[ENH] BEP018: Genetic information

src/04-modality-specific-files/08-genetic-descriptor.md

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+# Genetic Descriptor
+
+Support for genetic descriptors was developed as a [BIDS Extension Proposal](https://github.com/bids-standard/bids-specification/blob/master/src/06-extensions.md#bids-extension-proposals).
+The extension was primarily developped by Cyril Pernet and Clara Moreau with contributions from Tom Nichols and Jessica Turner.
+
+The goal of the genetic descriptor is to link imaging and genetic data. 
+This is necessary as genetic data are typically stored in dedicated repositories, separately from the imaging data. 
+The descriptor provides basics information about:
+-   where to find genetic information associated with the imaging data
+-   what type of genetic information is available
+
+## dataset_description.json
+
+In order to link a genetic database entry, the key `GeneticDataBase` MUST be present and
+the value is an object with the following fields:
+
+| Field name           | Definition                                                                     |
+|----------------------|--------------------------------------------------------------------------------|
+| Genetics.Dataset     | REQUIRED. URI where data can be retrieved.                                     |
+| Genetics.Database    | OPTIONAL. URI of database where the dataset is hosted.                         |
+| Genetics.Descriptors | OPTIONAL. List of relevant descriptors (*e.g.*, journal articles) for dataset. |
+
+`dataset_description.json` example:
+```JSON
+{
+  "Name": "Human Connectom Project",
+  "BIDSVersion":  "1.2.0",
+  "License": "CC0",
+  "Authors": ["1st author", "2nd author"],
+  "Funding": "list your funding sources",
+  "Genetics": {
+     "Dataset": "dataset",
+     "Database": "database",
+     "Descriptors": "descriptors"
+     }
+}
+```
+
+## Subject naming and Participants file
+
+If the same participants have different identifiers in the genetic and imaging datasets,
+the column `GeneticID` SHOULD be added to the `participants.tsv` file to associate
+the BIDS participant 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 `participants.tsv` file by adding optional columns.
+
+`participants.tsv` example:
+
+```Text
+participant_id  age sex group GeneticID	IDH Mutation
+sub-control01 34  M control 124587	yes
+sub-control02 12  F control 548936	yes
+sub-patient01 33  F patient 489634	no
+```
+
+## genetic_info.json
+
+This file is the descriptor of the genetic information available either in the participant tsv file and/or the genetic database described in the dataset_description.json. The `GeneticLevel` and `SampleOrigin` are the only two mandatory fields.
+
+| Field name         | Definition                                                                       | Values                                                                                                                                                                                                                                                                                                                              |
+| :----------------- | :------------------------------------------------------------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| GeneticLevel       | MANDATORY Describes the level of analysis                                        | `Genetic`, `Genomic`, `Epigenomic`, `Transcriptomic`, `Metabolomic`, or `Proteomic`                                                                                                                                                                                                                                                 |
+| AnalyticalApproach | OPTIONAL Methodology used to analyse the GeneticLevel                            | Value must be taken from [gapsolr](https://www.ncbi.nlm.nih.gov/projects/gapsolr/facets.html) under /Study/Molecular Data Type, for instance `SNP Genotypes (Array)` or `Methylation (CpG)`                                                                                                                                         |
+| SampleOrigin       | MANDATORY Describes from which tissue the genetic information was extracted from | `blood`, `saliva`, `brain`, `csf`, `breast milk`, `bile`, `amniotic fluid`, `other biospecimen`                                                                                                                                                                                                                                     |
+| TissueOrigin       | OPTIONAL Describes the type of tissue analyzed for SampleOrigin `brain`          | `gray matter`, `white matter`, `csf`, `meninges`, `macrovascular` or `microvascular`                                                                                                                                                                                                                                                |
+| BrainLocation      | OPTIONAL Refers to the location in space of the TissueOrigin                     | `MNI coordinate` or a `label` taken from the [Allen Brain Atlas](http://atlas.brain-map.org/atlas?atlas=265297125#atlas=265297125&plate=112360888&structure=4392&x=40348.15104166667&y=46928.75&zoom=-7&resolution=206.60&z=3) possibly `layer` to refer to layer-specific gene expression, which can also tie up with laminar fMRI |
+| CellType           | OPTIONAL Describes the type of cell analyzed                                     | Value should come from the [cell ontology](http://obofoundry.org/ontology/cl.html)                                                                                 |
+
+`genetic_info.json` example:
+
+```JSON
+{
+  "GeneticLevel": "Genetic",
+  "AnalyticalApproach": "SNP Genotypes", "SampleOrigin": "brain",
+  "TissueOrigin": "gray matter",
+  "CellType":  "neuron",
+  "BrainLocation": "[-30 -15 10]"
+}
+```