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AppleBreed DataBase (DB) aims to store genotypic and phenotypic data from multiple …


Biology Articles » Agriculture » Plant Production » A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase » Methods

Methods
- A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase

AppleBreed DB is intended to be a functional tool for geneticistsand breeders. Its data model combines conceptual and logicaldata models. The aim is to represent the implementation levelof information. The conceptual data model (CDM) was the firststep in processing the database design, followed by the logicaldata model (LDM). The CDM includes the main entities/structuresand the relationships among them, without specifying attributesor primary keys. Here, the highest levels in the relationshipsamong the different entities are identified. The CDM is dividedinto super-classes, classes and sub-classes. By definition,a class includes entities characterized by the same profile(e.g. the class marker includes the identities SSR, RFLP, SCARand AFLP). A super-class is a generalization of the classes.For example, the molecular markers, alleles and map classesgive different information on the genome and can be groupedat a superior level into a super-class called ‘Moleculardata’. The same principle is used to define the sub-classes. The LDM features specify all the entities and links definedin the model, as well as the attributes and the primary andforeign keys (keys identifying the link established betweendifferent entities). In line with examples of data models describedin the literature and with our objectives, the relational datamodel was chosen to ensure traceability of the collected data.To facilitate access to the database by users, a web interfacehad to be developed. Consequently, database management applicationswere chosen that would be accessible through the web (e.g. MySQL)and preferably based on open source programmes and operatingsystems (e.g. Linux).

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