ReferenceGenome
Summary of SMaHT Portal object type ReferenceGenome . Its derived types are: DonorSpecificAssembly. Types referencing this type are: AlignedReads, OutputFile, SupplementaryFile, VariantCalls. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.Tip
See actual ReferenceGenome data hereRequired Properties
| Property | Type | Description |
|---|---|---|
| identifier | string | See below for more details. |
| title | string | See below for more details. |
| At least one of the following ... | ||
| 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 |
Identifying Properties
| Property | Type | Description |
|---|---|---|
| accession | string | See below for more details. |
| aliases | array of string | See below for more details. |
| identifier | 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 |
| files | File array of string | See below for more details. |
| submission_centers | SubmissionCenter array of string | See below for more details. See values here |
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.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| 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.] |
| code | string | Code used in file naming scheme. Must adhere to (regex) pattern: ^[A-Za-z0-9_]{2,}$ |
| 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 | - |
| files | File • array of string • min items: 1 • unique | Files associated with the reference genome. |
| genbank_assembly | string | GenBank assembly accession. Must adhere to (regex) pattern: ^GCA_[0-9].[0-9]{1,}$ |
| identifier | string • min length: 2 • unique | Unique, identifying name for the item. Must adhere to (regex) pattern: ^[A-Za-z0-9-_]+$ |
| refseq_assembly | string | RefSeq assembly accession. Must adhere to (regex) pattern: ^GCF_[0-9].[0-9]{1,}$ |
| 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 |
| 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|_-]+$ |
| title | string • min length: 3 | Title for the item. |
| url | string • format: uri | An external resource with additional information about the item. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | Version for the item. Must adhere to (regex) pattern: ^[A-Za-z0-9_-.]{3,}$ |