Assay

last updated at 2022-12-13

Addition of assays

⚠️ Make sure to close all isa.*.xlsx files before submitting a new command to the command line, as otherwise the information cannot be saved by the ARC Commander.

An assay may consist of experimentally measured data together with experimental protocols.
An assay folder structure can be created by using arc a init. Under assays an assay folder named after the assay identifier is created which includes:
- dataset
- protocol
- assay.isa.xlsx
- README.md
An existing assay can be registered to the investigation by using arc a register.
To create the folder structure and afterwards register the new assay arc a add can be used. This command combines init and register.

⚠️ An assay identifier also sets the folder name, so ensure to avoid special characters!

Field	Description	Input
StudyIdentifier	Name of the study in which the assay is situated
AssayIdentifier (Mandatory)	Name of the assay of interest	GelBasedProteomicsWT
MeasurementType	A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein identification). The term can be free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and Term Source REF fields below are required.	Proteomics
MeasurementTypeTermAccessionNumber	The accession number from the Term Source associated with the selected term.
MeasurementTypeTermSourceREF	The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference section.
TechnologyType	Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass spectrometry. The term can be free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and Term Source REF fields below are required.	Mass spectrometry
TechnologyTypeTermAccessionNumber	The accession number from the Term Source associated with the selected term.
TechnologyTypeTermSourceREF	Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to match one of the Term Source Names declared in the Ontology Source Reference section.
TechnologyPlatform	Manufacturer and platform name, e.g. Bruker AVANCE	AB Sciex TT6600

If no study identifier is given, a study is created with the assay identifier as study identifier. Instead of using the editor, the following command can be used:
arc assay add -a GelBasedProteomicsM21 --measurementtype Proteomics --technologytype "Mass spectrometry" --technologyplatform "AB Sciex TT6600"

Listing and inspecting registered assays

Registered assays can be listed by arc a list.
To get detailed information about a specific entry use arc a get. If no arguments are specified an editor will request study and assay identifier (mandatory) to print all registered information into the shell.

Editing assay information

An assay can be edited using arc a edit.
- If no further arguments are specified an editor opens, that asks for the assay and study identifier that should be edited.
- If the assay exists, another editor opens with information already known for the respective assay. The required values can be edited.
Instead of using the editor, the following command can be used. To circumvent editor pop ups, not arc a edit, but arc a update must be used:
arc a update -s GelBasedProteomicsWT -a GelBasedProteomicsWT --technologyplatform "AB Sciex TT6600"

Removing assays

An assay can be unregistered from the investigation by using arc a unregister.
An assay folder structure can be deleted by using arc a delete.
To both, delete the assay folder structure and unregister it from the investigation arc a remove can be used.
Supply a study identifier and assay identifier to directly use these commands via command line, i.e.:
- arc a unregister -s <study identifier> -a <assay identifier>
- arc a delete -s <study identifier> -a <assay identifier>
- arc a remove -s <study identifier> -a <assay identifier>

💡 To remove, unregister, or delete an assay both study identifier and assay identifier are required to ensure the correct assay is chosen.

Moving assays

If an assay was mis-assigned to an incorrect study, or some assays should be grouped together (e.g. when a new study is created and some old assays would fit better to this new study), an assay can be moved from one study to another by using arc a move. After definition of the assay identifier together with old, and target study identifier, the assay is moved. If no study exist, that matches the given target study identifier, a new study is registered.
Instead of using the editor, the following command can be used:
arc a move -s GelBasedProteomicsWT -a GelBasedProteomicsWT -t WTProteomics

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