Assay

Summary of SMaHT Portal object type Assay . Types referencing this type are: AlignedReads, File, HistologyImage, Library, 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.

Tip

See actual Assay data here

Required Properties

Property	Type	Description
code	string	See below for more details.
identifier	string	See below for more details.
title	string	See below for more details.
valid_molecules	array of enum	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.
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
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.]
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_method  • PCR  • PCR-free  • WGA	enum of string	Amplification method used in the assay.
category  • ATAC-seq  • Bulk RNA-seq  • Bulk WGS  • Cut&Tag  • Dip-C  • Duplex-seq WGS  • Hi-C  • NT-seq  • Repeat Element Targeted Sequencing  • Single-cell RNA-seq  • Single-cell WGS  • Strand-seq  • WGA	enum of string	Category of assay.
cell_isolation_method  • Bulk  • Microbulk  • Single-cell	enum of string	Method of isolating cells used in the assay.
code	string • unique	Code used in file naming scheme. Must adhere to (regex) pattern: ^[0-9]$
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	-
identifier	string • min length: 2 • unique	Unique, identifying name for the item. Must adhere to (regex) pattern: ^[A-Za-z0-9-_]+$
molecule_specificity  • Duplex-sequencing  • Not Applicable  • Single-molecule	enum of string	Level of specificity of sequencing molecules.
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.
uuid	string	Unique ID by which this object is identified.
valid_molecules  • DNA  • RNA	array of enum • min items: 1 • unique • restricted	Molecules that are compatible with the assay.
valid_sequencers  • bgi_dnbseq_g400  • element_aviti  • illumina_hiseq_x  • illumina_novaseq_6000  • illumina_novaseq_x  • illumina_novaseq_x_plus  • ont_minion_mk1b  • ont_promethion_24  • ont_promethion_2_solo  • pacbio_revio_hifi	array of enum • min items: 1 • unique • restricted	Sequencers that are compatible with the assay.