Skip to content

Latest commit

 

History

History
2955 lines (2701 loc) · 61.8 KB

Macaque-Donor-and-Tissue-Metadata-README.md

File metadata and controls

2955 lines (2701 loc) · 61.8 KB

BICAN Macaque Donor and Tissue Metadata Schema

Document Status: Accepted by MOWG

Version: 1.0

Owner: HMBA

Reviewers: @mgiglio99, @puja-trivedi, @patrick-lloyd-ray

License: CC-BY-4.0

Date Created: 08-07-2024

Background

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 Macaque Donor and 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]

This document has the following sections:

General Requirements

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.

PatchSeq

The data in patchseq is the metadata essential for macaque patchseq experiments.

The following tables describe the patchseq 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
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.
Aliases subject_id
Data Type text

Repository

BICAN Field Name repository
BICAN UUID 408682ed-0e27-41e2-b9fa-f05674366d6e
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.
Aliases repository
Data Type inclusive_categorical

Donor Source

BICAN Field Name donor source
BICAN UUID 0d0cf732-0f76-409d-9a73-7a96d829d3d3
Definition The origin of the donor/subject in this experiment.
Aliases donor_source
Data Type inclusive_categorical

Sex at Birth

BICAN Field Name sex at birth
BICAN UUID c819b9d5-2fde-40b2-bf0d-e07b56f96ac9
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.
Aliases sex
Data Type exclusive_categorical

Age Value (Years)

BICAN Field Name age value (years)
BICAN UUID 14eb923a-161d-45e2-889d-81fea7b632b6
Definition A time quality inhering in a bearer by virtue of how long the bearer has existed.
Aliases age_of_death
Data Type numeric

Year of Death

BICAN Field Name year 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

Manner of Death

BICAN Field Name manner of death
BICAN UUID 36eeb35b-5020-4a9e-a74b-6e1104415e0e
Definition The manner of death is the determination of how the injury or disease leads to death. There are five manners of death (natural, accident, suicide, homicide, and undetermined).
Aliases manner_of_death
Data Type exclusive_categorical

Medical Records Available

BICAN Field Name medical records available
BICAN UUID ee2c9223-f7d1-4c64-a1da-cd7408309955
Definition The status (available, unavailable) of the medical records of the subject/donor.
Aliases medical_records_available
Data Type exclusive_categorical

Medical Records Reviewed

BICAN Field Name medical records reviewed
BICAN UUID 6139b159-c36c-4501-9176-fe2741e3d448
Definition The status (reviewed, not reviewed) of the medical records of the subject/donor.
Aliases medical_records_reviewed
Data Type exclusive_categorical

Hemisphere

BICAN Field Name hemisphere
BICAN UUID 68b7a28b-d695-4ec9-800b-6a27ca206081
Definition One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.
Aliases hemisphere
Data Type exclusive_categorical

Post Mortem Interval

BICAN Field Name post mortem interval
BICAN UUID 6fd5c5ac-b128-4a4a-ae98-09eaeba22f92
Definition The length of the temporal interval between the time of death of the subject/donor and the time at which the specimen is made.
Aliases post_mortem_interval
Data Type numeric

Left Hemisphere Preparation

BICAN Field Name left hemisphere preparation
BICAN UUID 57d5378f-a451-4bf5-a472-cc88d0d29586
Definition The type of preparation method used for the left hemisphere.
Aliases left_hemisphere_preparation
Data Type exclusive_categorical

Left Hemisphere Preparation Specify

BICAN Field Name left hemisphere preparation specify
BICAN UUID 002e915e-01c3-4570-a1f3-76680dcb2c33
Definition Specific details about the type of preparation method used for the left hemisphere.
Aliases left_hemisphere_preparation_specify
Data Type text

Right Hemisphere Preparation

BICAN Field Name right hemisphere preparation
BICAN UUID 477c2600-f979-43c5-9c61-ab61fd771584
Definition The type of preparation method used for the right hemisphere.
Aliases right_hemisphere_preparation
Data Type exclusive_categorical

Right Hemisphere Preparation Specify

BICAN Field Name right hemisphere preparation specify
BICAN UUID efd50be4-f7cf-4146-a08e-28f25680728c
Definition Specific details about the type of preparation method used for the right hemisphere.
Aliases right_hemisphere_preparation_specify
Data Type text

Photo 2D Available

BICAN Field Name photo 2d available
BICAN UUID 611beda8-1ac6-4183-a284-04a30bb474f3
Definition The status (available, unavailable) of two-dimensional photos of a subject/donor/specimen.
Aliases photo_2d_available
Data Type exclusive_categorical

Antemortem MRI Available

BICAN Field Name antemortem MRI available
BICAN UUID 43a04caa-4f28-47ac-8a9d-74c40f10776f
Definition The status (available, unavailable) of antemortem MRI images of a subject/donor/specimen.
Aliases antemortem_mri_available
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

Test Name

BICAN Field Name test name
BICAN UUID b6865e15-7538-4890-be99-a6f9e9920af3
Definition The name of the test that has been performed.
Aliases test_name
Data Type exclusive_categorical

Result

BICAN Field Name test result
BICAN UUID c14ea006-662c-4666-bfd1-6ff580c403ed
Definition The result(s) of the test that has been performed.
Aliases test_result
Data Type exclusive_categorical

Testing Tissue Source

BICAN Field Name testing tissue source
BICAN UUID 42f8e11b-d9a3-48fe-ac1e-cd6f4469de46
Definition The tissue sample location or identifier that is the subject of a test.
Aliases tissue_source
Data Type exclusive_categorical

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

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

Region of interest

BICAN Field Name region of interest
BICAN UUID 71611b58-f98e-4a69-ad88-c0029a377cbe
Definition The brain region, structure, or area from which a brain tissue source derives.
Aliases ROI
Data Type exclusive_categorical

Behavorial Testing

BICAN Field Name behavioral scoring available
BICAN UUID ea33881a-9813-4111-979b-135355e8141e
Definition The status (available, unavailable) of the behavioral scoring results for a subject/donor/specimen.
Aliases behavioral_scoring_available
Data Type exclusive_categorical

Behavorial Testing Type

BICAN Field Name behavioral scoring type
BICAN UUID 0a7a1eeb-8682-4261-8221-82d587dde0fa
Definition The type of behavioral scoring that is available for a subject/donor/specimen.
Aliases behavioral_scoring_type
Data Type text

Non Brain Diagnosis Description

BICAN Field Name non brain diagnosis description
BICAN UUID 4ba7c8cc-563c-4f0b-ab57-ae9c9762943f
Definition The description (text) of a non-brain diagnosis for a subject/donor/specimen.
Aliases non_brain_diagnosis_description
Data Type text

Population

The data in population is the metadata essential for macaque population studies.

The following tables describe the population 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
Definition
Aliases subject_id
Data Type text

Repository

BICAN Field Name repository
BICAN UUID 408682ed-0e27-41e2-b9fa-f05674366d6e
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.
Aliases repository
Data Type inclusive_categorical

Donor Source

BICAN Field Name donor source
BICAN UUID 0d0cf732-0f76-409d-9a73-7a96d829d3d3
Definition The origin of the donor/subject in this experiment.
Aliases donor_source
Data Type inclusive_categorical

Sex at Birth

BICAN Field Name sex at birth
BICAN UUID c819b9d5-2fde-40b2-bf0d-e07b56f96ac9
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.
Aliases sex
Data Type exclusive_categorical

Age Value (Years)

BICAN Field Name age value (years)
BICAN UUID 14eb923a-161d-45e2-889d-81fea7b632b6
Definition A time quality inhering in a bearer by virtue of how long the bearer has existed.
Aliases age_of_death
Data Type numeric

Year of Death

BICAN Field Name year 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

Autopsy Report

BICAN Field Name autopsy report
BICAN UUID 3f787b64-0985-4d0f-9523-54475164b7ad
Definition A document assembled by an author for the purpose of providing information regarding the cause of death of a subject for the audience.
Aliases autopsy_report
Data Type exclusive_categorical

Cause of Death

BICAN Field Name cause of death
BICAN UUID fa970a03-41ea-473b-a8ce-427fec92cdff
Definition The circumstance or condition that results in the death of a living being. [NCIT]
Aliases cause_of_death
Data Type text

Cause of Death Code

BICAN Field Name cause of death code
BICAN UUID 61374624-2d3c-477e-95b3-9bd30974b52a
Definition The ISO code that denotes the circumstance or condition that results in the death of a living being.
Aliases cause_of_death_code
Data Type text

Manner of Death

BICAN Field Name manner of death
BICAN UUID 36eeb35b-5020-4a9e-a74b-6e1104415e0e
Definition The manner of death is the determination of how the injury or disease leads to death. There are five manners of death (natural, accident, suicide, homicide, and undetermined).
Aliases manner_of_death
Data Type exclusive_categorical

Medical Records Reviewed

BICAN Field Name medical records reviewed
BICAN UUID 6139b159-c36c-4501-9176-fe2741e3d448
Definition The status (reviewed, not reviewed) of the medical records of the subject/donor.
Aliases medical_records_reviewed
Data Type exclusive_categorical

Hemisphere

BICAN Field Name hemisphere
BICAN UUID 68b7a28b-d695-4ec9-800b-6a27ca206081
Definition One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.
Aliases hemisphere
Data Type exclusive_categorical

Post Mortem Interval

BICAN Field Name post mortem interval
BICAN UUID 6fd5c5ac-b128-4a4a-ae98-09eaeba22f92
Definition The length of the temporal interval between the time of death of the subject/donor and the time at which the specimen is made.
Aliases post_mortem_interval
Data Type numeric

Left Hemisphere Preparation

BICAN Field Name left hemisphere preparation
BICAN UUID 57d5378f-a451-4bf5-a472-cc88d0d29586
Definition The type of preparation method used for the left hemisphere.
Aliases left_hemisphere_preparation
Data Type exclusive_categorical

Left Hemisphere Preparation Specify

BICAN Field Name left hemisphere preparation specify
BICAN UUID 002e915e-01c3-4570-a1f3-76680dcb2c33
Definition Specific details about the type of preparation method used for the left hemisphere.
Aliases left_hemisphere_preparation_specify
Data Type text

Right Hemisphere Preparation

BICAN Field Name right hemisphere preparation
BICAN UUID 477c2600-f979-43c5-9c61-ab61fd771584
Definition The type of preparation method used for the right hemisphere.
Aliases right_hemisphere_preparation
Data Type exclusive_categorical

Right Hemisphere Preparation Specify

BICAN Field Name right hemisphere preparation specify
BICAN UUID efd50be4-f7cf-4146-a08e-28f25680728c
Definition Specific details about the type of preparation method used for the right hemisphere.
Aliases right_hemisphere_preparation_specify
Data Type text

RIN

BICAN Field Name RIN
BICAN UUID cd472c0d-0b64-45c9-a38e-e54d15cea953
Definition The RNA integrity number value of a specimen.
Aliases rin
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
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.
Aliases rine
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
Definition The value of a measurement of acidity or basicity of a tissue, sample, or specimen.
Aliases ph
Data Type numeric

Brain Weight

BICAN Field Name brain weight measurement
BICAN UUID 546fc32d-f8a2-4c00-924a-8c4730f11f51
Definition The weight of a brain specimen.
Aliases brain_weight
Data Type numeric

Brain Tissue Weighed Type

BICAN Field Name brain tissue weighed type
BICAN UUID a7463e3f-0c61-4718-a7d0-60fd2116908a
Definition The state of a brain specimen when it is weighed (fresh, frozen, fixed).
Aliases weighed_type
Data Type exclusive_categorical

Photo 2D Available

BICAN Field Name photo 2d available
BICAN UUID 611beda8-1ac6-4183-a284-04a30bb474f3
Definition The status (available, unavailable) of two-dimensional photos of a subject/donor/specimen.
Aliases photo_2d_available
Data Type exclusive_categorical

Scan 3D Available

BICAN Field Name scan 3d available
BICAN UUID 658e8a80-e232-438f-8c1e-d5f38724dc55
Definition The status (available, unavailable) of three-dimensional scans of a subject/donor/specimen.
Aliases scan_3d_available
Data Type exclusive_categorical

Antemortem MRI Available

BICAN Field Name antemortem MRI available
BICAN UUID 43a04caa-4f28-47ac-8a9d-74c40f10776f
Definition The status (available, unavailable) of antemortem MRI images of a subject/donor/specimen.
Aliases antemortem_mri_available
Data Type exclusive_categorical

Postmortem MRI Available

BICAN Field Name postmortem MRI available
BICAN UUID 0badd072-0c25-48c6-9357-44d5b5bc0818
Definition The status (available, unavailable) of postmortem MRI images of a subject/donor/specimen.
Aliases postmortem_mri_available
Data Type exclusive_categorical

Postmortem MRI Type

BICAN Field Name postmortem MRI type
BICAN UUID 64a607a9-21e6-4c73-8f2e-2d67b0dc51c8
Definition The type of postmortem MRI that is available (cadeveric, fresh ex vivo, fixed ex vivo).
Aliases postmortem_mri_type
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 (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 (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

Social Group

BICAN Field Name social group
BICAN UUID 7759b09d-a685-49fe-b7d8-e7f2b4772f52
Definition The social group to which the subject belongs.
Aliases social_group
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 numeric

Perfusion

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

Perfusate 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 time

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 time

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 time

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 time

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 exclusive_categorical

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 exclusive_categorical

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 time

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 numeric

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 time

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 numeric

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 time

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

Trapping Date

BICAN Field Name trapping date
BICAN UUID e2603f30-af26-4d24-b9e7-dcbd47e09914
Definition The date on which the subject/specimen was trapped.
Aliases trapping_date
Data Type date

Trapping Time

BICAN Field Name trapping time
BICAN UUID cc2ec53a-cd90-4bf5-9c49-c99ebb81498f
Definition The time at which the subject/specimen was trapped.
Aliases trapping_time
Data Type time

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 matriline
Data Type

Behavioral Scoring Available

BICAN Field Name behavioral scoring available
BICAN UUID ea33881a-9813-4111-979b-135355e8141e
Definition The status (available, unavailable) of the behavioral scoring results for a subject/donor/specimen.
Aliases behavioral_scoring_available
Data Type exclusive_categorical

Behavioral Scoring Type

BICAN Field Name behavioral scoring type
BICAN UUID 0a7a1eeb-8682-4261-8221-82d587dde0fa
Definition The type of behavioral scoring that is available for a subject/donor/specimen.
Aliases behavioral_scoring_type
Data Type exclusive_categorical

Ordinal Dominance Rank

BICAN Field Name ordinal dominance rank
BICAN UUID 080685e2-756a-446e-8d9d-5585c9ddd998
Definition The dominance rank of the organism/subject/donor (ordinal).
Aliases ordinal_dominance_rank
Data Type

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 Type

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 Stain Type

BICAN Field Name histological stains type
BICAN UUID 6723e756-e4c1-42c7-bf2d-ee2e300b88ff
Definition The type of histological stains available for a specimen.
Aliases histological_stain_type
Data Type exclusive_categorical

Whole Brain Spatial Omics

The data in whole brain spatial omics is the metadata essential for whole brain spatial omics experiments.

The following tables describe the whole brain spatial omics 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
Definition
Aliases subject_id
Data Type text

Repository

BICAN Field Name repository
BICAN UUID 408682ed-0e27-41e2-b9fa-f05674366d6e
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.
Aliases repository
Data Type inclusive_categorical

Donor Source

BICAN Field Name donor source
BICAN UUID 0d0cf732-0f76-409d-9a73-7a96d829d3d3
Definition The origin of the donor/subject in this experiment.
Aliases donor_source
Data Type inclusive_categorical

Sex at Birth

BICAN Field Name sex at birth
BICAN UUID c819b9d5-2fde-40b2-bf0d-e07b56f96ac9
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.
Aliases sex
Data Type exclusive_categorical

Age Value (Years)

BICAN Field Name age value (years)
BICAN UUID 14eb923a-161d-45e2-889d-81fea7b632b6
Definition A time quality inhering in a bearer by virtue of how long the bearer has existed.
Aliases age_of_death
Data Type numeric

Year of Death

BICAN Field Name year 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
Definition One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.
Aliases hemisphere
Data Type exclusive_categorical

Post Mortem Interval

BICAN Field Name post mortem interval
BICAN UUID 6fd5c5ac-b128-4a4a-ae98-09eaeba22f92
Definition The length of the temporal interval between the time of death of the subject/donor and the time at which the specimen is made.
Aliases post_mortem_interval
Data Type numeric

RIN

BICAN Field Name RIN
BICAN UUID cd472c0d-0b64-45c9-a38e-e54d15cea953
Definition The RNA integrity number value of a specimen.
Aliases rin
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

Brain Weight

BICAN Field Name brain weight measurement
BICAN UUID 546fc32d-f8a2-4c00-924a-8c4730f11f51
Definition The weight of a brain specimen.
Aliases brain_weight
Data Type numeric

Photo 2D Available

BICAN Field Name photo 2d available
BICAN UUID 611beda8-1ac6-4183-a284-04a30bb474f3
Definition The status (available, unavailable) of two-dimensional photos of a subject/donor/specimen.
Aliases photo_2d_available
Data Type exclusive_categorical

Scan 3D Available

BICAN Field Name scan 3d available
BICAN UUID 658e8a80-e232-438f-8c1e-d5f38724dc55
Definition The status (available, unavailable) of three-dimensional scans of a subject/donor/specimen.
Aliases scan_3d_available
Data Type exclusive_categorical

Antemortem MRI Available

BICAN Field Name antemortem MRI available
BICAN UUID 43a04caa-4f28-47ac-8a9d-74c40f10776f
Definition The status (available, unavailable) of antemortem MRI images of a subject/donor/specimen.
Aliases antemortem_mri_available
Data Type exclusive_categorical

Appendix