MHC Restriction Ontology (MRO)

Download the latest release of MRO.

Download the development version of MRO.

We recommend Protégé 5 beta for viewing MRO in OWL format.

MHC molecules form a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology (MaHCO) and created MRO to represent MHC molecules as they relate to immunological experiments. MRO models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multichain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO Foundry. We link to well-established MHC nomenclature resources of the international ImMunoGeneTics information system (IMGT) for human data and The Immuno Polymorphism Database (IPD) for non-human species.

Vita et al., An Ontology for Major Histocompatibility Restriction, Journal of Biomedical Semantics, 2016.

This is work in progress. Here are some remaining tasks:

• model evidence codes
• have an expert review rat terms
• add sequences for the remaining chains, where possible
• review modelling with others ontology developers and domain experts
• add textual definitions and additional annotations

Build Instructions

We use ROBOT and GNU Make to build MRO from template files, applying the Quick Term Template (QTT) approach (see Overcoming the ontology enrichment bottleneck with Quick Term Templates).

The index.tsv contains the master list of MRO terms. The ontology/ directory contains template files, with one file for the core (upper-level) terms:

• core.tsv

and then one file per branch of the ontology:

• genetic-locus.tsv
• haplotype.tsv
• serotype.tsv
• chain.tsv
• molecule.tsv
• haplotype-molecule.tsv
• serotype-molecule.tsv
• mutant-molecule.tsv
• evidence.tsv
• chain-sequence.tsv

Two other files contain all remaining terms:

• import.txt lists the external ontology terms that we import
• external.tsv declares some external ontology terms

With GNU Make and ROBOT installed, building is as simple as running:

make

Testing

We use a combination of ROBOT and Python (3.x) scripts for validating the MRO outputs. Install the Python requirements:

python3 -m pip install -r requirements.txt

Then run:

make test

This will run the following checks:

• ROBOT report (writes to build/report.csv - fails on ERROR-level violations)
• ROBOT verify (writes query results to build/ - if any queries return results, this is an error)
• validation of iedb/mhc_allele_restriction.tsv table (writes errors to build/mhc_allele_restriction_errors.tsv)

The build will fail on any error from these steps.