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.
"What is CropStoreDB?", project outline, news and information
Design principlesThe design philosophy for CropStoreDB took into account the requirement to provide an explicit relationship between database tables and the entities that are commonly manipulated by plant geneticists. Providing a means to explain such relationships visually is proving to be beneficial in encouraging those who generate datasets to be responsible for, and involved in, the curation and data validation process. This approach is appropriate in many institutions or projects where there is insufficient investment to carry the overhead of developing and modifying sophisticated data-checking software, and where reference datasets are generated over long periods of time.
Eexcerpt from the poster presented at PAG XVIII, January 2010, San Diego (Poster available via the brassica.info website)
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. Finally 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.
An Excel file has been collated containing a list of all tables found in CropStoreDB (version cs_schema_9_1), with MySQL field definitions, BNF nomenclature with examples, comments, and field dependencies. (last updated January 2016)
- Geolocation geometry and SRID fields have been included in relevant tables
- Any future updates to the schema will be listed here as they occur.