23
Jun

Hackathon on plant breeding APIs

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Dr Rathore at the plant breeding API hackathon organized by the Bill & Melinda Gates Foundation.Photo: C. Sarma, ICRISAT

A hackathon was organized by the Bill & Melinda Gates Foundation on plant Breeding Application Programming Interface (BrAPI). The Breeding API specifies a standard interface for plant phenotype/genotype databases to serve their data to various crop breeding applications. BrAPIs are shared and open APIs are used by all data providers and data consumers.

The hackathon was organized to discuss and implement various use cases which included:

  • Working on the BrAPI validation test suite;
  • Interfacing with handheld devices;
  • Working with genebanks;
  • Linking breeding system to genomic data management systems;
  • Integration of FlapJack (a multi-platform application providing interactive visualizations of high-throughput genotype data);
  • Analytical pipelines including Galaxy (a software system that enables researchers without informatics expertise to perform computational analyses through the web);
  • Discussions on models to wire up Galaxy to use BrAPI;
  • Discussions on exchange between systems such as breeding system and data warehouse;
  • Discussion on defining a sample and enabling its proper tracking and information exchange between various data management systems. A general opinion on treating a sample as an observational unit was formed and modification of APIs was proposed;
  • Extension and modification of Minimum Information About a Plant Phenotyping Experiment (MIAPPE) was discussed. Existing APIs were reviewed and modified to make BrAPI able to pass MIAPPE datasets;
  • Future need of APIs for being HATEOS or JSON-LD compliant was also discussed and emphasis was given to adaptation of Findable, Accessible, Interoperable, Reusable (FAIR) principles (https://www.nature.com/articles/sdata201618).

Module 5 of Excellence in Breeding Initiative (EiB) team has volunteered to try to secure funding for the above BrAPI, including putting in place a coordinator or developer to take BrAPI development forward.

ICRISAT staff Dr Abhishek Rathore, Theme Leader, Statistics, Bioinformatics & Data Management and Mr Chaitanya Sarma, Scientific Officer, participated in the hackathon at Seattle from 12-16 June.

This work contributes to UN Sustainable Development Goals

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