AIH-HSP V1.0 Data Types – Genomic Processing Type

The Genomic Processing Type defines the allowable operations, methods, and processing descriptors used for Genomic (DNA/RNA) data.
It reuses Common Definitions for: Header, Algorithm, Algorithms, FeatureClass, Features.

The Genomic Processing Type shall:

• Fix Domain = Genomics.
• Validate Operation against genomics‑specific enumerations.
• Validate Method against genomics computational techniques.
• Allow Algorithm to be a string identifier or an AlgorithmObject.
• Allow Algorithms to be an array of Algorithm items.
• Require Features to be a non‑empty array of unique strings.

Label	Description
Header	Genomic Processing Type Header, Standard “AIH‑GNT‑Vx.y”.
Domain	Constant value "Genomics". Processing Type applies exclusively to genomic data.
Operation	Specifies the genomics‑specific processing step. Enumerated list includes: QualityControl, Alignment, VariantCalling, VariantFiltering, Annotation, GeneExpressionQuantification, DifferentialExpression, CopyNumberAnalysis, HaplotypeReconstruction, EpigenomicProcessing.
QualityControl	Operation performing read‑level QC (quality checks, trimming, adapter removal).
Alignment	Operation mapping sequencing reads to a reference genome.
VariantCalling	Operation identifying SNPs, indels, or structural variants.
VariantFiltering	Operation filtering variants using quality thresholds or rules.
Annotation	Operation adding functional/clinical annotations to variants or genes.
GeneExpressionQuantification	Operation quantifying gene/isoform expression from RNA‑seq.
DifferentialExpression	Operation comparing expression levels across groups/conditions.
CopyNumberAnalysis	Operation detecting genomic amplifications or deletions (CNV).
HaplotypeReconstruction	Operation phasing variants into haplotypes.
EpigenomicProcessing	Operation analysing methylation or chromatin accessibility signals.
Method	Processing technique used to implement the operation. Must be one of: FastQC, Cutadapt, Trimmomatic, BWA, Bowtie2, STAR, HISAT2, GATK, FreeBayes, DeepVariant, ANNOVAR, VEP, Salmon, Kallisto, DESeq2, EdgeR, CNVkit.
Algorithm	String identifier or AlgorithmObject from CommonDefinitions. Represents the algorithm used.
AlgorithmObject.Name	Required algorithm name (e.g., “GATK‑HC”, “DeepVariant‑Model”).
AlgorithmObject.Version	Optional version identifier.
AlgorithmObject.Params	Free‑form object containing algorithm configuration parameters.
Algorithms	Array of Algorithm entries, each either a string ID or an AlgorithmObject.
FeatureClass	Category describing type of genomic features (e.g., variant features, expression features, CNV features).
Features	Non‑empty array of unique genomic feature names (e.g., SNP_Count, TPM_FoldChange, CNV_Events).
Trace	Provenance information and Time.
DescrMetadata	Descriptive Metadata