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Assay Schema

This reference document defines the structural properties of the ISAAssayJSONSchema object and explains how its experimental data graphs map onto a flat, tab-separated assay matrix file (a_*.txt).

Object Properties

Section titled “Object Properties”

The ISAAssayJSONSchema object models a distinct experimental test or measurement block within a study and contains the following parameters:

Property Type Description
@type "Assay" Mandatory type metadata token.
@id string Optional JSON-LD identifier.
@context string Optional JSON-LD context string.
filename string The target file name assigned when writing out this assay matrix (typically a_*.txt).
measurementType ISAOntologyReferenceSchema Ontology term representing what is being measured.
technologyType ISAOntologyReferenceSchema Ontology term representing the technology platform used.
technologyPlatform string A string detailing the explicit manufacturer or instrument layout.
dataFiles ISADataSchema[] Array of associated raw or derived data assets generated by this assay.
materials { "sources": SourceSchema[], "samples": SampleSchema[], "otherMaterials": MaterialSchema[]} Object containing the materials used in the assay.
unitCategories OntologyAnnotationSchema[] List of all the units defined in the study.
processSequence ISAProcessOrProtocolApplicationSchema...[] The execution tracking graph connecting assay inputs, protocols, and data nodes.
comments ISACommentSchema[] It corresponds to ISA Comment objects.

Matrix Generation & Column Architecture

Section titled “Matrix Generation & Column Architecture”

When converting an ISA Study structure using convertTable(tableData: ISAAssayJSONSchema) into horizontal, tab-delimited files, columns are dynamically generated by evaluating linear sequences via a graph model.

1. Structural Element Columns

Section titled “1. Structural Element Columns”

Assay sequences typically terminate in data files or specialized material extracts. Columns are ordered by processing sequence:

  • Assay Material & Data Nodes: Generates column headers dynamically matching the underlying node type (e.g., Extract Name, Labeled Extract Name, Raw Data File). Cells output the string literal name of the entity.
  • Workflow Steps: Intermediary execution steps generate a Protocol REF column matching the protocolName on the corresponding process edge.

2. Annotation & Qualifier Modifiers

Section titled “2. Annotation & Qualifier Modifiers”

Just like the Study matrix, nodes and process boundaries append descriptive qualifiers to their immediate right if ontology metadata or comments exist:

Node Attributes (Characteristics & Comments)

Section titled “Node Attributes (Characteristics & Comments)”
  • Characteristics [Category]: Generated if an assay node includes items in its characteristics collection. The category label is extracted from characteristicType.annotationValue.
    • Generates two trailing qualifier tracking columns: Term Accession Number and Term Source REF.
  • Comment [Name]: Appends a column for entries inside a node’s comments array matching the targeted comment configuration.

Protocol Attributes (Parameters)

Section titled “Protocol Attributes (Parameters)”
  • Parameter Value [Name]: Generated when a workflow step applies discrete parameter values. The bracketed name reflects parameterName.annotationValue.
    • Generates two trailing qualifier tracking columns: Term Accession Number and Term Source REF.

Output Structural Integrity Constraints

Section titled “Output Structural Integrity Constraints”
  • Cell Compiling: All string tokens within generated body cells are strictly wrapped inside double-quotes ("") and broken down by uniform tab delimiters (\t).
  • Intermediary Null Safe Fallbacks: If shorter alternate pathways exist within the graph topology, columns belonging strictly to longer parallel routes evaluate cleanly to empty strings ("") to preserve structural row symmetry.
  • Termination Rule: If the input processSequence contains zero entries, calls to the matrix compiler break immediately and return an empty string ('').