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Master database structure

Piotr Majka edited this page Apr 23, 2020 · 2 revisions

Marmoset Brain Architecture Project SQLite Database Structure Documentation

This wiki page describes the structure (schema) of the master database which aggregates the results of the connectivity studies. You can use the database to retrieve many types of data using custom SQL queries for the purpose of your research.

Please note that the data is distributed under the terms of the CC BY-SA 4.0 licence licence. When using the data, please acknowledge the following article:

  • Majka P., Bai S., Bakola S., Bednarek S., Chan J.C., Jermakow N., Passarelli L., Reser D.H., Theodoni P., Worthy K.H., Wang X-J., Wójcik D.K., Mitra P.P. & Rosa M.G.P. (2020). Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey. Nature Communications. http://doi.org/10.1038/s41467-020-14858-0.

  • Majka, P., Chaplin, T. A., Yu, H.-H., Tolpygo, A., Mitra, P. P., Wójcik, D. K., & Rosa, M. G. P. (2016). Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. Journal of Comparative Neurology, 524(11), 2161–2181. http://doi.org/10.1002/cne.24023.

SQLite export (version 1.0) schema overview:

The master database comprises the following tables:

  1. Experiment cases
  2. Table to store injection metadata
  3. Table to store information about labelled cells
  4. Table to store connectivity strength data
  5. Table to store the hierarchical structure of marmoset brain areas
  6. Table to store structure info of marmoset brain areas
  7. Table to store information about tracers used in marmoset studies

The figure below illustrates the relations between the tables DB schema Map

Column Data Type Description
case_id TEXT The unique ID in database to refer to the case, this is intended for machine processing only
display_name TEXT The user-friendly name to be shown in publications and websites
sex CHAR The sex of the animal studied
weight NUMERIC The weight of the animal at the time of surgery (in grams)
hemisphere TEXT The hemisphere studied in this case
date_of_birth DATE The animal's date of birth
injection_date DATE The date of injection performed
perfusion_date DATE The date the brain is extracted and perfused
survival_days INT The number of days between surgery and brain is extracted
sectioning_plane, STRING The sectioning plane of the brain, possible candidates are coronal or sagittal
comment TEXT Expert anatomist comment on the animal and the experiment
total_cells INT Total number of cells label by tracer(s)
extrinsic_cells INTEGER Total number of extrinsic cells labeled by the tracer(s)
intrinsic_cells INTEGER Total number of intrinsic cells labeled by the tracer(s)
created DATETIME The timestamp this case metadata was created
modified DATETIME The timestamp this case metadata was last modified
Column Data Type Description
case_id TEXT The Foreign Key to reference the cases table of this injection
tracer_id TEXT The Foreign Key to reference the tracers table of the tracer used in this injection
hemisphere CHAR The hemisphere of the brain which the injection hit
comment TEXT Expert anatomist comment aimed at helping detailed interpretation the injection
injection_structure INT The Foreign Key to reference the structure table by id, which is the target of the injection
total_cells INTEGER Total number of cells labeled by the tracer in this injection
extrinsic_cells INTEGER Total number of extrinsic cells labeled by the tracer in this injection
intrinsic_cells INTEGER Total number of intrinsic cells labeled by the tracer in this injection
Column Data Type Description
id INTEGER Primary key of the cell in table
cell_number INTEGER
case_id TEXT Foreign key to reference table cases by case_id
section TEXT The section which injection hit to
tracer_id TEXT Foreign key to reference table tracers by tracer_id
x REAL The position of the cell located in the section in A-P direction (in millimeter)
y REAL The position of the cell located in the section in M-L direction (in millimeter)
z REAL The position of the cell located in the section in D-V direction (in millimeter)
structure_id INTEGER Foreign key to reference table structures by structure_id
laminar_position INT Column to describe laminar position 1 for supragranular and 0 for infragranular
Column Data Type Description
case_id TEXT The case this connectivity info is derived
tracer_id TEXT The tracer used in this injection
target VARCHAR (30) The target area of the connectivity
source VARCHAR (30) The source area of the connectivity
cell_count INTEGER The number of extrinsic cells labeled by tracer
supra_count The number of extrinsic cells in supragranular layer labeled by tracer
infra_count The number of extrinsic cells in infragranular layer labeled by tracer
SLN
ILN
injection_structure The targeted area of the injection
leaf_node BOOLEAN The flag to define if this connectivity strength is between leaf nodes of the area (structure)
Column Data Type Description
id INTEGER The integer primary key for easy reference
parent_id INT The parent node of the link
child_id INT The child node of the link
Column Data Type Description
id INTEGER Database primary integer key for easy reference
caf_uid INT The unique id referring to CAF file
parent_id INT If the structure is a child of a parent node, this refers to the record of its parent
path_id STRING The sequence id for the path
path TEXT A string separated by forward slash to indicate the traversal path from the root node to the current structure node
color_r INT The color coding used to draw this area, the red component (max: 255)
color_b INT The color coding used to draw this area, the blue component (max: 255)
color_g INT The color coding used to draw this area, the green component (max: 255)
abbrev VARCHAR (30) The abbreviation code to use in programming interfaces
human_abbrev VARCHAR (30) The human-readable abbreviation for the area
display_name TEXT The common name of the area
is_leaf_node BOOLEAN The flag to indicate if the current node is a leaf in the tree structure
Column Data Type Description
tracer_id TEXT The unique id to reference this tracer
comment TEXT More information about the tracer
color_r INT The color code used to draw the tracer, the red component (max: 255)
color_g INT The color code used to draw the tracer, the green component (max: 255)
color_b INT The color code used to draw the tracer, the blue component (max: 255)
inj_color_r INT The color code used to draw the injection by this tracer, the red component (max: 255)
inj_color_g INT The color code used to draw the injection by this tracer, the green component (max: 255)
inj_color_b INT The color code used to draw the injection by this tracer, the blue component (max: 255)
display_name TEXT The human-friendly short form of the tracer displayed in publications and websites
display_name_long TEXT The human-friendly full name of the tracer displayed in publications and websites