CropStore
Low Maintenance, Explicit Curation and Management of Integrated Datasets For Crop Plant Genetics
Graham King, Pierre Carion et al., Rothamsted Research.see large size schema
Three primary database modules (cs_PLANT, cs_LINKAGE_MAP, cs GENETIC_MARKER). have been defined in order to organise sets of tables relating to specific activities or analyses. The cs_PLANT modulemanages information relating to experimental plant materials, associated plant varieties, trials, traits and scoring occasions. There is a clear distinction between genetic entities such as plant line and individual plant accessions and specific plants from which experimental data may be acquired.
The cs_LINKAGE_MAP module manages information relating to genetic linkage maps, their constituent linkage groups and associated marker loci. An important aspect of this module is the ability to distinguish between different versions of maps and to associated these with relevant plant_populations or sub-populations. This module also provides the opportunity to manage information relating to Quantitative Trait Loci (QTL), where the trait relates directly to a well defined trait_descriptor. mapping_locus is the core entity within this module reflecting the
The cs_GENETIC_MARKER module is the most complex, reflecting both the widespread use of different types of genetic marker for use in genetic mapping, as well as their application to the assessment of genetic diversity. Given the considerable ambiguity of nomenclature present in the literature and different databases, an effort has been made to distinguish clearly between the entities of marker assays, genetic loci and alleles, as well as to the zygote genotypes that may be assigned to different marker fragments that are commonly resolved in marker assays.
Input template spreadsheets - Download Here
A series of MSExcel workbooks have been generated to facilitate the curation process. These comprise individual sheets where the column headings correspond directly in order and type to field names within the corresponding CropStore table. Default and example values are provided. Standard Operating Procedures have been developed that describe the recommended series of steps to ensure the curation process is able to be managed to a high standard.Nomenclature conventions
A series of nomenclature conventions are proposed based on experience accumulated over the past decade in attempts to provide unambiguous assignment of name to distinct entities, within context of a particular set of resources or experimental occasions and observations. The value of establishing some level of standardisation and adoption for such nomenclature convention lies in the ability to.. However, this does require a level of agreement, co-ordination and supervision in order to maintain. The level at which adoption of agreed nomenclatures become particularly valuable is where a research community has expressed a desire to establish a registry of entities that are commonly exchanged (eg linkage maps, loci etc) and where the benefits of such a concerted effort are tangible to those who participate.Draft nomenclature conventions are available for inspection here
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Implementations and interfaces
- MySQL implementation will be available for download here shortly, with update history
- MS Excel input template spreadsheets and Standard Operating Procedures will be available here soon
- An early prototype interface
based on the Germinate database system was developed in 2005/6 by Fady Mohareb and Mark Quinton-Tulloch - Web and Windows based interfaces will be available soon for testing
