Query data by germplasm/genotype

Description

To find sources of resistance to stem rust (UG99) and tolerance to drought conditions in bread wheat along with passport information of the germplasms (sources) and genotypic information such as molecular markers, genes associated with stem rust.

Data types

Phenotypic data and genotypic data

Challenges

Phenotypic and genotypic data are generally stored in different databases and there is no easy way to link such databases. For example: GrinGlobal is used for the passport data associated with the germplasms, phenotypic data in IWIS (International wheat information system) or/and BMS (Breeding Management System) and gene sequences in NCBI, EMBL, low density marker data in GDMS and high density marker data in HDF5 databases.

Concerns

  1. How do we link these databases to each other?
  2. Do we have well-documented metadata to make a query?

What could be common entities in all these information to pull out the information? Looking at the query description, the data should be to germplasm (name or identifier) and traits using ontology.

Written by: Effie Tsiflidou, Thomas Francart, Richard Fulss, Rosemary Shrestha
Published on: 02 October 2014
Updated on: 30 October 2014

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