Linking data management systems to analytics is an important step in breeding digitalization. Breeders can use this R package to Query the Breeding Management System(s) like BMS, BreedBase, and GIGWA (using BrAPI calls) and help them to retrieve phenotypic and genotypic data directly into their analyzing pipelines developed in R statistical environment.
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.
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.packages("remotes")
remotes::install_github("icarda-git/QBMS")If you are not already an active BMS user, you can contact IBP support to get access to a trial BMS server.
# load the QBMS library
library(QBMS)
# config your BMS connection (by providing your BMS login page URL)
set_qbms_config("https://www.bms-uat-test.net/ibpworkbench/controller/auth/login")
# 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 current bms server
list_crops()
# select a crop by name
set_crop("maize")
# list all breeding programs in the selected crop
list_programs()
# select a breeding program by name
set_program("MC Maize")
# list all studies/trials in the selected program
list_trials()
# filtered by year of starting date
list_trials(2020)
# select a specific study/trial by name
set_trial("2018 PVT")
# 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("2018 PVT Environment Number 1")
# select a specific study by location name (first match)
studies <- list_studies()
set_study(studies[studies$locationName == "BASF Bremen", "studyName"][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()
# get the pedigree table
pedigree_table <- get_pedigree_table(germplasm, "germplasmName", "pedigree")
# retrieve multi-environment trial data of the selected study/trial
MET <- get_trial_data()
# retrieve all environments/locations information in the selected program
program_studies <- get_program_studies()
# retrieve observations data of given germplasm aggregated from all trials
# in the selected program
germplasm_observations <- get_germplasm_data("BASFCORN-2-1")
# retrieve germplasm attributes for a given germplasm in a crop
germplasm_attributes <- get_germplasm_attributes("BASFCORN-2-1")