Systems Science of Biological Dynamics database (SSBD:database)

Submitted by Perrine on Tue, 09/08/2020 - 13:37

This database provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, gene expression nuclei, etc. Quantitative biological data and microscopy image are collected from a variety of species, sources and methods. These include data obtained from both experiment and computational simulation. Images are downloadable as uploaded raw files. SSBD utilises OMERO internally to manage microscopic images and their metadata. SSBD also provides a REST API allowing 3rd party applications, such as R, Python, Java and C/C++ to access the data directly from the database. In addition, SSBD provides Resource Description Framework (RDF) formatted meta-information of the quantitative data and microscopy images at RIKEN Meta Database and NBDC RDF Portal.  It is a japenese initiative. 

has Ground truth

It also stores all the qualitative data (i.e. segmented data or ROIs) separately as numerical datasets. Quantitative data are represented by using a unified data format, the Biological Dynamics Markup Language.

has imaging details

Diverse microscopes (mostly light microscopy, but some electronic microscopy as well). SSBD tries to store and curate 4D datasets, ie images that are 3D together with time element.