Taxonomy and Germplasm


Any type of data in CarrotOmics that references the taxonomy of a particular organism will have a corresponding organism page for that organism. These can be viewed either from the "Species" menu by selecting "Organism Summary", or from the home page Quick Start "Species List". The organisms listed in CarrotOmics have been derived from any of several sources:


Germplasm accessions can be viewed and searched through the "Search" menu "Germplasm Search" option, or from the home page Quick Start "Germplasm Search". Germplasm accessions can be searched by name, by keywords such as a trait or germplasm collection, by taxonomy, country of origin, and cultivar pedigree. Germplasm accessions will also in some case be found as cross-references on analysis or publication pages.

Biological Samples and Materials

CarrotOmics stores the information about biological samples from NCBI under a corresponding CarrotOmics Biological Sample page, for example SAMN17775433. These pages will link to CarrotOmics analyses and projects, and have references to corresponding NCBI entries. Information about other types of biological samples, such as a plant that has been evaluated for one or more phenotypes, is not represented by its own page, but will be found in the data files linked to the phenotyping project or analysis, for example 2013 Alternaria Resistance Evaluation

Phylogenetic Trees

A list of publications providing taxonomic trees can be accessed from the Trees page. All of the taxonomic trees within a given publication are collected under a single analysis that represents all trees in a publication, for example TreeBASE Study S15477. Each individual tree has a corresponding sub-analysis, listed in the Relationship field, which will ideally further describe analysis methods that were used to generate that tree, and each sub-analysis will have a link to the actual phylogenetic tree.