New schema update to specimen_from_organism schema

[ami-day]

For which schema is a change/update being suggested?

I would like to request an update to the specimen_from_organism schema.

What should the change/update be?

Adding new fields

I would like to add the following new fields to this schema to allow data contributors to get information on the Regions of Interest (ROI) used when NanoString Digital Spatial Profiling technology is used for library construction. This is required for the interpretation of the spatial data linked to the sequencing data:

specimen_from_organism.region_of_interest.id
specimen_from_organism.region_of_interest.area
specimen_from_organism.region_of_interest.markers
specimen_from_organism.region_of_interest.morphology
specimen_from_organism.region_of_interest.segment_id
specimen_from_organism.region_of_interest.segment_area
specimen_from_organism.region_of_interest.segment_markers
specimen_from_organism.region_of_interest.segment_morphology

This update constitutes a minor change to the schema(s) it affects.

What new field(s) need to be changed/added?

specimen_from_organism.region_of_interest.id
specimen_from_organism.region_of_interest.area
specimen_from_organism.region_of_interest.markers
specimen_from_organism.region_of_interest.morphology
specimen_from_organism.region_of_interest.segment_id
specimen_from_organism.region_of_interest.segment_area
specimen_from_organism.region_of_interest.segment_markers
specimen_from_organism.region_of_interest.segment_morphology

Field name
region_of_interest.id
region_of_interest.area
region_of_interest.markers
region_of_interest.morphology
region_of_interest.segment_id
region_of_interest.segment_area
region_of_interest.segment_markers
region_of_interest.segment_morphology

Field description
region_of_interest.id: an identifier for a Region Of Interest (ROI).
region_of_interest.area: the area of a Region Of Interest (ROI) in mm2.
region_of_interest.markers: A list of markers used to identify a Region of Interest (ROI).
region_of_interest.morphology: The morphology used to describe a Region of Interest (ROI).
region_of_interest.segment_id: an identifier for a Segment defined within a Region Of Interest (ROI).
region_of_interest.segment_area: the area of a Segment within a Region Of Interest (ROI) in mm2.
region_of_interest.segment_markers: A list of markers used to identify a Segment within a Region of Interest (ROI).
region_of_interest.segment_morphology: The morphology used to describe a Segment within a Region of Interest (ROI).

Field type
str
integer
enum
str
str
integer
enum
str

Required
no
no
no
no
no
no
no
no

Examples
region_of_interest.id: region 1
region_of_interest.area: 94541.01
region_of_interest.markers: PanCk+
region_of_interest.morphology: alveolar
region_of_interest.segment_id: segment 1
region_of_interest.segment_area: 23321.01
region_of_interest.segment_markers: PanCk+||alphaSMA-
region_of_interest.segment_morphology: alveolar

CV or enum
no
no
no
no
no
no
no
no

Why is the change requested?

To allow data contributors to get information on the Regions of Interest (ROI) used when NanoString Digital Spatial Profiling technology is used for library construction. This is required for the interpretation of the spatial data linked to the sequencing data.