Contents

AIRR Ontologies and Vocabularies Team

Summary

The “Ontologies and Vocabularies Team” was formed as a joint interest group of the Common Repository (ComRepo) and the Minimal Standards (MiniStd) working groups of the AIRR Community. The long-term aim of the Team is to define standard vocabularies and ontologies to be used by AIRR-compliant databases.

Ontology Data Representation

The nodes in an ontology are typically either concepts (e.g., capital) or instances thereof (e.g., Paris). These nodes have local IDs (often numbers), which are unique within an ontology. They also typically have labels, which is the human-readable name of the node. Ontology entities in the AIRR Data Standard reflect this model, with each AIRR field that is represented as an ontology recorded with a global ontology ID (id) and the corresponding label (label).

Within the AIRR Standards, Compact URIs (CURIEs) are used to represent ontology IDs. CURIEs are a standardized way to abbreviate International Resource Identifiers (IRI, [RFC3987]), which includes URIs as a subset. They were originally conceived to simplify the handling of attributes, e.g. in XML or SPARQL, by making them more compact and readable. CURIEs are also used by IEDB databases to reduce redundancies (mainly in the leading part of IRIs).

For example, a typical CURIE would look like NCBITAXON:9258. In this case, NCBITAXON is the prefix, a custom string that will be replaced by a repository-defined IRI component (e.g., http://purl.obolibrary.org/obo/NCBITaxon_). Note that there is no connection between NCBITAXON in the CURIE and NCBITaxon in the IRI, the former one is just a placeholder.

The AIRR schema will provide a list of AIRR approved CURIE prefixes along with a list of at least one IRI prefix (i.e., replacement string) for each them. This list serves two purposes:

  1. It provides a controlled namespace for CURIE prefixes used in the AIRR schema. For now, custom additions to or replacements of these prefixes in the schema are prohibited. This does not affect the ability of repositories to use such custom prefixes internally.

  2. It simplifies resolution of CURIEs by non-repositories. The lists of IRI prefixes for each CURIE prefix should not be considered to be exhaustive. However, when using custom IRI prefixes, it must be ensured that they refer to the same ontology as the provider prefixes.

It should be explicitly noted that the IRI prefix list should not be interpreted as any kind of recommendation for certain providers. It is left up to users to decide how to resolve the resulting IRIs, e.g., via DNS/HTTP (if possible) or by using a provider of their choice.

Approved Ontologies

  • Cell ontology (CL)

    • used in:

    • CURIE summary

      • CURIE Prefix: CL

      • CURIE IRI Prefix: http://purl.obolibrary.org/obo/CL_

    • example AIRR use

      • “cell_subset.id” : “CL:0000542”

      • “cell_subset.label” : “lymphocyte”

    • default root node

      • label: lymphocyte

      • local id: CL_0000542

      • path: ``

    • license: CC BY

    • latest release (as of 2020-05-20): 2020-03-02

    • repo: https://github.com/obophenotype/cell-ontology

    • maintainer: Alexander Diehl, Buffalo, NY, US (addiehl@buffalo.edu)

  • Human disease ontology (DOID)

    • used in:

    • CURIE summary

      • CURIE Prefix: DOID

      • CURIE IRI Prefix: http://purl.obolibrary.org/obo/DOID_

    • example AIRR use

      • “disease_diagnosis.id” : “DOID:9538”

      • “disease_diagnosis.label” : “multiple myeloma”

    • default root node

      • label: disease

      • local ID: DOID:4

      • path: disease

    • license: CC0

    • latest release (as of 2020-05-20): 2020-04-20

    • repo: https://github.com/DiseaseOntology/HumanDiseaseOntology

    • maintainer: Lynn Schriml, U Maryland, MD, US (lynn.schriml@gmail.com)

    • notes: Features ICD cross-reference

  • NCBI organismal taxonomy (NCBITAXON)

    • used in:

    • CURIE summary

      • CURIE Prefix: NCBITAXON

      • CURIE IRI Prefixes: http://purl.obolibrary.org/obo/NCBITaxon_, http://purl.bioontology.org/ontology/NCBITAXON/

    • example AIRR use

      • “species.id” : “NCBITAXON:9606”

      • “species.label” : “Homo sapiens”

    • default root node

      • label: Gnathostomata

      • local ID: 7776

      • path: cellular organisms/Eukaryota/Opisthokonta/Metazoa/Eumetazoa/Bilateria/Deuterostomia/Chordata/Craniata/Vertebrata/Gnathostomata

    • license: UMLS

    • latest release (as of 2020-05-20): 2020-04-18

    • repo: https://github.com/obophenotype/ncbitaxon

    • maintainer: NCBI (info@ncbi.nlm.nih.gov)

  • NCI thesaurus (NCIT)

    • used in:

      • Study type (study_type, Study)

    • CURIE summary

      • CURIE Prefix: NCIT

      • CURIE IRI Prefixes: http://purl.obolibrary.org/obo/NCIT_, http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#

    • example AIRR use

      • “study_type.id” : “NCIT:C15197”

      • “study_type.label” : “Case-Control Study”

    • default root node

      • label: Study

      • local ID: C63536

      • path: Activity/Clinical or Research Activity/ Research Activity/Study

    • license: Public domain, credit of NCI is requested

    • repo: https://github.com/NCI-Thesaurus/thesaurus-obo-edition

    • latest release (as of 2020-05-20): 2020-05-04

    • maintainer: NCI (ncicbiitappssupport@mail.nih.gov)

  • Units of measurement ontology (UO)

    • used in:

    • CURIE summary

      • CURIE Prefix: UO

      • CURIE IRI Prefix: http://purl.obolibrary.org/obo/UO_

    • example AIRR use

      • “age_unit.id” : “UO:0000036”

      • “age_unit.label” : “year”

    • default root node

      • label: time unit

      • local ID: UO_0000003

      • path: unit/time unit

    • license: CC BY (per Github repo)

    • repo: https://github.com/bio-ontology-research-group/unit-ontology

    • latest release (as of 2020-05-20): 2020-05-18

    • maintainer: unknown

  • Uber-anatomy ontology (Uberon)

    • used in:

    • CURIE summary

      • CURIE Prefix: UBERON

      • CURIE IRI Prefix: http://purl.obolibrary.org/obo/UBERON_

    • example AIRR use

      • “tissue.id” : “UBERON:0002371”

      • “tissue.label” : “bone marrow”

    • default root node

      • label: multicellular anatomical structure

      • local ID: UBERON:0010000

      • path: /BFO_0000002/BFO_0000004/anatomical entity/material anatomical entity/anatomical structure/multicellular anatomical structure

    • license: CC BY

    • repo: https://github.com/obophenotype/uberon

    • latest release (as of 2020-05-20): 2019-11-22

    • maintainer: Chris Mungall, LBL, CA, US (cjmungall@lbl.gov)

AIRR Data Commons API V1 OntoVoc Report - Sprint 11/2018