Skip to content

Commit

Permalink
rearrange content, add header paragraphs
Browse files Browse the repository at this point in the history
  • Loading branch information
BrapiCoordinatorSelby committed May 8, 2024
1 parent 0311693 commit 561dbbd
Show file tree
Hide file tree
Showing 35 changed files with 17 additions and 44 deletions.
7 changes: 0 additions & 7 deletions content/03.01.--.HEADER.Data_Collection.md

This file was deleted.

3 changes: 3 additions & 0 deletions content/03.01.--.HEADER.Phenotyping.md
Original file line number Diff line number Diff line change
@@ -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.
File renamed without changes.
File renamed without changes.
File renamed without changes.
6 changes: 0 additions & 6 deletions content/03.02.--.HEADER.Data_Management.md

This file was deleted.

3 changes: 3 additions & 0 deletions content/03.02.--.HEADER.Genotyping.md
Original file line number Diff line number Diff line change
@@ -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.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
8 changes: 0 additions & 8 deletions content/03.03.--.HEADER.Federation_Infrastructure.md

This file was deleted.

3 changes: 3 additions & 0 deletions content/03.03.--.HEADER.Germplasm_Management.md
Original file line number Diff line number Diff line change
@@ -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.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
3 changes: 3 additions & 0 deletions content/03.04.--.HEADER.Data_Management.md
Original file line number Diff line number Diff line change
@@ -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.
6 changes: 0 additions & 6 deletions content/03.04.--.HEADER.Data_Visualization.md

This file was deleted.

File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
7 changes: 2 additions & 5 deletions content/03.05.--.HEADER.Analytics.md
Original file line number Diff line number Diff line change
@@ -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.
3 changes: 3 additions & 0 deletions content/03.06.--.HEADER.Infrastructure.md
Original file line number Diff line number Diff line change
@@ -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.
6 changes: 0 additions & 6 deletions content/03.06.--.HEADER.Samples_and_Genotypes.md

This file was deleted.

File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
6 changes: 0 additions & 6 deletions content/03.07.00.HEADER.Data_Portals.md

This file was deleted.

0 comments on commit 561dbbd

Please sign in to comment.