWA.md
rename to content/03.02.04.GIGWA.md
diff --git a/content/03.06.02.PHG.md b/content/03.02.05.PHG.md
similarity index 100%
rename from content/03.06.02.PHG.md
rename to content/03.02.05.PHG.md
diff --git a/content/03.03.--.HEADER.Federation_Infrastructure.md b/content/03.03.--.HEADER.Federation_Infrastructure.md
deleted file mode 100644
index a255818..0000000
--- a/content/03.03.--.HEADER.Federation_Infrastructure.md
+++ /dev/null
@@ -1,8 +0,0 @@
-### Federated Data Management Infrastructures
-<!-- 
-(AGENT, INCREASING, EURISCO, DataPLANT, NFDI4BioDiversity, FAIRAgro)
-
-* General use case description(s) -  AgrosystemIntegration of germplasm collections in context of data trustee models among private economy and public research, integration of ex-situ genebanks (EU H2020 projects AGENT, INCREASING), integrated agrosystems and plant research infrastructure
-* Specific tool examples - BraPI endpoints for AGENT, IPK-Genebank, MIAPPE ISA-TAB2BRAPI service
-* Alternate solutions/ why is it better with BrAPI - Schema.ORG lightweight meta data harvesting, ARCs as collaborative data decoration, API and publication pipeline
-* future related use cases, areas to improve - LIMS to BrAPI proxies -->
diff --git a/content/03.03.--.HEADER.Germplasm_Management.md b/content/03.03.--.HEADER.Germplasm_Management.md
new file mode 100644
index 0000000..11122c0
--- /dev/null
+++ b/content/03.03.--.HEADER.Germplasm_Management.md
@@ -0,0 +1,3 @@
+### Germplasm Management
+
+The vast quantity of new accessions, variants, and lines being created each year means germplasm data management is critical to keeping things organized. This is true at the level of a single breeding program, on a national scale, and on the international scale. BrAPI supports the transmission of germplasm passport data, as well as pedigree trees and crossing metadata. The BrAPI community has developed BrAPI compliant tools for storing, searching, and visualizing this metadata. There are even some plans in place to build federated networks of genebank data, connected via BrAPI. 
diff --git a/content/03.02.08.MGIS.md b/content/03.03.01.MGIS.md
similarity index 100%
rename from content/03.02.08.MGIS.md
rename to content/03.03.01.MGIS.md
diff --git a/content/03.03.01.AGENT_Portal.md b/content/03.03.02.AGENT_Portal.md
similarity index 100%
rename from content/03.03.01.AGENT_Portal.md
rename to content/03.03.02.AGENT_Portal.md
diff --git a/content/03.04.02.Helium.md b/content/03.03.03.Helium.md
similarity index 100%
rename from content/03.04.02.Helium.md
rename to content/03.03.03.Helium.md
diff --git a/content/03.07.02.GLIS.md b/content/03.03.04.GLIS.md
similarity index 100%
rename from content/03.07.02.GLIS.md
rename to content/03.03.04.GLIS.md
diff --git a/content/03.07.03.FLORILEGE.md b/content/03.03.05.FLORILEGE.md
similarity index 100%
rename from content/03.07.03.FLORILEGE.md
rename to content/03.03.05.FLORILEGE.md
diff --git a/content/03.07.01.FAIDARE.md b/content/03.03.06.FAIDARE.md
similarity index 100%
rename from content/03.07.01.FAIDARE.md
rename to content/03.03.06.FAIDARE.md
diff --git a/content/03.04.--.HEADER.Data_Management.md b/content/03.04.--.HEADER.Data_Management.md
new file mode 100644
index 0000000..fede9ab
--- /dev/null
+++ b/content/03.04.--.HEADER.Data_Management.md
@@ -0,0 +1,3 @@
+### Breeding Data Management
+
+While specialty data management is important for some use cases, often breeders want a central repository of critical data. General breeding data management systems support some level phenotypic, genotypic, and germplasm data, as well as trial, equipment, and people management. By enabling BrAPI support, these larger systems can connect with smaller tools and specialty systems to provide more functionality under the same user interface. There are several breeding data management systems developed in the BrAPI community, each with their own pros and cons. 
diff --git a/content/03.04.--.HEADER.Data_Visualization.md b/content/03.04.--.HEADER.Data_Visualization.md
deleted file mode 100644
index 64a4888..0000000
--- a/content/03.04.--.HEADER.Data_Visualization.md
+++ /dev/null
@@ -1,6 +0,0 @@
-### Data visualization 
-<!-- 
-* General use case description(s)
-* Specific tool examples 
-* Alternate solutions/ why is it better with BrAPI
-* future related use cases, areas to improve -->
diff --git a/content/03.02.02.DeltaBreed.md b/content/03.04.01.DeltaBreed.md
similarity index 100%
rename from content/03.02.02.DeltaBreed.md
rename to content/03.04.01.DeltaBreed.md
diff --git a/content/03.02.03.BMS.md b/content/03.04.02.BMS.md
similarity index 100%
rename from content/03.02.03.BMS.md
rename to content/03.04.02.BMS.md
diff --git a/content/03.02.04.Breedbase.md b/content/03.04.03.Breedbase.md
similarity index 100%
rename from content/03.02.04.Breedbase.md
rename to content/03.04.03.Breedbase.md
diff --git a/content/03.02.05.BIMS.md b/content/03.04.04.BIMS.md
similarity index 100%
rename from content/03.02.05.BIMS.md
rename to content/03.04.04.BIMS.md
diff --git a/content/03.02.06.Germinate.md b/content/03.04.05.Germinate.md
similarity index 100%
rename from content/03.02.06.Germinate.md
rename to content/03.04.05.Germinate.md
diff --git a/content/03.05.--.HEADER.Analytics.md b/content/03.05.--.HEADER.Analytics.md
index f2a62cf..9808bf9 100644
--- a/content/03.05.--.HEADER.Analytics.md
+++ b/content/03.05.--.HEADER.Analytics.md
@@ -1,6 +1,3 @@
 ### Analytics
-<!-- 
-* General use case description(s)
-* Specific tool examples 
-* Alternate solutions/ why is it better with BrAPI
-* future related use cases, areas to improve -->
+
+While other tools listed above have the capability to do specialized analytics on certain types of data, general analytics tools can cover a wide range of data types and analytical models. The tools developed by the BrAPI community, can pull in data from multiple BrAPI compatible data sources and provide enhanced analytical functionality. In many cases, there is no longer a need to import and export large data files to a local computational environment just to run standard analytical models. These tools are able to extract the data they need from a data source without much human intervention or human error. 
diff --git a/content/03.06.--.HEADER.Infrastructure.md b/content/03.06.--.HEADER.Infrastructure.md
new file mode 100644
index 0000000..8945a43
--- /dev/null
+++ b/content/03.06.--.HEADER.Infrastructure.md
@@ -0,0 +1,3 @@
+### General Infrastructure 
+
+Adopting BrAPI compatibility into an existing system can be difficult sometimes. The BrAPI Community has developed several tools to make adoption easier. This includes things like pre built code libraries, connectors to other technology standards, and mappers to alternate data types or data files. THe goal here is always to lower the barrier to entry for the BrAPI community, making it easier for other groups to get started and connect their existing data to the standard. 
diff --git a/content/03.06.--.HEADER.Samples_and_Genotypes.md b/content/03.06.--.HEADER.Samples_and_Genotypes.md
deleted file mode 100644
index 41f529a..0000000
--- a/content/03.06.--.HEADER.Samples_and_Genotypes.md
+++ /dev/null
@@ -1,6 +0,0 @@
-### Samples and Genotypes
-
-<!-- * General use case description(s)
-* Specific tool examples 
-* Alternate solutions/ why is it better with BrAPI
-* future related use cases, areas to improve -->
diff --git a/content/03.03.02.MIAPPE_MIRA.md b/content/03.06.01.MIAPPE_MIRA.md
similarity index 100%
rename from content/03.03.02.MIAPPE_MIRA.md
rename to content/03.06.01.MIAPPE_MIRA.md
diff --git a/content/03.03.03.MIAPPE_BrAPI2ISA.md b/content/03.06.02.MIAPPE_BrAPI2ISA.md
similarity index 100%
rename from content/03.03.03.MIAPPE_BrAPI2ISA.md
rename to content/03.06.02.MIAPPE_BrAPI2ISA.md
diff --git a/content/03.03.04.BrAPIMapper.md b/content/03.06.03.BrAPIMapper.md
similarity index 100%
rename from content/03.03.04.BrAPIMapper.md
rename to content/03.06.03.BrAPIMapper.md
diff --git a/content/03.07.04.Zendro.md b/content/03.06.04.Zendro.md
similarity index 100%
rename from content/03.07.04.Zendro.md
rename to content/03.06.04.Zendro.md
diff --git a/content/03.07.00.HEADER.Data_Portals.md b/content/03.07.00.HEADER.Data_Portals.md
deleted file mode 100644
index f656416..0000000
--- a/content/03.07.00.HEADER.Data_Portals.md
+++ /dev/null
@@ -1,6 +0,0 @@
-### Data Portal
-
-<!-- * General use case description(s)
-* Specific tool examples 
-* Alternate solutions/ why is it better with BrAPI
-* future related use cases, areas to improve -->