Managing Phenotypic Data through the IBP’s Breeding Management System

Presented at the Workshop on Managing Crop Phenotype Data, PAG XXIII by Graham McLaren and Rebecca Berrigan

Date Saturday 10th January 2015, San Diego, California.

The IBDB Phenotyping Data Model

Title of presentation/Author Image courtesy of FreeDigitalPhotos.net

STUDY AND DATASET INFORMATION

• study labels and levels • define data labels and • measurement variates

TRIAL DESIGN • observation units • sampling plans • experimental design

TRIAL ENVIRONMENT • georeference • location names • environment levels • link to LMM

GERMPLASM ENTRY • germplasm

identifiers • characterization

levels • link to GMS

ONTOLOGY • properties • methods • scales • standard

variables • valid values

OBSERVATION

• variate values • Links to valid

values

IBDBV2 – Data Model

MAPPING TO THE CHADO NATURAL DIVERSITY SCHEMA

cv, cvterm, cvtermsynonym, cvterm_relationship

Project, projectprop, Project_relationship

Stock, stockprop

nd_experiment, nd_experimentprop

nd_geolocation, nd_geolocationprop

Phenotype

Data Annotation

Property eg Trait

Method eg Protoocol

Scale eg Units

Variable Label or Variate

Trai

t Dic

tiona

ry

Community curated trait dictionaries for each crop at www.cropontology.org

Data Access - API

Phenotyiping Data Access/Rebecca Berrigan

API : Application Programming Interface

• Protects data consumers from data storage changes

• Allows data to be provided in forms that are easier to consume

Title of presentation/Author Image courtesy of FreeDigitalPhotos.net

Phenotyping Data BMS/Rebecca Berrigan Image courtesy of FreeDigitalPhotos.net

Phenotyping Data BMS/Rebecca Berrigan Image courtesy of FreeDigitalPhotos.net

Let’s see an API http://api.leafnode.io:8080/

Phenotyping Data BMS/Rebecca Berrigan Image courtesy of FreeDigitalPhotos.net

http://api.leafnode.io:8080/study/10104 {“id”:10104, “name”:”basicNurseryTemplate”, “type”:”N”, “dataset”: [{ …… “measuredTraits”:” ……”, “environment”:” ……..”, }