Modules and data field definitions

In order to maximize the impact of high quality crop science, there is a continuing need for explicit management of complex datasets relating to plant and crop genetics. We are addressing the first stage in dataset curation and dissemination, by providing a data model and tools that reflect the relationships understood and manipulated by researchers and breeders.

Modules

CropStoreDB is curated within five interconnected modules:

• CS_PLANT manages the plant population and line data. A clear distinction is made between genetic entities such as plant line and individual plant accessions.
• CS_TRAIT deals with trials, experimental designs, trait descriptions, and scores. This module allows detailed methods, including any variations, to be captured.
• CS_LINKAGE_MAP contains the data for linkage maps, linked to plant populations, genetic markers and genome alignment data in AlignStoreDB.
• CS_GENETIC_MARKER is used to link markers to sequence in SeqStoreDB.
• CS_QTL is used to capture quantitative trait loci based on explicitly described experimental traits. This includes summary statistics for the trait data used to calculate QTL.

Field definitions

A detailed set of field definitions have been developed for each table within CropStoredDB.

• Definitions and nomenclature standards are provided in an Excel workbook
• This includes a collated list of all tables found in CropStoreDB (version cs_schema_9_2), with MySQL field definitions, BNF nomenclature with examples, comments, and field dependencies.