.. _Database Structure:


MSD Database Structure
======================


MSD database has a hierarchical structure. We have the concepts of **Projects**, **Organisms**, **Samples**, and **Datasets**.
As a user has defined a project, the new project can host various *organisms*, *samples* and *datasets*. A defined *organism*
can have several samples assigned to and similarly each *sample* might have various *datasets*.

Imgaine this hypothetical situation: research project in featuring three mice.
In this case each mouse would be an *organism* at MSD. Suppose it is important to compare two types of samples 
(colon biopsy and feces) and two microbiome analysis methods (16S amplicon and Shotgun sequencing). In 
order to achieve this it is required to attempt one sampling for each sample type and get enough sample for 
each sample type to send for different sequencing methods. It means that 2 samples from each mouse  will be taken
and from each sample 2 datasets would be produced. Thus, all three mice should be defined as *organism* at MSD and 
for each of them only **2** *samples* are defined for which **2** *datasets* would get generated and uploaded to MSD. The table below
shows the case.

.. _Concepts Relaion:
.. csv-table:: Relation of entities at MSD
   :header: "No.", "Project", "Organism", "Sample", "Dataset Type"
   :widths: 5, 10, 10, 20

   "1", "My_Project", "Mouse_1", "M1_Biopsy_1", "M1_Biopsy_1_16S"
   "2", "My_Project", "Mouse_1", "M1_Biopsy_1", "M1_Biopsy_1_shotgun"
   "3", "My_Project", "Mouse_1", "M1_feces_1", "M1_feces_1_16S"
   "4", "My_Project", "Mouse_1", "M1_feces_1", "M1_feces_1_Shotgun"
   "5", "My_Project", "Mouse_2", "M2_Biopsy_1", "M2_Biopsy_1_16S"
   "6", "My_Project", "Mouse_2", "M2_Biopsy_1", "M2_Biopsy_1_Shotgun"
   "7", "My_Project", "Mouse_2", "M2_feces_1", "M2_feces_1_16S"
   "8", "My_Project", "Mouse_2", "M2_feces_1", "M2_feces_1_Shotgun"
   "9", "My_Project", "Mouse_3", "M3_Biopsy_1", "M3_Biopsy_1_16S"
   "10", "My_Project", "Mouse_3", "M3_Biopsy_1", "M3_Biopsy_1_Shotgun"
   "11", "My_Project", "Mouse_3", "M3_feces_1", "M3_feces_1_16S"
   "12", "My_Project", "Mouse_3", "M3_feces_1", "M3_feces_1_Shotgun"

The table above shows that each mouse has 4 samples and each sample has 2 datasets. In total, there are 12 datasets.

.. include:: MSD-ID_explanations.rst

.. note::
   Definition of a *sample* refers to each attempt of sampling. For example, two samples, both taken from
   feces, at the same time point would be considered two distinguished samples so that two different sample 
   objects at MSD.


.. image:: /media/crc_base.jpg
   :scale: 50 %
   :alt: MSD Database Structure