Ontologies & Terminologies
RareLink uses a variety of ontologies and terminologies to standardise the representation of data and facilitate interoperability between different data sources. These ontologies and terminologies are used to describe the phenotypic and genotypic features of rare diseases (RDs) and their associated genes, as well as the relationships between them. The use of standardised vocabularies ensures that data can be easily integrated and queried across different databases and platforms.
- Terminology:
refers to a collection of preferred or officially recognized terms within a specific domain. In the medical field, one of the most significant terminologies for information retrieval is the Medical Subject Headings (MeSH), which serves as a framework for indexing and searching literature in Medline.
- Ontologies:
…on the other hand, go beyond mere vocabulary. They establish and define relationships between concepts, enabling computational reasoning and inference.
Tip
For more detail please read: Classification, Ontology, and Precision Medicine (Haendel MA et al., 2018)
Ontologies used in RareLink
The following codesystems are used in the RareLink Core Framework:
- ICD-10 & ICD-11:
The International Statistical Classification of Diseases is used for documenting morbidity in healthcare systems, encoding mortality statistics, and billing purposes. The ICD-11 encodes rare diseases more comprehensively.
- ORDO:
The Orphanet Rare Disease Ontology is an open-access ontology for rare diseases enabling queries of rare disorders and capturing relationships between diseases.
- MONDO:
The Monarch Initiative Disease Ontology aims to harmonize disease definitions across the world. It is a semi-automatically constructed ontology merging multiple disease resources.
- OMIM:
Online Mendelian Inheritance in Man is an authoritative catalogue focusing on genetic variation and phenotypic expressions. While OMIM_g codes refer to specific genes, OMIM_p codes refer to phenotypes or clinical manifestations associated with genetic disorders.
- SNOMED CT:
The Systematized Nomenclature of Medicine Clinical Terms is a comprehensive clinical healthcare terminology providing codes, terms, and definitions used in documentation.
- LOINC:
Logical Observation Identifiers Names and Codes is widely used terminology for clinical observations and laboratory findings by providing identifiers.
- UO:
The Units of Measurement Ontology is an ontology for units of measurement used in scientific data.
- NCBITaxon:
The NCBI Taxonomy is a hierarchical classification of living organisms.
- HGNC:
The Human Genome Organisation - Gene Nomenclature Committee approves unique symbols and names for human loci.
- HGVS:
The Human Genome Variation Society provides guidelines for cataloguing variations in DNA, RNA, and protein sequences.
- NCIT:
The National Cancer Institute Thesaurus is a reference terminology for cancer and biomedical research.
- GENO:
The Genotype Ontology is an ontology for describing genetic variation and related concepts.
- SO:
The Sequence Ontology provides standardized vocabulary for genomic annotation components, enhancing sharing and analysis of genomic information.
- MAXO:
The Medical Action Ontology (MAxO) provides a structured vocabulary for medical procedures, interventions, therapies, and treatments for disease with an emphasis on rare disease (RD). MAxO provides a vocabulary to annotate diseases and phenotypes with recommended treatments and interventions.
Note
The versions used by the RareLink Core Framework can be found here: RareLink Ontologies.
Further Reading
The Sequence Ontology: a tool for the unification of genome annotations
Ordo: an ontology connecting rare disease, epidemiology and genetic data
A 20-year evaluation of LOINC in the United States’ largest integrated health system
HGVS recommendations for the description of sequence variants: 2016 update