PathologyReport
Summary of SMaHT Portal abstract (cannot be created directly) object type PathologyReport . Its derived types are: BrainPathologyReport, NonBrainPathologyReport. Types referencing this type are: HistologyImage. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.Description: A pathology report for a tissue sample.
Tip
See actual PathologyReport data hereRequired Properties
| Property | Type | Description |
|---|---|---|
| outcome | string | See below for more details. |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
| submitted_id | string | See below for more details. |
| tissue_name | string | See below for more details. |
| tissue_samples | TissueSample array of string | See below for more details. |
Identifying Properties
| Property | Type | Description |
|---|---|---|
| accession | string | See below for more details. |
| submitted_id | string | See below for more details. |
| uuid | string | See below for more details. |
Reference Properties
| Property | Type | Description |
|---|---|---|
| consortia | Consortium array of string | See below for more details. See values here |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
| tissue_samples | TissueSample array of string | See below for more details. |
Properties
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| additional_notes | string | Additional notes or other findings related to the sample. |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| anatomical_sample_location | string | Anatomical location from which the sample was taken. |
| consortia | Consortium • array of string • unique | Consortia associated with this item. See values here |
| description | string | Plain text description of the item. |
| display_title | string • calculated | - |
| final_review_determination • No • Yes | enum of string | Whether a final review determination was made for the sample. |
| is_indeterminate • No • Yes | enum of string | Whether the tissue sample is indeterminate. |
| non_target_tissues | array of object | - |
| non_target_tissues . non_target_tissue_description | string | Description of other non-target tissue present in the sample. |
| non_target_tissues . non_target_tissue_percentage • [0-10] • [11-25]] • [26-49] • [50-100] | enum of string | Percentage range of the sample that was the non-target tissue subtype (%). |
| non_target_tissues . non_target_tissue_present • No • Yes | enum of string | Whether the non-target tissue subtype was present in the sample. |
| non_target_tissues . non_target_tissue_subtype | string | Subtype of non-target tissue in sample. |
| outcome • Acceptable • Unacceptable | enum of string | Outcome of the pathology report. |
| pathologic_findings | array of object | - |
| pathologic_findings . finding_description | string | Description of pathologic/unexpected finding. |
| pathologic_findings . finding_percentage • [0-10] • [11-25]] • [26-49] • [50-100] | enum of string | Percentage range of the sample that displayed the pathologic/unexpected finding (%). |
| pathologic_findings . finding_present • No • Yes | enum of string | Whether pathologic/unexpected finding is present in the sample. |
| pathologic_findings . finding_type | string | Type of pathologic/unexpected finding present in the sample. |
| status • deleted • draft • in review ← default • obsolete • public • released • restricted | enum of string • default: in review | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_PATHOLOGY-REPORT_[A-Z0-9-_.]{4,}$ |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| target_tissues | array of object | - |
| target_tissues . target_tissue_autolysis_score | integer • min value: 0 • max value: 3 | Autolysis score of the target tissue in the sample. 0=None, 1=mild , 2=moderate, 3=severe. |
| target_tissues . target_tissue_percentage • [0-10] • [11-25]] • [26-49] • [50-100] | enum of string | Percentage range of the sample that was the target tissue subtype (%). |
| target_tissues . target_tissue_present • No • Yes | enum of string | Whether the target tissue subtype was present in the sample. |
| target_tissues . target_tissue_subtype | string | Subtype of target tissue in sample. |
| tissue_autolysis_score | integer • min value: 0 • max value: 3 | Overall tissue autolysis score of the sample. 0=None, 1=mild , 2=moderate, 3=severe. |
| tissue_name | string | Name of the type of tissue the sample was taken from. |
| tissue_samples | TissueSample • array of string | Link to associated tissue samples. |
| unacceptable_description | string | Description of unacceptable review determination. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | Version for the item. Must adhere to (regex) pattern: ^([0-9]+.)*[0-9]+$ |