Germplasm Ontology
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Introduction
- Ian Delacy's presentation on the topic is here.
Components of the Ontology
- Germplasm generative relationships
- Germplasm derivative relationships
- Germplasm management relationships
- Germplasm genetic constitution
Protege files for uploading (models as of 10th March 2005):
Overview of the Scope of Germplasm Ontology
The function of Genealogy Management System (GMS) in ICIS is:
- To provide a unique identifier for all packets of seed of a germplasm (collection of genitors as you have vegetatively reproduced germplasms) that have or do exist(note almost all progenitors of present germplasm do not exist anymore but we must know them to trace pedigrees and calculate COP, etc.).
- To manage all the names attached to the packet of seed (homonyms, synonyms, abbreviations – a nightmare)
- To provide a breeding history of the germplasm
The last item, breeding history, naturally results in the posing of questions such as:
- What are its parents, grandparents, ancestors, descendents, relatives?
- What probability do they have of having genes in common?
- What proportion of genes is expected to come from a list of ancestors?
- What parents do they have in common?
- Given an allele of a gene which ancestor did it come from?
Questions such as the following often need to be answered before the above questions can be answered:
- Does the germplasm belong to an out breeding, in breeding or vegetatively reproduced species?
- Is the germplasm homozygous or heterozygous?
- Is the germplasm homogeneous or heterogeneous?
- What type of cultivar (fixed lines, hybrid, clone etc) is formed?
- How has the germplasm been stored?
- Where did this germplasm come from (how did I get it)?
- Did I import it?
- Did I seed increase it?
Questions such as the following do not need to be asked:
- Questions on the cytological constitution of the germplasms – questions such as
- what is the ploidy level of the germplasm?
- What is the somy level?
