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The Brain Research Through Advancing Innovative Neurotechnologies® (BRAIN) Initiative Cell Atlas Network (BICAN) aims to transform our understanding of brain cell types and the precise tools needed to access them, bringing us one step closer to unraveling the complex workings of the human brain.
Building on findings from the BRAIN Initiative Cell Census Network (BICCN), BICAN takes the next step in mapping brain cells and circuits across multiple species, with an emphasis on humans. The aim of BICAN is to generate a complete reference atlas of cell types in the human brain across the lifespan, which can be shared and used throughout the research community. In addition to developing a “parts list” detailing the vast array of neurons and non-neuronal cells in the human brain, the project also aims to map cell interactions that underlie a wide range of brain disorders.
To this end, BICAN aims to support the publication, sharing, and exploration of datasets generated in the course of the project. Creating a complete reference atlas from multiple datasets requires vast harmonization of metadata. In order to facilitate the harmonization of metadata, we require datasets include a small set of metadata available from data submitters.
This document describes a schema, a type of contract, that BICAN requires of all donor to alignment datasets to enable searching, filtering, and integration of datasets.
Note that the requirements in the schema are just the minimum required information. Datasets often have additional metadata, which is preserved in datasets submitted to the data archives.
Overview
The BICAN Developing Human and NHP Tissue Metadata schema describes metadata associated with and produced from the preparation of macaque donor and tissue in the HMBA and BICAN. [more detail needed here]
Organisms. Data must be from a Metazoan organism and defined in the NCBI organismal classification.
Redundant Metadata. It is STRONGLY RECOMMENDED to avoid multiple metadata fields containing identical or similar information.
Developing Nonhuman Primate
The data in developing nonhuman primate is the metadata essential for developing nonhuman primate experiments.
The following tables describe the developing nonhuman primate metadata. If an entry in the table is empty, the schema does not have any other requirements on data in those layers beyond the ones listed above.
Curators must annotate the following columns:
local donor ID
BICAN Field Name
local donor ID
BICAN UUID
f8af20f7-e8b8-47b5-8a68-9ec1f913ffdf
Aliases
subject_id
Definition
An identifier that uniquely denotes objects only within the scope of a specific object aggregate and that is not registered in an identifier registry.
Data Type
text
repository
BICAN Field Name
repository
BICAN UUID
408682ed-0e27-41e2-b9fa-f05674366d6e
Aliases
repository
Definition
Repository' trailing modifier (qualifier, 'repository') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to the public source-code repository where the given data format is developed or maintained.
Data Type
inclusive_categorical
donor source
BICAN Field Name
donor source
BICAN UUID
0d0cf732-0f76-409d-9a73-7a96d829d3d3
Aliases
donor_source
Definition
The origin of the donor/subject in this experiment.
Data Type
inclusive_categorical
sex at birth
BICAN Field Name
sex at birth
BICAN UUID
c819b9d5-2fde-40b2-bf0d-e07b56f96ac9
Aliases
sex
Definition
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
Data Type
exclusive_categorical
age value (years)
BICAN Field Name
age value (years)
BICAN UUID
14eb923a-161d-45e2-889d-81fea7b632b6
Aliases
age_of_death
Definition
A time quality inhering in a bearer by virtue of how long the bearer has existed.
Data Type
numeric
date of death
BICAN Field Name
date of death
BICAN UUID
60445046-d9d8-4f00-959e-9a4c42613e5e
Definition
The year wherein the subject or donor has ceased to exist.
Aliases
year_of_death
Data Type
date
hemisphere
BICAN Field Name
hemisphere
BICAN UUID
68b7a28b-d695-4ec9-800b-6a27ca206081
Aliases
hemisphere
Definition
One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.
Data Type
exclusive_categorical
post mortem interval
BICAN Field Name
post mortem interval
BICAN UUID
6fd5c5ac-b128-4a4a-ae98-09eaeba22f92
Aliases
post_mortem_interval
Definition
The length temporal interval between the time of death of the subject/donor and the time at which the specimen is made.
Data Type
numeric
left hemisphere preparation
BICAN Field Name
left hemisphere preparation
BICAN UUID
57d5378f-a451-4bf5-a472-cc88d0d29586
Aliases
left_hemisphere_preparation
Definition
The type of preparation method used for the left hemisphere.
Data Type
exclusive_categorical
left hemisphere preparation specify
BICAN Field Name
left hemisphere preparation specify
BICAN UUID
002e915e-01c3-4570-a1f3-76680dcb2c33
Aliases
left_hemisphere_preparation_specify
Definition
Specific details about the type of preparation method used for the left hemisphere.
Data Type
text
right hemisphere preparation
<
BICAN Field Name
right hemisphere preparation
BICAN UUID
477c2600-f979-43c5-9c61-ab61fd771584
Aliases
right_hemisphere_preparation
Definition
The type of preparation method used for the right hemisphere.
Data Type
exclusive_categorical
right hemisphere preparation specify
BICAN Field Name
right hemisphere preparation specify
BICAN UUID
efd50be4-f7cf-4146-a08e-28f25680728c
Aliases
right_hemisphere_preparation_specify
Definition
Specific details about the type of preparation method used for the right hemisphere.
Data Type
text
RIN
BICAN Field Name
RIN
BICAN UUID
cd472c0d-0b64-45c9-a38e-e54d15cea953
Aliases
rin
Definition
The RNA integrity number value of a specimen.
Data Type
numeric
RIN tissue source
BICAN Field Name
RIN tissue source
BICAN UUID
d547ee51-9ec3-489c-8e49-7d8cd94080a8
Definition
The tissue sample location or identifier that is used for calculating the RNA integrity number.
Aliases
rin_tissue_source
Data Type
text
RIN testing organization
BICAN Field Name
RIN testing organization
BICAN UUID
cfed831e-9a62-4a32-bf92-532873420eb3
Definition
The organization that determines the RNA integrity number of a sample/specimen.
Aliases
rin_testing_organization
Data Type
text
RINe
BICAN Field Name
RINe
BICAN UUID
1210148d-d8fb-45aa-b51a-4b19b6d09bec
Aliases
rine
Definition
A type of RIN (RNA integrity number) value that represents the relative ratio of the signal in the fast zone to the 18S peak signal fpr a specimen.
Data Type
numeric
RINe tissue source
BICAN Field Name
RINe tissue source
BICAN UUID
7d5fd9af-82a1-4bdb-a3c6-9225d1717c53
Definition
The tissue sample location or identifier that is used for calculating the RINe number.
Aliases
rine_tissue_source
Data Type
text
RINe testing organization
BICAN Field Name
RINe testing organization
BICAN UUID
15a6d162-a3ca-4852-b626-a911c37c04c9
Definition
The organization that determines the RINe number.
Aliases
rine_testing_organization
Data Type
text
pH
BICAN Field Name
pH
BICAN UUID
9e67af02-c081-43e1-a42c-bf9603cae616
Aliases
ph
Definition
The value of a measurement of acidity or basicity of a tissue, sample, or specimen.
Data Type
numeric
brain weight measurement
BICAN Field Name
brain weight measurement
BICAN UUID
546fc32d-f8a2-4c00-924a-8c4730f11f51
Aliases
brain_weight
Definition
The weight of a brain specimen.
Data Type
numeric
brain tissue weighed type
BICAN Field Name
brain tissue weighed type
BICAN UUID
a7463e3f-0c61-4718-a7d0-60fd2116908a
Aliases
weighed_type
Definition
The state of a brain specimen when it is weighed (fresh, frozen, fixed).
Data Type
exclusive_categorical
photo 2d available
BICAN Field Name
photo 2d available
BICAN UUID
611beda8-1ac6-4183-a284-04a30bb474f3
Aliases
photo_2d_available
Definition
The status (available, unavailable) of two-dimensional photos of a subject/donor/specimen.
Data Type
exclusive_categorical
non-brain tissue available
BICAN Field Name
non-brain tissue available
BICAN UUID
3a064c96-a956-4cf3-8b77-056b8e392f99
Definition
The status (yes, no) of whether non-brain tissue from this organism is available.
Aliases
non_brain_tissue_available
Data Type
exclusive_categorical
tissue type
BICAN Field Name
tissue type
BICAN UUID
33ccbc85-ae35-44d6-8bc6-c2fb91116cf7
Definition
The type of tissue (non-brain) that is available from this organism.
Aliases
tissue_type
Data Type
exclusive_categorical
tissue type details
BICAN Field Name
tissue type details
BICAN UUID
f551cf87-2c6e-4b92-888d-6310e6a500d8
Definition
The details of the non-brain tissue that is available from this organism.
Aliases
tissue_type_details
Data Type
text
birth weight value (lbs)
BICAN Field Name
birth weight value (lbs)
BICAN UUID
69d9a60d-32d5-4c3a-a26a-802d8f030c8d
Definition
The weight (at birth) of the subject/donor in pounds.
Aliases
birth_weight_lbs
Data Type
numeric
birth weight value (oz)
BICAN Field Name
birth weight value (oz)
BICAN UUID
b6f30050-f762-4427-8533-31738e737ea2
Definition
The weight (at birth) of the subject/donor in ounces.
Aliases
birth_weight_oz
Data Type
numeric
gestational age value (weeks)
BICAN Field Name
gestational age value (weeks)
BICAN UUID
6d8a9b3f-792c-48c2-bd3c-56e52bb51672
Definition
The gestational age of the subject/donor in weeks.
Aliases
gestational_age_value_weeks
Data Type
numeric
gestational age value (days)
BICAN Field Name
gestational age value (days)
BICAN UUID
4e532e52-6e4c-46cd-9fde-96f97ef3b034
Definition
The gestational age of the subject/donor in days.
Aliases
gestational_age_value_days
Data Type
numeric
species
BICAN Field Name
species
BICAN UUID
d11fb2ce-bfdb-4735-9b17-b6ba606520b1
Definition
The species of a subject/donor/sample/specimen.
Aliases
species
Data Type
exclusive_categorical
body weight
BICAN Field Name
body weight
BICAN UUID
f2673501-b48f-4703-bb7e-d642b73c2ad4
Definition
The weight of the whole organism/donor/subject.
Aliases
body_weight
Data Type
premortem perfusion done
BICAN Field Name
premortem perfusion done
BICAN UUID
1fc487d8-2403-4d7c-952f-7e502d5f8359
Definition
The status of premortem perfusion (done, not done).
Aliases
perfusion
Data Type
exclusive_categorical
premortem perfusion buffer type
BICAN Field Name
premortem perfusion buffer type
BICAN UUID
78d62e29-4323-4927-aec8-6fc8dc59a889
Definition
The type of premortem perfusion buffer that was used for premortem perfusion.
Aliases
perfusate_type
Data Type
text
head off time
BICAN Field Name
head off time
BICAN UUID
00ab5986-a8c4-4a7f-bf2b-6b5f08a97b25
Definition
The time at which the head was removed from the organism/donor/subject.
Aliases
head_off_time
Data Type
brain extraction time
BICAN Field Name
brain extraction time
BICAN UUID
06be5810-7b9c-452e-b7ca-13eeb15179ca
Definition
The time at which the brain was extracted from the organism/donor/subject.
Aliases
brain_extraction_time
Data Type
brain fixed time
BICAN Field Name
brain fixed time
BICAN UUID
2a09ecb4-0096-4a6c-b4f0-9b68cb231413
Definition
The time at which the brain specimen was fixed.
Aliases
brain_fixed_time
Data Type
brain frozen time
BICAN Field Name
brain frozen time
BICAN UUID
fb01ce0d-1417-404a-978d-aad708c0404f
Definition
The time at which the brain specimen was frozen.
Aliases
brain_frozen_time
Data Type
brain fixation method
BICAN Field Name
brain fixation method
BICAN UUID
8e0a01a9-ab7a-49a5-bf44-cc0af47719b1
Definition
The method used for fixing the brain specimen.
Aliases
brain_fixation_method
Data Type
brain freeze method
BICAN Field Name
brain freeze method
BICAN UUID
71237def-9b50-481f-a01d-65dc99e3493f
Definition
The method used for freezing the brain specimen.
Aliases
brain_freeze_method
Data Type
sedation start time
BICAN Field Name
sedation start time
BICAN UUID
0ad6cca0-d4ce-4cd8-bbce-520bc01db061
Definition
The time at which sedation of the organism/donor/subject began.
Aliases
sedation_start_time
Data Type
sedation total dose
BICAN Field Name
sedation total dose
BICAN UUID
3c895613-4526-4b87-8620-7b42eff94fee
Definition
The total dose of sedation used on the organism/donor/subject.
Aliases
sedation_total_dose
Data Type
euthanasia time
BICAN Field Name
euthanasia time
BICAN UUID
14c541ab-7db3-4438-9328-c5f3098f5ff7
Definition
The time at which euthanasia of the organism/donor/subject occurred.
Aliases
euthanasia_time
Data Type
euthanasia dose
BICAN Field Name
euthanasia dose
BICAN UUID
d87c6869-c0d1-46b3-bb32-95dc3e3d5ed4
Definition
The dose of compouds used to euthanize the organism/donor/subject.
Aliases
euthanasia_dose
Data Type
perfusion time start
BICAN Field Name
perfusion time start
BICAN UUID
7f94f8ad-82b7-4827-9614-838555a1f046
Definition
The time at which perfusion began.
Aliases
perfusion_time_start
Data Type
perfusion time end
BICAN Field Name
perfusion time end
BICAN UUID
6c873444-8306-4b3f-9e5a-97f6d34c88b3
Definition
The time at which perfusion ended.
Aliases
perfusion_time_end
Data Type
matriline
BICAN Field Name
matriline
BICAN UUID
ae0447a3-0504-43a3-95d5-4248e53d3224
Definition
The relavant matriline and patriline information for a subject/donor/sample/specimen.
Aliases
family_history
Data Type
text
brain size anterior-posterior
BICAN Field Name
brain size anterior-posterior
BICAN UUID
0830564a-26ba-41eb-888a-33d0c39ead8f
Definition
The size of the brain specimen in the anterior-posterior axis.
Aliases
brain_size_anterior_posterior
Data Type
numeric
brain size medial-lateral
BICAN Field Name
brain size medial-lateral
BICAN UUID
4722f739-71f6-4001-9784-afef8f9f2d0e
Definition
The size of the brain specimen in the medial-lateral axis.
Aliases
brain_size_medial_lateral
Data Type
numeric
brain size dorsal-ventral
BICAN Field Name
brain size dorsal-ventral
BICAN UUID
e683f5ee-696f-4baf-a9bf-2f12226ceb4a
Definition
The size of the brain specimen in the dorsal-ventral axis.
Aliases
brain_size_dorsal_ventral
Data Type
numeric
brain size unit
BICAN Field Name
brain size unit
BICAN UUID
4d0c44c6-e620-455d-989e-126c3c81ec91
Definition
The unit that the brain size measurements are recorded.
Aliases
brain_size_unit_type
Data Type
exclusive_categorical
histological stains available
BICAN Field Name
histological stains available
BICAN UUID
4b868ba6-dba8-45e3-a43e-88e421625cab
Definition
The status (available, unavailable) of histological stainings of a specimen.
Aliases
histological_stains_available
Data Type
exclusive_categorical
histological stains type
BICAN Field Name
histological stains type
BICAN UUID
6723e756-e4c1-42c7-bf2d-ee2e300b88ff
Definition
The type of histological stains available for a specimen.