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BICAN Developing Tissue Metadata Schema

Document Status: Approved by MOWG

Version: 1.0

Owner: HMBA

Reviewers: @MariahKenney, @licongcui, @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 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]

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.

Developing Tissue

The data in developing tissue is the metadata essential for developing tissue experiments.

The following tables describe the developing tissue 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:

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 text

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

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

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

left hemisphere tissue inventory

BICAN Field Name left hemisphere tissue inventory
BICAN UUID 05e2821e-e7dc-4e33-94dc-7b55c372e5a0
Definition The inventory (list) of the tissue samples for a specific left hemisphere specimen.
Aliases left_hemisphere_tissue_inventory
Data Type

left hemisphere tissue sampling history

BICAN Field Name left hemisphere tissue sampling history
BICAN UUID b02f7dd7-4535-4b41-b8df-73786b8983bc
Definition The history of the tissue sampling for a specific left hemisphere specimen.
Aliases left_hemisphere_tissue_sampling_history
Data Type

right hemisphere preparation

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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

right hemisphere tissue inventory

BICAN Field Name right hemisphere tissue inventory
BICAN UUID 8b6b910f-beb7-4e2b-881a-7f862ef5d588
Definition The inventory (list) of the tissue samples for a specific right hemisphere specimen.
Aliases right_hemisphere_tissue_inventory
Data Type

right hemisphere tissue sampling history

BICAN Field Name right hemisphere tissue sampling history
BICAN UUID 60d2efe0-bf7f-48f7-96fc-71cdf03226dd
Definition The history of the tissue sampling for a specific right hemisphere specimen.
Aliases right_hemisphere_tissue_sampling_history
Data Type

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 measurement

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

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

matriline and patriline

BICAN Field Name matriline and patriline
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

Appendix