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Concepts

Usage of animal subjects in neuroscience

Many data pipelines in neuroscience retain information about the experimental subjects (e.g., date of birth, sex). For animal models, this can also include owner, cage and sacrificing information. Many researchers also retain genotyping information (e.g., line, zygosity). Labs that perform their own genotyping need to keep track of even more information, such as breeding pairs, litters, and genotyping tests. Element Animal can help researchers organize all this information in connection with a broader experimental pipeline.

Key Partnerships

Over the past few years, several labs have developed DataJoint-based pipelines for animal management. Our team collaborated with several of them during their projects. Additionally, we interviewed these teams to understand their experiment workflow, associated tools, and interfaces. These teams include:

Through our interviews and direct collaboration with the precursor projects, we identified the common motifs in the animal subject schemas to create the Animal Management Element. This element works for diverse downstream pipelines and is always used in combination with other elements for specific experiments. As such it is validated jointly with the processing elements such as the Array Ephys Element and Calcium Imaging Element.

Element architecture

There are three modules in element-animal:

  • subject: contains the basic information of subject, including Strain, Line, Subject, Zygosity, and SubjectDeath information
  • genotyping: this module is designed for labs that keep track of colony management and genotyping results, containing information of breeding, weaning, housing, and genotyping.
  • surgery: this module maintains records of subject implantations including, for example, fiberphotometry.

Subject Diagram

Subject schema diagram

Genotyping Diagram

Genotyping schema diagram

Surgery Diagram

Surgery schema diagram

subject schema (API docs)

  • Although not required, most choose to connect the Session table to a Subject table.
Table Description
Strain Genetic strain of an animal. (e.g. C57Bl/6)
Allele Store allele information
Line Genetic line
Subject Animal subject information
SubjectDeath Subject death information
SubjectCull Subject culling information
Zygosity Information about zygosity of a subject

genotyping schema (API docs)

Table Description
Sequence Gene sequence information
AlleleSequence Allele sequence information
BreedingPair Information about male-female pair used for breeding
Litter Information about litter (group of animals born to a breeding pair)
Weaning Information about weaning (maternal separation)
SubjectLitter Subject and its litter
Cage Cage information
SubjectCaging Information about subject and its cage.
GenotypeTest Information about genotype test

surgery schema (API docs)

Table Description
CoordinateReference Coordinate reference system
BrainRegion Brain region of a given surgery
Hemisphere Brain region hemisphere
ImplantationType Type of implantation
Implantation Implantation of a device