Library
Summary of SMaHT Portal object type Library . Types referencing this type are: AlignedReads, File, FileSet, 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: Library items contain information on sequencing libraries prepared from analytes.
Tip
See actual Library data hereRequired Properties
| Property | Type | Description |
|---|---|---|
| analytes | Analyte array of string | See below for more details. |
| assay | Assay 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. |
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 |
|---|---|---|
| analytes | Analyte array of string | See below for more details. |
| assay | Assay string | See below for more details. |
| consortia | Consortium array of string | See below for more details. See values here |
| library_preparation | LibraryPreparation string | See below for more details. |
| protocols | Protocol 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 |
|---|---|---|
| a260_a280_ratio | number • min value: 0 | Ratio of nucleic acid absorbance at 260 nm and 280 nm, used to determine a measure of DNA purity. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| adapter_name | string | Name of sequencing adapter. |
| adapter_sequence | string | Base sequence of sequencing adapter. |
| 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.] |
| amplification_cycles | integer • min value: 0 | Number of PCR Cycles used for additional amplification. |
| analyte_weight | number • min value: 0 | Weight of analyte used to prepare library (mg). |
| analytes | Analyte • array of string • min items: 1 • unique | Links to associated analytes. |
| antibody | array of string | Antibody used for affinity enrichment. |
| assay | Assay • string | Link to associated assay. |
| barcode_sequences | array of string • min items: 1 • unique | Barcode sequence for multiplexed sequencing. |
| comments | array of string | Additional comments for library. |
| concatenated_reads • • No • Not applicable • Yes | enum of string | Whether or not the library contains concatenated reads. Relevant for Kinnex. |
| 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 | - |
| dna_target | array of string • min items: 1 • unique | DNA target used in insert selection. |
| external_id | string | External ID for the item provided by submitter. Must adhere to (regex) pattern: ^[A-Za-z0-9-_]{3,}$ |
| fragment_mean_length | number • min value: 0 | Mean length of the sequenced fragments, e.g. as predicted by Agilent Bioanalyzer (bp). |
| guide_sequence | array of string • min items: 1 • unique | Guide sequence. Relevant for Cas9 capture experiments. |
| insert_coefficient_of_variation | number • min value: 0 | Coefficient of variation of the length of the sample molecule in the fragments to be sequenced. |
| insert_maximum_length | integer • min value: 0 | Maximum length of the sample molecule in the fragments to be sequenced (bp). |
| insert_mean_length | number • min value: 0 | Mean length of the sample molecule in the fragments to be sequenced (bp). |
| insert_minimum_length | integer • min value: 0 | Minimum length of the sample molecule in the fragments to be sequenced (bp). |
| library_preparation | LibraryPreparation • string | Link to associated library preparation. |
| preparation_date | string • format: date | Date of library preparation. |
| protocols | Protocol • array of string • min items: 1 • unique • restricted | Protocols providing experimental details. |
| 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,}_LIBRARY_[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_fragment_size | integer • min value: 0 | Targeted fragment size for library (bp). |
| target_insert_maximum_length | integer • min value: 0 | Target maximum length of the insert (bp). |
| target_insert_minimum_length | integer • min value: 0 | Target minimum length of the insert (bp). |
| target_monomer_size | integer • min value: 0 | For libraries with concatenated reads, the target monomer size (bp). Relevant for Kinnex. |
| uuid | string | Unique ID by which this object is identified. |