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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 Donor to Alignment Metadata schema describes [@lydiang fill in description 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.
Alignment
The data in Alignment is the metadata that essential for the alignment processes and entities.
The following table describes the alignment 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:
alignment output label
BICAN Field Name
alignment_output_label
Annotator
Curator
Data Type
string
Definition
A string that serves as a label (name) for an alignment output.
BICAN UUID
1ca34909-2923-4219-848e-c7c250ec92cd
alignment output created by process id
BICAN Field Name
alignment_output_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of the process that created an alignment output.
BICAN UUID
66caedfa-add6-4e8a-bb45-03cc9d90c149
alignment output path
BICAN Field Name
alignment_output_path
Annotator
Curator
Data Type
string
Definition
A path to the alignment output for a specific alignment process.
BICAN UUID
6015464d-6820-4baf-bc7a-a601c0507085
alignment output barcoded cell sample label
BICAN Field Name
alignment_output_barcoded_cell_sample_label
Annotator
Curator
Data Type
string
Definition
A label of the barcoded cell sample associated with an alignment output.
BICAN UUID
754281ea-94c6-47d8-aab4-7443b6132004
alignment output entity label
BICAN Field Name
alignment_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary output entity (alignment output) of an alignment process.
BICAN UUID
0d27affc-bb94-405e-81df-ffdbbc735e5d
alignment process id
BICAN Field Name
alignment_process_id
Annotator
Curator
Data Type
string
Definition
An identifier used to refer to an alignment process.
BICAN UUID
ae61d258-5f16-42a2-90cc-1279d87384a6
alignment input entity label
BICAN Field Name
alignment_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary input entity (library_aliquot) of an alignment process.
BICAN UUID
ec7344d5-e6f9-46ed-8f0c-d6d0591b3656
alignment input process id
BICAN Field Name
alignment_input_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of the alignment input process.
BICAN UUID
671b4be4-a12b-4d34-856d-300fa28a3c69
alignment input library pool sequencing process id
An identifier of the library pool sequencing process for alignment input.
BICAN UUID
d8fa34ad-ab7c-418b-b0ce-a48ced53dff6
alignment input barcoded cell sample id
BICAN Field Name
alignment_input_barcoded_cell_sample_id
Annotator
Curator
Data Type
string
Definition
A label of the barcoded cell sample associated with the input library aliquot.
BICAN UUID
2f2b32db-0a86-499a-b4e4-08fbef3eab96
Library Pool
The data in the library pool is the metadata that essential for library pool generation and identification.
The following table describes the library pool 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:
library pool sequencing output created by process id
An identifer of a library aliquot associated with a fastq file.
BICAN UUID
7325a944-f9d6-4314-8e96-323496242736
library pool sequencing input entity label
BICAN Field Name
library_pool_sequencing_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary input of a library pool sequencing process.
BICAN UUID
a6ee19dc-8e46-4993-9da9-81aeb0f63462
library pool sequencing process id
BICAN Field Name
library_pool_sequencing_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a library pool sequencing process.
BICAN UUID
f5f0d55e-006e-4b0e-a502-f4a7f5673e8c
library pool sequencing vendor read count
BICAN Field Name
library_pool_sequencing_vendor_read_count
Annotator
Curator
Data Type
integer
Definition
The number of pass filter reads assigned to an indexed library aliquot.
BICAN UUID
c3f96263-7f6b-4031-b715-f17ee1ccaf7a
library pool label
BICAN Field Name
library_pool_label
Annotator
Curator
Data Type
string
Definition
A string that refers to a library pool.
BICAN UUID
29e0578b-6427-4c93-b29b-bde27fbadeec
library pool created by process id
BICAN Field Name
library_pool_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a process that created a library pool.
BICAN UUID
871fe632-54f2-433c-8734-6045d5f9203f
library pool tube avg size bp
BICAN Field Name
library_pool_tube_avg_size_bp
Annotator
Curator
Data Type
integer
Definition
The average size of the pooled libraries given in terms of base pairs.
BICAN UUID
cf1b7c96-cdc1-4eed-8e76-ac44fbd151f7
library pool tube contents nm
BICAN Field Name
library_pool_tube_contents_nm
Annotator
Curator
Data Type
string
Definition
The concentration of the library pool in terms of nM (nMol/L).
BICAN UUID
32f2d02b-7300-4554-aa93-6de6e456eda7
library pool tube internal label
BICAN Field Name
library_pool_tube_internal_label
Annotator
Curator
Data Type
string
Definition
An internal label for a library pool tube container.
BICAN UUID
f1fdea98-7849-4def-a62f-a04cbbf98922
library pool construction output entity label
BICAN Field Name
library_pool_construction_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary output entity (library pool ) of a library pool construction process.
BICAN UUID
0129624c-3cec-46e6-aa8c-49df75937c56
library pool construction process id
BICAN Field Name
library_pool_construction_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a library pool construction process.
BICAN UUID
b26ed5a7-ad3e-4457-9fdd-cf9895980a34
library pool construction input entity label
BICAN Field Name
library_pool_construction_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of an input entity (library aliquot) of a library pool construction process.
BICAN UUID
296c8571-b1b2-4f06-a0f2-60bbdd050797
library pool construction input process id
BICAN Field Name
library_pool_construction_input_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a library pool construction process input.
BICAN UUID
d25187b3-bc2d-4f99-953f-10cae0b56122
Library Aliquot
The data in library aliquot is the metadata that essential for...
The following table describes the library aliquot 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:
library aliquot label
BICAN Field Name
library_aliquot_label
Annotator
Curator
Data Type
string
Definition
A label of a library aliquot.
BICAN UUID
34191bad-d167-4335-8224-ade897d3728e
library aliquot created by process id
BICAN Field Name
library_aliquot_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a process that created a library aliquot.
BICAN UUID
f7471219-1424-4bcc-ae5d-fbc50b2639dd
library aliquot input quantity fmol
BICAN Field Name
library_aliquot_input_quantity_fmol
Annotator
Curator
Data Type
float
Definition
The number of library molecules in an aliquoted portion of a library, as expressed in femtomoles.
BICAN UUID
21fa7764-92d5-400c-b73e-5a8caece5a16
library aliquot library label
BICAN Field Name
library_aliquot_library_label
Annotator
Curator
Data Type
string
Definition
A label of the library which a library aliquot is portioned from.
BICAN UUID
2d073310-911c-4e09-856a-a2ce6c015827
library aliquoting input entity label
BICAN Field Name
library_aliquoting_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary input of a library aliquoting process.
BICAN UUID
a5accf6d-98b8-4d0d-af3f-dd967e1ce077
library aliquoting output entity label
BICAN Field Name
library_aliquoting_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary output of a library aliquoting process.
BICAN UUID
6163e49b-a523-4adc-a45e-c93fbc6911dd
library aliquoting process id
BICAN Field Name
library_aliquoting_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a library aliquoting process.
BICAN UUID
e42425e2-8ceb-4c0a-93f4-6dffbfc57df3
Library
The data in library is the metadata that essential for...
The following table describes the library 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:
library label
BICAN Field Name
library_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a specific library.
BICAN UUID
f717e254-3630-4342-be7b-4d56376e7afe
library created by process id
BICAN Field Name
library_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a process that creates a library.
BICAN UUID
8255bc41-528a-4559-83f2-c93528c4092e
library avg size bp
BICAN Field Name
library_avg_size_bp
Annotator
Curator
Data Type
integer
Definition
The average size of a library in terms of base pairs. This is used to calculate the molarity before pooling and sequencing.
BICAN UUID
f851eba9-56d1-4472-9d0c-d7f8bc33000a
library r1 sequence
BICAN Field Name
library_r1_sequence
Annotator
Curator
Data Type
string
Definition
A sequence of i7 index required by sequencing instrument for demultiplexing (could be sense or antisense).
BICAN UUID
ccb0553d-4146-45ee-b731-77563cb805cd
library r2 sequence
BICAN Field Name
library_r2_sequence
Annotator
Curator
Data Type
string
Definition
A sequence of i5 index required by sequencing instrument for demultiplexing (could be sense or antisense).
BICAN UUID
0ee7f272-01d9-453d-94a3-eefd1a86718e
library creation date
BICAN Field Name
library_creation_date
Annotator
Curator
Data Type
datetime
Definition
The date of a library creation.
BICAN UUID
9c2f575d-1b64-451d-894f-656861afe07a
library input ng
BICAN Field Name
library_input_ng
Annotator
Curator
Data Type
string
Definition
The amount of cDNA going into library construction in nanograms.
BICAN UUID
3db770eb-078e-4b41-92b9-e2e551660753
library prep pass fail
BICAN Field Name
library_prep_pass_fail
Annotator
Curator
Data Type
categorical
Definition
A result (pass or fail) of a test for library preparation based on library yield and size.
BICAN UUID
6817ede2-7ead-402d-9dbc-131aca627c6c
library method
BICAN Field Name
library_method
Annotator
Curator
Data Type
string
Definition
A technique or method that is used to generate a library (specific to the alignment method required for the library). For example, 10xV3.1 (for RNASeq single assay), 10xMult-RSeq (for RNASeq multiome assay), and 10xMult-ATAC (for ATACSeq multiome assay).
BICAN UUID
7b60d59e-fdd7-4b27-a2d4-cae9b69103a6
Library Quantification
The data in library quantification is the metadata that essential for...
The following table describes the library quantification 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:
library quantification ng
BICAN Field Name
library_quantification_ng
Annotator
Curator
Data Type
string
Definition
The amount of library generated in nanograms.
BICAN UUID
318b2d3a-dae7-4c63-bfbb-93862b92f63e
library quantification nm
BICAN Field Name
library_quantification_nm
Annotator
Curator
Data Type
string
Definition
The concentration of library in terms of nM (nMol/L). The number of molecules is needed for accurate pooling of the libraries and for generating the number of target reads/cell in sequencing.
BICAN UUID
c4771566-82bf-4a0a-8a57-3d1b687e3851
library quantification fmol
BICAN Field Name
library_quantification_fmol
Annotator
Curator
Data Type
string
Definition
The amount of library generated in femtomoles
BICAN UUID
4c09ada7-c116-48bc-8fb1-0dcf5c4b939a
library r1 index
BICAN Field Name
library_r1_index
Annotator
Curator
Data Type
string
Definition
The library index used for Read-1 sequence. Indexes allow libraries to be pooled together for sequencing. Sequencing output (fastq) are demultiplexed by using the indexes for each library. The name will be associated with a oligo (string of bases). The required direction of the sequence (sense or antisense) of the index can differ depending on sequencing instruments.
BICAN UUID
be6b81ef-c02d-4aaf-bd8d-5891ad919a9e
library r2 index
BICAN Field Name
library_r2_index
Annotator
Curator
Data Type
string
Definition
The library index used for Read-2 sequence. Indexes allow libraries to be pooled together for sequencing. Sequencing output (fastq) are demultiplexed by using the indexes for each library. The name will be associated with a oligo (string of bases). The required direction of the sequence (sense or antisense) of the index can differ depending on sequencing instruments.
BICAN UUID
f82e3576-36fb-4399-8485-70cbf4911e8f
Library Construction
The data in library construction is the metadata that essential for...
The following table describes the library construction 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:
library construction input entity label
BICAN Field Name
library_construction_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary input of a library construction process.
BICAN UUID
e2d7623d-7313-4d6c-b58d-0795f91a1f45
library construction output entity label
BICAN Field Name
library_construction_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary output of a library construction process.
BICAN UUID
af4dbe52-7ae5-493e-b044-05abbb9fa981
library construction process date
BICAN Field Name
library_construction_process_date
Annotator
Curator
Data Type
datetime
Definition
The date when a library construction process occurred.
BICAN UUID
ab4ae9709-3fc4-45e0-a477-80099f102410
library construction process id
BICAN Field Name
library_construction_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a library construction process.
BICAN UUID
d7393dd2-2406-4984-badb-5b85547f4640
cDNA Amplification
The data in cDNA amplification is the metadata that essential for...
The following table describes the cDNA amplification 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:
amplified cdna label
BICAN Field Name
amplified_cdna_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a portion of amplified cdna.
BICAN UUID
e2606a11-114e-472f-9e05-33f9b6fc3089
amplified cdna created by process id
BICAN Field Name
amplified_cdna_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a process that created a portion of amplified cdna.
BICAN UUID
d695c983-07ff-450f-bbff-53a8638cd6d8
amplified cdna amplified quantity ng
BICAN Field Name
amplified_cdna_amplified_quantity_ng
Annotator
Curator
Data Type
float
Definition
The amount of cDNA produced from an amplification process in nanograms.
BICAN UUID
0db79d05-8612-4896-b9d3-eb1558841449
amplified cdna method
BICAN Field Name
amplified_cdna_method
Annotator
Curator
Data Type
string
Definition
A method used to generate cDNA (eg 10xV3.1, 10xMultiome-Rseq).
BICAN UUID
995369ca-3e05-4f7b-80a8-92427b90e8fa
amplified cdna pcr cycles
BICAN Field Name
amplified_cdna_pcr_cycles
Annotator
Curator
Data Type
integer
Definition
The number of PCR cycles used during cDNA amplification for a cDNA.
BICAN UUID
3827634c-3f8f-4760-b358-86ce4b030238
amplified cdna percent cdna longer than 400bp
BICAN Field Name
amplified_cdna_percent_cdna_longer_than_400bp
Annotator
Curator
Data Type
float
Definition
A QC metric that describes quantifies mRNA degradation of cDNA. Higher % is higher quality starting material.
BICAN UUID
8d150467-f69e-461c-b54c-bcfd22f581e5
amplified cdna rna amplification pass fail
BICAN Field Name
amplified_cdna_rna_amplification_pass_fail
Annotator
Curator
Data Type
categorical
Definition
A result (pass or fail) based on cDNA yield and size.
BICAN UUID
bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5
cdna amplification input entity label
BICAN Field Name
cdna_amplification_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary input of a cDNA amplification process.
BICAN UUID
3e8c5ad4-6a15-478e-ad1c-e68a06b61181
cdna amplification input entity label
BICAN Field Name
cdna_amplification_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of the primary input of a cDNA amplification process.
BICAN UUID
ee5b7407-284a-44d1-813c-746fc934a398
cdna amplification process date
BICAN Field Name
cdna_amplification_process_date
Annotator
Curator
Data Type
datetime
Definition
The date when a cDNA amplification process occurred.
BICAN UUID
6cc333e7-9b98-497f-b7b1-eae904db2400
cdna amplification process id
BICAN Field Name
cdna_amplification_process_id
Annotator
Curator
Data Type
string
Definition
An identifier a cDNA amplification process.
BICAN UUID
a4d2b272-64e2-4adb-8886-38ee822488c9
Cell Barcoding
The data in cell barcoding is the metadata that essential for...
The following table describes the cell barcoding 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:
barcoded cell sample label
BICAN Field Name
barcoded_cell_sample_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a barcoded cell sample.
BICAN UUID
4c0e6380-e53f-4173-a474-d41e836fefe3
barcoded cell sample created by process id
BICAN Field Name
barcoded_cell_sample_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a process that created a barcoded cell sample.
BICAN UUID
1c78b561-d595-4f73-adb0-0de6a2c743e9
barcoded cell sample port well
BICAN Field Name
barcoded_cell_sample_port_well
Annotator
Curator
Data Type
string
Definition
A position of a load port of a 10x chip.
BICAN UUID
aca38100-d245-4be4-9be3-ba27192779fe
barcoded cell sample quantity count
BICAN Field Name
barcoded_cell_sample_quantity_count
Annotator
Curator
Data Type
integer
Definition
The number of barcoded cells expected after barcoding (usually a calculated fraction of the number of cells going into cell_barcoding).
BICAN UUID
dd6abb3c-b671-48eb-a924-13945484de71
cell barcoding input entity label
BICAN Field Name
cell_barcoding_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary input of a cell barcoding process.
BICAN UUID
b5d251bd-0944-4c48-9508-74492185376e
cell barcoding output entity label
BICAN Field Name
cell_barcoding_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary output of a cell barcoding process.
BICAN UUID
12bc4988-4c21-4eac-93f5-e7c2b17a2b32
cell barcoding process id
BICAN Field Name
cell_barcoding_process_id
Annotator
Curator
Data Type
string
Definition
An identifier for a cell barcoding process.
BICAN UUID
a352af1b-1f33-4c8b-865f-7a6865ae5748
Cell Dissociation
The data in cell dissociation is the metadata that essential for...
The following table describes the cell dissociation 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:
dissociated cell sample label
BICAN Field Name
dissociated_cell_sample_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a dissociated cell sample.
BICAN UUID
65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
dissociated cell sample created by process id
BICAN Field Name
dissociated_cell_sample_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a process that created a dissociated cell sample.
BICAN UUID
a155d7f4-0126-430c-a7fb-20b8dd35134d
dissociated cell sample cell prep type
BICAN Field Name
dissociated_cell_sample_cell_prep_type
Annotator
Curator
Data Type
string
Definition
A type of cell preparation; for example, cells, or nuclei.
BICAN UUID
baae4ac3-f959-4594-b943-3a82ec19bd34
dissociated cell sample facs population plan
BICAN Field Name
dissociated_cell_sample_facs_population_plan
Annotator
Curator
Data Type
string
Definition
A fluorescent marker label used to enrich cell dissociation for desired cell types.
BICAN UUID
a6f16756-4e52-4c37-b9dc-4ee5714f79b5
dissociated cell sample number of cells collected
BICAN Field Name
dissociated_cell_sample_number_of_cells_collected
Annotator
Curator
Data Type
integer
Definition
The total number of dissociated cells or nuclei going into a cell barcoding process.
BICAN UUID
e2922a9e-e549-448a-8983-7e7f4f2338a9
cell dissociation input entity label
BICAN Field Name
cell_dissociation_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary input of a cell dissociation process.
BICAN UUID
5ed1a311-e060-4d00-9f24-9615503f9b7b
cell dissociation output entity label
BICAN Field Name
cell_dissociation_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary output of a cell dissociation process.
BICAN UUID
cd94154e-8062-4156-a503-53bf09e32ba4
cell dissociation process id
BICAN Field Name
cell_dissociation_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a cell dissociation process.
BICAN UUID
7151ff55-0b40-4caf-b008-818a79e6e9f6
Tissue Dissectioning
The data in tissue dissectioning is the metadata that essential for...
The following table describes the tissue dissectioning 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:
tissue sample label
BICAN Field Name
tissue_sample_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a tissue sample.
BICAN UUID
2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
tissue sample created by process id
BICAN Field Name
tissue_sample_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a process that created a tissue sample.
BICAN UUID
4bb1e57a-3038-4e44-86cf-238eb1874c50
tissue sample roi plan
BICAN Field Name
tissue_sample_roi_plan
Annotator
Curator
Data Type
string
Definition
BICAN UUID
e7dda557-bda0-4392-ac7f-2651688549b3
tissue dissectioning input entity label
BICAN Field Name
tissue_dissectioning_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary input of a tissue dissectioning process.
BICAN UUID
98ad4077-9cb2-4e03-bad7-6358796aa78c
tissue dissectioning output entity label
BICAN Field Name
tissue_dissectioning_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary output of a tissue dissectioning process.
BICAN UUID
d294e15a-6823-4ecd-aafe-5ce98c2adadf
tissue dissectioning process id
BICAN Field Name
tissue_dissectioning_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a tissue dissectioning process.
BICAN UUID
fc5ddba7-d297-410c-942d-e46ecf657dcb
tissue dissectioning input entity label
BICAN Field Name
tissue_dissectioning_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary input entity of a tissue dissectioning process.
BICAN UUID
d906ee29-f041-4642-8ba2-c1a54af213ea
tissue dissectioning input process id
BICAN Field Name
tissue_dissectioning_input_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of an associated tissue dissectioning process.
BICAN UUID
9cfb3a49-ac05-4ce5-8ed9-c9d82d6ff761
Brain Sections, Segments, Extractions
The data in brain sections, segments, extractions is the metadata that essential for...
The following table describes the brain specimens 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:
brain section label
BICAN Field Name
brain_section_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a brain section.
BICAN UUID
e3bd9517-80e1-4158-981d-bb73baabceca
brain section created by process id
BICAN Field Name
brain_section_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a process that created a brain section.
BICAN UUID
a6e62b20-8c2d-4e40-a03b-41d943ec11cb
brain section ordinal
BICAN Field Name
brain_section_ordinal
Annotator
Curator
Data Type
integer
Definition
A sequential number of a section used to track the relative positional order of sections from a segment.
BICAN UUID
d97be176-d39e-413c-8c1f-14e47f23da66
brain segment sectioning input entity label
BICAN Field Name
brain_segment_sectioning_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary input of a brain segment sectioning process.
BICAN UUID
e41e854d-b68a-4c69-b23f-d1d39891dff0
brain segment sectioning process id
BICAN Field Name
brain_segment_sectioning_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a brain segment sectioning process.
BICAN UUID
3d426c44-47b2-4329-a06a-addd323bbf46
brain segment label
BICAN Field Name
brain_segment_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a brain segment.
BICAN UUID
befeefc1-4be3-4974-a54e-929fd83cbf28
brain segment created by process id
BICAN Field Name
brain_segment_created_by_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a process that created a brain segment.
BICAN UUID
03856361-d1b5-4983-a0fb-ae5a75d8ec6e
brain segment anatomical division
BICAN Field Name
brain_segment_anatomical_division
Annotator
Curator
Data Type
string
Definition
The anatomical division that describes the brain segment; for example, whole brain, cerebrum, cerebellum, brainstem.
BICAN UUID
ec2565cc-1a11-4d1d-9c98-7eeeca27fd82
brain segment barcode
BICAN Field Name
brain_segment_barcode
Annotator
Curator
Data Type
string
Definition
A physical barcode label for a vessel holding a brain segment.
BICAN UUID
516560ed-0715-475a-b717-6ccfa3ec2934
brain extraction input entity label
BICAN Field Name
brain_extraction_input_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary input of a brain extraction process.
BICAN UUID
29442943-7d3d-4126-8817-9c10e34c8b83
brain extraction output entity label
BICAN Field Name
brain_extraction_output_entity_label
Annotator
Curator
Data Type
string
Definition
A label of a primary output of a brain extraction process.
BICAN UUID
583a312a-43de-4c00-91ad-ec65f6fed2df
brain extraction process id
BICAN Field Name
brain_extraction_process_id
Annotator
Curator
Data Type
string
Definition
An identifier of a brain extraction process.
BICAN UUID
d1549808-92c8-4cf8-8e88-ad98a123d645
Donor Metadata
The data in donor metadata is the metadata that essential for...
The following table describes the donor 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:
donor label
BICAN Field Name
donor_label
Annotator
Curator
Data Type
string
Definition
A label that refers to a donor.
BICAN UUID
cb8ebdda-c8d2-4c29-b6cd-fcb5d0d6e720
donor age at death
BICAN Field Name
donor_age_at_death
Annotator
Curator
Data Type
string
Definition
The age of a donor at the time of death.
BICAN UUID
3df398ff-c5ee-4754-aeb8-2dd86027622e
donor date of birth
BICAN Field Name
donor_date_of_birth
Annotator
Curator
Data Type
datetime
Definition
The date of birth of a donor.
BICAN UUID
4c376dcd-cf1f-4ccb-9d93-28ca73f53019
donor date of death
BICAN Field Name
donor_date_of_death
Annotator
Curator
Data Type
datetime
Definition
The date of death of a donor.
BICAN UUID
4cbe0de6-0d4d-4a7d-b38b-c483deaa0e3a
donor full genotype
BICAN Field Name
donor_full_genotype
Annotator
Curator
Data Type
string
Definition
The full genotype of a donor.
BICAN UUID
0a4c3a68-b41f-47e6-8128-257abc2ccaa5
donor ncbitaxonomyid
BICAN Field Name
donor_ncbitaxonomyid
Annotator
Curator
Data Type
string
Definition
The NCBI taxonomy identifier of the organism type of this donor.
BICAN UUID
6837cb02-6bd7-4fb8-838c-9062ead96ba4
donor sex
BICAN Field Name
donor_sex
Annotator
Curator
Data Type
categorical
Definition
The sex of a donor organism; for example, M or F.
BICAN UUID
632d3d3f-f85b-4efc-a1ab-010fe417ae81
age label
BICAN Field Name
age_label
Annotator
Curator
Data Type
string
Definition
A label that refers to an age.
BICAN UUID
0630a265-4a63-48f4-8853-66b929002306
age reference point
BICAN Field Name
age_reference_point
Annotator
Curator
Data Type
string
Definition
The reference point for an age interval; for example, birth or conception.
BICAN UUID
3bed1f94-9d82-4ed7-afdf-79d896b24dbb
age unit
BICAN Field Name
age_unit
Annotator
Curator
Data Type
categorical
Definition
The unit used for representing the donor age from the reference point.
BICAN UUID
b5436e99-f0a7-4c30-825d-56b88ee2ac1d
age value
BICAN Field Name
age_value
Annotator
Curator
Data Type
string
Definition
The value representing the donor age from the reference point.