Output annotated metadata as BIDS compatible data dictionary

[surchs]

One of the outputs we generate with this tool could be a BIDS compatible data dictionary. This could allow us to encode all of the harmonizations inside the data dictionary and leave the original participants.tsv file as is.

Example

We start with this

participant_id	age	sex	handedness	group
sub-01	Y034	M	right	PD
sub-02	Y012	F	right	CTL
sub-03	Y009	F	n/a	PD

And this data dictionary:

{
    "age": {
        "Description": "age of the participant",
        "Units": "years"
    },
    "sex": {
        "Description": "sex of the participant as reported by the participant",
        "Levels": {
            "M": "male",
            "F": "female"
        }
    },
    "handedness": {
        "Description": "handedness of the participant as reported by the participant",
        "Levels": {
            "left": "left",
            "right": "right"
        }
    },
    "group": {
        "Description": "diagnostic group the participant belonged to",
        "Levels": {
            "CTL": "Control subject",
            "PD": "Parkinson Patient"
        }
    }
}

Then we annotate things with our tool and end up with this data dictionary:

{
    "age": {
        "Description": "age of the participant",
        "Units": "years",
       "bagel": {
           "type": "age",
           "map": "[1-9]+"
           }
    },
    "sex": {
        "Description": "sex of the participant as reported by the participant",
        "Levels": {
            "M": "male",
            "F": "female"
        },
        "bagel": {
        	"type": "gender"
        	"map": None
    },
    "handedness": {
        "Description": "handedness of the participant as reported by the participant",
        "Levels": {
            "left": "left",
            "right": "right"
        }
    },
    "group": {
        "Description": "diagnostic group the participant belonged to",
        "Levels": {
            "CTL": "Control subject",
            "PD": "Parkinson Patient"
        },
        "bagel": {
        	"type": "diagnosis",
        	"map": {
        		"CTL": "https://normalcontrol.org",
        		"PD": "https://SNOMED.Parkinson.org"
        		}
	    }
	}
    
}

[surchs]

This is not a focus right now but we should revisit this in order to add compatibility with BIDS and OpenNeuro at a later stage

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

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[github-actions]

We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 30 days.
We have applied the stale-issue label to indicate that this issue should be reviewed again and then either prioritized or closed.

[surchs]

I'm closing this because we are implementing and tracking it in #305 now