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Overview

openBIS has a hierarchical data structure:

  1. Space: folder with only Code and Description
  2. Project: folder with only Code and Description
  3. Experiment/Collection: folder with Code + user-defined properties
  4. Object: entity with Code + user-defined properties 
  5. Data set: folder where data files are stored. A data set has Code + user-defined properties


Access to openBIS is controlled either at the Space level or Project level.


Data model in openBIS ELN-LIMS 

In the openBIS ELN-LIMS the following structure is used.

Inventory

The inventory is usually 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 following structure is used in the Inventory:


Materials (=Space)

Methods (=Space)


In the generic ELN-LIMS, the Materials folder is empty and everything has to be defined by an admin user.

The Methods folder has default folders for general protocols defined:


Methods (=Space)

Protocols (=Project)

General Protocols (=Collection)


In the ELN-LIMS for life sciences, some folders are already predefined in the Materials folder. For example:


Materials (=Space)

Reagents (=Project)

Chemicals Collection (=Collection)

Enzymes Collection (=Collection)

Antibodies Collection (=Collection)


An openBIS Instance admin can customise the Inventory folders for the lab and create the needed Object types (Register Master Data via the Admin Interface).

Lab Notebook

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


Username (=Space)

Master thesis project (=Project)

Experiment 1 (=Experiment)

Experimental step 1 (=Object)

Experimental step 2 (=Object)

Raw Data (=Data set)



Some labs prefer to organise their lab notebook using a classification 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. Example structure:


SNF projects (=Space)

Project 1 (=Project)

Experiment (=Experiment)

Experimental Step (=Object)

Raw Data (=Data set)

Project 2 (=Project)

Experiment (=Experiment)

Experimental step 1 (=Object)

Experimental step 2 (=Object)

Raw Data (=Data set)


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

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


  2. One Experimental step is written following a protocol stored in the Inventory and using a sample stored in the inventory. The protocol and the sample are the parents of the Experimental Step. 

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


Protocols

Protocols are standard procedures that can be followed to perform given experiments in a lab. Usually protocols are stored in the common inventory and are linked to Experimental procedures using the parent-child relationships described above. 

The protocol contains the standard steps to follow. The parameters measured during one experiment following a give protocol should be recorded in the Experimental Step.

Not all labs have standard procedures in place. In this case, the Methods section of the Inventory does not need to be used.

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