QBMS

R package to Query the Breeding Management System database (using BrAPI calls) in favor of scientists/researchers as targeted end-users who want to retrieve their experiments data directly into R statistical analyzing environment.

Package Author and Maintainer: Khaled Al-Shamaa <k.el-shamaa (at) cgiar (dot) org>

Package Contributor: Mariano Omar CRIMI <m.crimi (at) cgiar (dot) org>

Package Contributor: Zakaria Kehel <z.kehel (at) cgiar (dot) org>

Package Copyright Holder: International Center for Agricultural Research in the Dry Areas (ICARDA)

Breeding Management System

Breeding Management System (BMS) is an information management system developed by the Integrated Breeding Platform to help breeders manage the breeding process, from programme planning to decision-making. The BMS is customizable for most crop breeding programs, and comes pre-loaded with curated ontology terms for many crops (bean, cassava, chickpea, cowpea, groundnut, maize, rice, sorghum, soybean, wheat, and others). The BMS is available as a cloud application, which can be installed on local or remote servers and accessed by multiple users.

BrAPI

The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. This community driven standard is free to be used by anyone interested in plant breeding data management.

Install

install.packages("devtools")
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")

devtools::install_github("khaled-alshamaa/QBMS")

If you are not already an active BMS user, you can contact IBP support to get access to a trial BMS server.

Example

# load the QBMS library
library(QBMS)

# config your BMS connection
set_qbms_config("bms.example.com", 443, "https://")

# login using your BMS account (interactive mode)
# or pass your BMS username and password as parameters (batch mode)
login_bms()

# list supported crops in the bms server
list_crops()

# select a crop by name
set_crop("Tutorial1")

# list all breeding programs in the selected crop
list_programs()

# select a breeding program by name
set_program("Training Breeding Program")

# list all studies/trials in the selected program (optional, filter by year)
list_trials()
list_trials(2017)

# select a specific study/trial by name
set_trial("CIDTN-2016")

# get observation variable ontology in the selected study/trial
ontology <- get_trial_obs_ontology()

# list all environments/locations information in the selected study/trial
list_studies()

# select a specific environment/location by name
set_study("CIDTN-2016 Environment Number 1")

# retrieve data, general information, and germplasm list of the selected environment/location
data <- get_study_data()
info <- get_study_info()
germplasm <- get_germplasm_list()

# retrieve multi-environment trial data of the selected study/trial
MET <- get_trial_data()

# retrieve observations data of given germplasm aggregated from all trials in the selected program
germplasm_observations <- get_germplasm_data("FLIP10-3C")

# retrieve all environments/locations information in the selected program
program_studies <- get_program_studies()