About ONGA
ONGA (Ontology for Genomic Annotations) provides controlled vocabularies for describing genomic data files. It defines two complementary vocabularies: - DataType: Computational output types (HOW data was produced) - FeatureType: Biological feature types (WHAT biology it represents) A file's DataType describes its computational origin (e.g., "peaks" from a peak caller). A file's FeatureType describes what biological phenomenon it captures (e.g., "TF binding sites"). The same DataType can represent different FeatureTypes depending on the experiment.
The Problem
When you have a genomic data file (like a BED file), what does it actually contain? Is it peaks from ChIP-seq? ATAC-seq? IDR-filtered peaks? Methylation states? Signal tracks?
The ENCODE consortium developed approximately 310 internal terms for describing file contents ("output types"), but these terms aren't formalized as an ontology, lack definitions, and aren't easily usable outside ENCODE.
Existing ontologies like EDAM cover broad bioinformatics concepts but lack the granularity needed for real-world genomic file annotation.
The Solution
ONGA formalizes this vocabulary with:
- Hierarchical organization — 22 categories organizing 237 specific terms
- Proper definitions — Each term has a description explaining its meaning
- Ontology mappings — 86 terms mapped to EDAM, Sequence Ontology, and OBI where applicable
- Clear provenance — Terms track their source (ENCODE, UCSC, etc.)
- Extension mechanism — New terms can be proposed and reviewed
Scope
In Scope
- File content types — Peaks, signals, quantifications, matrices, references
- Biospecimen classifications — Cell line, primary cell, tissue, organoid (planned)
- Track geometry types — Points, segments, valued points, step functions (planned)
Out of Scope (use existing ontologies)
- File formats → EDAM format branch
- Assay types → OBI/EFO (ChIP-seq, ATAC-seq, etc.)
- Organisms → NCBITaxon
- Cell types → Cell Ontology (CL)
- Anatomical terms → UBERON
- Sequence features → Sequence Ontology (SO)
Technical Details
- Version
- 0.1.0
- License
- CC BY 4.0
- Namespace
- https://databio.org/onga/
- Format
- LinkML
- Created by
- Nathan Sheffield
- Created
- 2026-05-20
Links
- GitHub repository
- ENCODE Project — Source of output_type vocabulary
- EDAM Ontology — Target for upstream contribution
- LinkML — Schema language used
- SSSOM — Mapping standard used
Contact
For questions, suggestions, or to propose new terms, please open an issue on GitHub.