Genetic Descriptor
Support for genetic descriptors was developed as a BIDS Extension Proposal. Please see Citing BIDS on how to appropriately credit this extension when referring to it in the context of the academic literature.
Genetic data are typically stored in dedicated repositories, separate from imaging data. A genetic descriptor links a BIDS dataset to associated genetic data, potentially in a separate repository, with details of where to find the genetic data and the type of data available.
Example datasets
The following example dataset with genetics data have been formatted using this specification and can be used for practical guidance when curating a new dataset.
Dataset Description
If information on associated genetic data is supplied as part of a BIDS dataset,
these "genetic descriptors" are encoded as an additional, REQUIRED entry in the
dataset_description.json
file.
Datasets linked to a genetic database entry include the following REQUIRED and OPTIONAL
keys in the Genetics
sub-object of dataset_description.json
:
Key name | Requirement Level | Data type | Description |
---|---|---|---|
Dataset | REQUIRED | string | URI where data can be retrieved. |
Database | OPTIONAL | string | URI of database where the dataset is hosted. |
Descriptors | OPTIONAL | string or array of strings | List of relevant descriptors (for example, journal articles) for dataset using a valid URI when possible. |
Example:
{
"Name": "Human Connectome Project",
"BIDSVersion": "1.3.0",
"License": "CC0",
"Authors": ["1st author", "2nd author"],
"Funding": ["P41 EB015894/EB/NIBIB NIH HHS/United States"],
"Genetics": {
"Dataset": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001364.v1.p1",
"Database": "https://www.ncbi.nlm.nih.gov/gap/",
"Descriptors": ["doi:10.1016/j.neuroimage.2013.05.041"]
}
}
Subject naming and Subjects file
If the same subjects have different identifiers in the genetic and imaging datasets,
the column genetic_id
SHOULD be added to the subjects.tsv
file to associate
the BIDS subject with a subject in the Genetics.Dataset
referred to in the
dataset_description.json
file.
Information about the presence/absence of specific genetic markers MAY be duplicated
in the subjects.tsv
file by adding optional columns (like idh_mutation
in the
example below).
Note that optional columns MUST be further described in an accompanying
subjects.json
file as described in
Tabular files.
subjects.tsv
example:
subject_id age sex group genetic_id idh_mutation
sub-control01 34 M control 124587 yes
sub-control02 12 F control 548936 yes
sub-patient01 33 F patient 489634 no
Genetic Information
Template:
genetic_info.json
The following fields are defined for genetic_info.json:
The genetic_info.json
file describes the genetic information available in the
subjects.tsv
file and/or the genetic database described in
dataset_description.json
.
Datasets containing the Genetics
field in dataset_description.json
or the
genetic_id
column in subjects.tsv
MUST include this file.
Key name | Requirement Level | Data type | Description |
---|---|---|---|
GeneticLevel | REQUIRED | string or array of strings | Describes the level of analysis. Values MUST be one of "Genetic" , "Genomic" , "Epigenomic" , "Transcriptomic" , "Metabolomic" , or "Proteomic" .For more information on these levels, see Multi-omics approaches to disease by Hasin et al. 2017. |
AnalyticalApproach | OPTIONAL | string or array of strings | Methodology or methodologies used to analyze the "GeneticLevel" . Values MUST be taken from the database of Genotypes and Phenotypes (dbGaP) under /Study/Molecular Data Type (for example, SNP Genotypes (Array) or Methylation (CpG). |
SampleOrigin | REQUIRED | string | Describes from which tissue the genetic information was extracted. Must be one of: "blood" , "saliva" , "brain" , "csf" , "breast milk" , "bile" , "amniotic fluid" , "other biospecimen" . |
TissueOrigin | OPTIONAL | string | Describes the type of tissue analyzed for "SampleOrigin" brain . Must be one of: "gray matter" , "white matter" , "csf" , "meninges" , "macrovascular" , "microvascular" . |
BrainLocation | OPTIONAL | string | Refers to the location in space of the "TissueOrigin" . Values may be an MNI coordinate, a label taken from the Allen Brain Atlas, or layer to refer to layer-specific gene expression, which can also tie up with laminar fMRI. |
CellType | OPTIONAL | string | Describes the type of cell analyzed. Values SHOULD come from the cell ontology. |
To ensure dataset description consistency, we recommend following Multi-omics approaches to disease by Hasin et al. 2017 to determine the GeneticLevel:
Genetic
: data report on a single genetic location (typically directly in thesubjects.tsv
file)Genomic
: data link to subjects' genome (multiple genetic locations)Epigenomic
: data link to subjects' characterization of reversible modifications of DNATranscriptomic
: data link to subjects RNA levelsMetabolomic
: data link to subjects' products of cellular metabolic functionsProteomic
: data link to subjects peptides and proteins quantification
genetic_info.json
example:
{
"GeneticLevel": "Genomic",
"AnalyticalApproach": ["Whole Genome Sequencing", "SNP/CNV Genotypes"],
"SampleOrigin": "brain",
"TissueOrigin": "gray matter",
"CellType": "neuron",
"BrainLocation": "[-30 -15 10]"
}