Tissue
Summary of SMaHT Portal object type Tissue . Its parent type is: SampleSource. Types referencing this type are: AlignedReads, Donor, File, HistologyImage, OutputFile, ReferenceFile, SubmittedFile, SupplementaryFile, UnalignedReads, VariantCalls. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.Description: Tissues collected from an individual.
Tip
See actual Tissue data hereRequired Properties
| Property | Type | Description |
|---|---|---|
| donor | Donor string | See below for more details. |
| external_id | 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. |
| uberon_id | OntologyTerm 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 |
| donor | Donor string | See below for more details. |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
| uberon_id | OntologyTerm 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.] |
| 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_location | string | Anatomical location of the tissue in the donor. |
| code | string • unique | Code used in file naming scheme. |
| consortia | Consortium • array of string • unique | Consortia associated with this item. See values here |
| display_title | string • calculated | - |
| donor | Donor • string | Link to the associated donor. |
| external_id | string | External ID for the item provided by submitter. Must adhere to (regex) pattern: ^[A-Za-z0-9-_]{3,}$ |
| ischemic_time | number • min value: 0 | Time interval of ischemia (hours). |
| pathology_notes | string | Notes from pathologist report on the tissue. |
| ph | number • min value: 0 • max value: 14 | pH of the tissue. |
| preservation_medium | string | Medium used for preservation. |
| preservation_type • Fixed • Fresh • Frozen • Snap Frozen | enum of string | Method of preservation. |
| prosector_notes | string | Notes from prosector report on the tissue recovery. |
| sample_count | integer • min value: 0 | Number of samples produced from the tissue. |
| size | number • min value: 0 | Size of the tissue. |
| size_unit • cm^2 • cm^3 | enum of string | Unit of measurement for size of the tissue. |
| 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,}_TISSUE_[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|_-]+$ |
| uberon_id | OntologyTerm • string | Uberon Ontology identifier for the tissue. |
| uuid | string | Unique ID by which this object is identified. |
| volume | number • min value: 0 | Volume of the tissue (mL). |
| weight | number • min value: 0 | Weight of the tissue (g). |