Software

Summary of SMaHT Portal object type Software . Types referencing this type are: AlignedReads, OutputFile, 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: Software used to generate files or perform analysis.

Tip

See actual Software data here

Required Properties

Property	Type	Description
category	array of enum	See below for more details.
title	string	See below for more details.
version	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.
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

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.]
binary_url	string • format: uri	An external resource to a compiled download of the software.
category  • Alignment  • Alignment Manipulation  • Assembly  • Basecaller  • Data Compression  • Feature Annotation  • Format Conversion  • Gene Quantification  • Quality Control  • Read Manipulation  • Transcript Quantification  • Variant Annotation  • Variant Calling  • Variant Manipulation	array of enum • min items: 1 • unique	-
code	string	Code used in file naming scheme. Must adhere to (regex) pattern: ^[A-Za-z0-9_]{2,}$
commit	string	The software commit hash.
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	-
gpu	string	GPU used for basecalling software, particularly for ONT data.
model	string	DNA model used for basecalling software, particularly for ONT data.
modification_tags  • 5mC  • 5mCG  • 5mCG_5hmCG  • 5mC_5hmC  • 6mA  • None  • m6A_DRACH	array of enum • min items: 1 • unique	Tags used to modify the basecaller software, particularly for ONT data.
name	string • min length: 3	Name of the item. Must adhere to (regex) pattern: ^[A-Za-z0-9-_]+$
source_url	string • format: uri	An external resource to the code base.
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,}_SOFTWARE_[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|_-]+$
title	string • min length: 3	The name of the software.
uuid	string	Unique ID by which this object is identified.
version	string	The version of the software. Must adhere to (regex) pattern: [A-Za-z0-9._-]+