Master database structure
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:
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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.
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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.
The master database comprises the following tables:
- Experiment cases
- Table to store injection metadata
- Table to store information about labelled cells
- Table to store connectivity strength data
- Table to store the hierarchical structure of marmoset brain areas
- Table to store structure info of marmoset brain areas
- Table to store information about tracers used in marmoset studies
The figure below illustrates the relations between the tables
| 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 |
