1 Definition 2 Functional Requirements 3 Syntax 4 Semantics

1 Definition

A Genomics Omics Qualifier specifies metadata describing a Genomics Omics Data instance and providing information about:

  • the Sub‑Type of the genomics/omics data (e.g., whole‑genome sequencing variants, RNA‑seq expression matrix, methylation profiles, proteomics abundance tables),
  • the Format used to encode the data (e.g., VCF variant representation, FASTQ/BAM reads, TSV/CSV matrices, HDF5‑based assay containers), and

The combination of Behavioural Signal Data and Behavioural Signal Qualifier is called Behavioural Signal Object, specified by AIH-HSP V1.0.

2 Functional Requirements

  • Genomics Omics Sub‑Type Identification: The Genomics Omics Qualifier shall specify the Sub‑Type of the Genomics Omics Data.
  • Genomics Omics Format Identification: The Genomics Omics Qualifier shall specify the Format used to encode the Genomics Omics Data.
  • Separation from Data: The Genomics Omics Qualifier shall not contain intrinsic genomics/omics samples; it shall only describe the Genomics Omics Data.
  • Interpretability of Data: The Genomics Omics Qualifier shall provide sufficient information to interpret the Genomics Omics Data.

Users needing additional entries in the Physiological Signal Qualifier or support of new Qualifiers should make a documented request to the MPAI Secretariat. Requests will be considered by the appropriate MPAI committee.

3 Syntax

https://schemas.mpai.community/TFA/V1.5/data/GenomicsOmicsQualifier.json

4 Semantics

  1. Sub‑Types
    1. DNA‑Based Data
      Whole‑genome variants
      Whole‑exome variants
      Targeted panel variants
      Structural variants
      Copy‑number profiles
    2. RNA‑Based Data
      Gene‑expression matrix (bulk RNA‑seq)
      Transcript‑level quantification
      Splicing / junction counts
    3. Epigenomic Data
      Methylation array profiles
      Bisulfite sequencing profiles
    4. Proteomics Data
      Protein abundance profiles
      Peptide quantification tables
    5. Metabolomics Data
      Metabolite abundance profiles
  2. Formats
    1. DNA‑Based Formats
      VCF
      BCF
      FASTQ (raw reads)
      BAM / CRAM (aligned reads)
      TSV/CSV (variant tables)
    2. RNA‑Based Formats
      FASTQ (raw reads)
      BAM / CRAM
      TSV/CSV (gene‑expression matrices)
      HDF5 (e.g., assay containers)
    3. Epigenomic Formats
      IDAT (array raw files)
      TSV/CSV (processed methylation profiles)
      HDF5
    4. Proteomics Formats
      TSV/CSV (protein/peptide quantification)
      HDF5
    5. Metabolomics Formats
      TSV/CSV
      HDF5

5 References