Package: QBMS 3.0.0

Khaled Al-Shamaa

QBMS: Query the Breeding Management System(s)

This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, 'Germinate' <https://germinateplatform.github.io/get-germinate/>, 'DeltaBreed' <https://sandbox.breedinginsight.net>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.

Authors:Khaled Al-Shamaa [aut, cre], Mariano Omar Crimi [ctb], Zakaria Kehel [ctb], Johan Aparicio [ctb], ICARDA [cph]

QBMS_3.0.0.tar.gz
QBMS_3.0.0.zip(r-4.7-any)QBMS_3.0.0.zip(r-4.6-any)QBMS_3.0.0.zip(r-4.5-any)
QBMS_3.0.0.tgz(r-4.6-any)QBMS_3.0.0.tgz(r-4.5-any)
QBMS_3.0.0.tar.gz(r-4.7-any)QBMS_3.0.0.tar.gz(r-4.6-any)
QBMS_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
QBMS/json (API)

# Install 'QBMS' in R:
install.packages('QBMS', repos = c('https://icarda.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/icarda/qbms/issues

Pkgdown/docs site:https://icarda.github.io

On CRAN:

Conda:

8.48 score 11 stars 1 packages 68 scripts 384 downloads 55 exports 53 dependencies

Last updated from:f38ebb0a75. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE127
source / vignettesOK182
linux-releaseNOTE135
macos-releaseNOTE90
macos-oldrelNOTE109
windows-develNOTE120
windows-releaseNOTE96
windows-oldrelNOTE82
wasm-releaseOK113

Exports:calc_biovarsdebug_qbmsget_germplasm_attributesget_germplasm_dataget_germplasm_listget_hwsd2get_marker_mapget_pedigree_tableget_program_studiesget_qbms_connectionget_study_dataget_study_infoget_terraclimateget_trial_dataget_trial_obs_ontologyget_trial_pedigreeget_variantsget_variantsetgigwa_get_allelematrixgigwa_get_markersgigwa_get_metadatagigwa_get_samplesgigwa_get_sequencesgigwa_get_variantsgigwa_list_dbsgigwa_list_projectsgigwa_list_runsgigwa_set_dbgigwa_set_projectgigwa_set_runini_hwsd2ini_terraclimatelist_cropslist_programslist_studieslist_trialslist_variantsetsloginlogin_bmslogin_breedbaselogin_germinatelogin_gigwalogin_oauth2qbms_wizardqbms_wizard_serverqbms_wizard_uiscan_brapi_endpointsset_cropset_programset_qbms_configset_qbms_connectionset_studyset_tokenset_trialset_variantset

Dependencies:askpassbase64encbitbit64blobbslibcachemclicodetoolscommonmarkcpp11curlDBIdigestfastmapfontawesomefsfuturefuture.applyglobalsgluehtmltoolshttpuvhttr2jquerylibjsonlitelaterlifecyclelistenvmagrittrmemoisemimeminiUIopensslotelparallellypkgconfigpromisesR6rappdirsRcpprlangRNetCDFRSQLiterstudioapisassshinysourcetoolssysterravctrswithrxtable

EBS Example
QBMS | EBS | BrAPI | OAuth 2.0 | Example | Connect and authenticate to EBS | Query data
Rendered fromebs_example.Rmdusingknitr::rmarkdown

Last update: 2026-08-23
Started: 2023-12-16

Connection Wizard
Overview | Option 1: Using the Wizard from the R Console | Option 2: Embedding the Wizard in a Shiny Application | Option 3: Embedding the Wizard in an Interactive R Markdown Document | Choosing the Right Interface | Result Object
Rendered fromwidget_example.Rmdusingknitr::rmarkdown

Last update: 2026-07-19
Started: 2026-06-17

DeltaBreed Example
QBMS | DeltaBreed | BrAPI | Example | Using the Connection Wizard
Rendered fromdeltabreed_example.Rmdusingknitr::rmarkdown

Last update: 2026-07-19
Started: 2026-07-19

GIGWA Example
QBMS | GIGWA | BrAPI | Example | Enhanced Allele Matrix Retrieval
Rendered fromgigwa_example.Rmdusingknitr::rmarkdown

Last update: 2026-06-11
Started: 2022-05-18

TerraClimate Example
QBMS | TerraClimate | Reference: | Example | Offline Mode
Rendered fromterraclimate_example.Rmdusingknitr::rmarkdown

Last update: 2026-03-26
Started: 2022-06-29

Germinate Example
QBMS | Germinate | BrAPI | Connect to a Germinate server | Work with Phenotypic Data | Work with Genotypic Data | Work with Pedigree Data
Rendered fromgerminate_example.Rmdusingknitr::rmarkdown

Last update: 2025-08-04
Started: 2025-07-23

BMS Example
QBMS | Breeding Management System | BrAPI | Example
Rendered frombms_example.Rmdusingknitr::rmarkdown

Last update: 2025-07-23
Started: 2022-05-18

BreedBase Example
QBMS | BreedBase | BrAPI | Example
Rendered frombreedbase_example.Rmdusingknitr::rmarkdown

Last update: 2025-07-23
Started: 2022-02-28

FAO HWSD v2 Example
QBMS | FAO HWSD v2 Soil Database | Example | Advanced Users
Rendered fromhwsd2_example.Rmdusingknitr::rmarkdown

Last update: 2024-03-07
Started: 2023-12-16

Readme and manuals

Help Manual

Help pageTopics
Internal Function for Core BrAPI GET Callsbrapi_get_call
BrAPI Mapping Tablebrapi_map
Internal Function Used for Core BrAPI POST Calls (Allele Matrix Search)brapi_post_search_allelematrix
Internal Function Used for Core BrAPI POST Callsbrapi_post_search_call
Building Pedigree Table Recursivelybuild_pedigree_table
Calculate the Bioclimatic Variablescalc_biovars
Debug Internal QBMS Status Objectdebug_qbms
Engine Workflow Step Definitionsengine_workflows
Asynchronously Fetch a Single API Pageget_async_page
Asynchronously Fetch Multiple API Pagesget_async_pages
Get Authentication Step Typeget_auth_step_type
Get the BrAPI Endpoint URL for a given QBMS functionget_brapi_url
Get Engine-Specific Configuration Parametersget_engine_config_params
Retrieve Attributes for a Specified Germplasmget_germplasm_attributes
Retrieve Observations Data for a Specified Germplasm.get_germplasm_data
Get Germplasm ID for a Specified Germplasm Nameget_germplasm_id
Get the Germplasm List of the Current Active Studyget_germplasm_list
Get HWSD v2 Soil Data for a Given Location(s)get_hwsd2
Login Pop-Up Windowget_login_details
Get marker position informationget_marker_map
Get Next Stepget_next_step
Get Direct Parentsget_parents
Get the Pedigree Tableget_pedigree_table
Get Previous Stepget_prev_step
Get the List of Trials, Studies, and Locations Information for the Current Selected Programget_program_studies
Retrieve the List of Trials for the Active Breeding Programget_program_trials
Get the QBMS Connectionget_qbms_connection
Get Full Step Sequenceget_step_sequence
Get the Observations Data of the Current Active Studyget_study_data
Get the Details/Metadata of the Current Active Studyget_study_info
Get TerraClimate Data for a Given Coordinate(s)get_terraclimate
Get the Observations Data of the Current Active Trialget_trial_data
Get the Traits Ontology/Metadata of the Current Active Trialget_trial_obs_ontology
Get the Pedigree table for the Selected Trialget_trial_pedigree
Get Marker Matrix from the Selected Variant Setget_variants
Get Marker Matrix from the Selected Variant Setget_variantset
Get Markers Matrix in the Selected GIGWA Rungigwa_get_allelematrix
Get Markers Map in the Selected GIGWA Rungigwa_get_markers
Get the Metadata of the Current Active GIGWA Rungigwa_get_metadata
Get the Samples List of the Current Active GIGWA Projectgigwa_get_samples
Get the Sequences of the Current Active GIGWA Projectgigwa_get_sequences
Get Available Variants in the Selected GIGWA Rungigwa_get_variants
List GIGWA Databasesgigwa_list_dbs
Get the List of All Projects in the Selected GIGWA Databasegigwa_list_projects
Get the List of the Run Names Available in the Selected GIGWA Projectgigwa_list_runs
Set the Current Active GIGWA Database by Namegigwa_set_db
Set the Current Active GIGWA Projectgigwa_set_project
Set the Current Active GIGWA Rungigwa_set_run
Download and Setup HWSD v2.0 Data Files to Extract their Data Offlineini_hwsd2
Download TerraClimate netCDF Data Files to Extract their Data Offlineini_terraclimate
Retrieve Supported Crops from the Serverlist_crops
Get the List of Locations Information of the Current Selected Croplist_locations
Retrieve Breeding Programs for the Active Croplist_programs
Get the List of Studies in the Current Active Triallist_studies
List Trials in the Current Active Breeding Programlist_trials
List Variant Sets in the Selected Studylist_variantsets
Login to a BrAPI Serverlogin
Login to the Serverlogin_bms
Login to the BreedBase Serverlogin_breedbase
Login to the Germinate Serverlogin_germinate
Login to the GIGWA Serverlogin_gigwa
Login using OAuth 2.0 Authenticationlogin_oauth2
Navigation Step UI Factorynavigation_step_ui
Normalize QBMS List Function Resultsnormalize_options
QBMS Connection Wizard (Console / Gadget mode)qbms_wizard
QBMS Wizard Module Serverqbms_wizard_server
QBMS Wizard Module UIqbms_wizard_ui
Make One Data.Table from a List of Manyrbindlistx
Combine Data Frames by Row, Filling in Missing Columnsrbindx
Scan BrAPI Endpointsscan_brapi_endpoints
Set the Current Active Cropset_crop
Set the Current Active Breeding Programset_program
Configure BMS Server Settingsset_qbms_config
Set the QBMS Connectionset_qbms_connection
Set the Current Active Studyset_study
Set Access Token Responseset_token
Set the Current Active Trialset_trial
Set the Active Variant Setset_variantset