openbis-data-modelling.md



openBIS Data Modelling

Overview
openBIS has the following data structure:


Space: entity with Code and Description


Project: entity with Code and Description


Experiment/Collection: entity with user-defined properties


Object: entity with user-defined properties 

Dataset: folder where data files are stored. A dataset has user-defined properties


Space is the top level. Below Spaces there are Projects and below Projects there are Experiments/Collections.
In the general openBIS data model, Objects can:

be shared across Spaces (i.e. they do not belong to any Space)
belong to a Space

belong to a Project

belong to an Experiment/Collection


Datasets can be associated only to Experiments/Collections or to Objects.
Access to openBIS is controlled at the Space level, Project level or openBIS instance level (see openBIS roles ).

Data model in openBIS ELN-LIMS 

In the openBIS ELN-LIMS a simplified data model is used, as shown below.
.
In this case, Objects can only belong to Experiments/Collections.

Inventory
The inventory is usually conceived to be shared by all lab members. The
inventory is used to store all materials and protocols (i.e. standard
operating procedures) used in the lab. It is possible to create
additional inventories, for example of instruments and equipment.
The picture below shows an example of an Inventory with the different openBIS levels.


Lab Notebook
By default, the lab notebook is organised per user. Each user has a
personal folder (=Space), where to create Projects, Experiments
and Experimental Steps (=Objects). Data files can be uploaded to Datasets. Example structure:

Some labs prefer to organise their lab notebook using an organization
per project rather than per user. In this case an openBIS Space would
correspond to a lab Project and an openBIS Project could be a
sub-project or a user folder (one folder per user working on the same project).

openBIS parents and children

Objects can be linked to other Objects, Datasets to other Datasets with
N:N relationship. In openBIS these connections are known as parents
and children.


Examples of parent-child relationships

One or more samples are derived from one main sample. This is the
parent of the other samples:


One Experimental step is performed following a protocol stored in the
inventory, on a sample stored in the inventory, using a given equipment. The protocol, the sample and the equipment are the parents of the Experimental step


One Experimental Step is done after another and we want to keep
track of the links between the steps: