A metadata is a piece of data used to define or describe another piece of data. In the case of a genome, the data is the sequence(s) and the metadata can describe the shape of the cell, its motility, the temperature at which it grows best, the known metabolic pathways, etc.
This page presents the metadata available in MicroScope. Those metadata can be used in the Advanced Selector to select objects. Note that we only support qualitative metadata for now.
Currently, there is only one source of metadata associated to the species of the genome (identified by its NCBI taxid).
Source of data¶
Species metadata are taken from Joshua S. Madin et al., A synthesis of bacterial and archaeal phenotypic trait data. Sci Data 7, 170 (2020). This article unifies phenotypic and quantitative genomic traits from 26 sources. The description of all available data can be seen here. We use version 1.2.
For our use, we have selected 9 qualitative metadata which are described in the table below:
|Trait name||Description||Exemple values|
|Cell shape||The typical shape of cells||bacillus, coccobacilus, …|
|Gram stain||Gram positive or negative||Gram positive, Gram negative|
|Motility||Capacity to move||motile/non motile, gliding, …|
|Sporulation||Can produce spores||sporulating/non sporulation|
|Metabolism||Oxygen usage||aerobic, microaerophilic, …|
|Range tmp||Coarse environmental preference||mesophilic, psychrophilic, …|
|Range salinity||Coarse environmental preference||stenohaline, halophilic, euryhaline, …|
|Pathways||List of metabolic pathways undertaken||aerobic_anoxygenic_phototrophy, fermentation, nitrate_reduction, …|
|Isolation source||Where the microbe was sourced from||host, biofilm, soil, …|
See the reference for more precise description and the meaning of the values.