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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.

Sprint Reports

• Report Sprint 11/2018
  • Objectives
  • General Considerations
  • Criteria for Ontologies
  • Selected Ontologies
  • Technical aspects
  • Footnotes
  • Appendix
• Report Sprint 04/2020
  • Objectives
  • General Policies
  • Decisions on Pending Items of Sprint 11/2018
  • New Ontologies
  • Technical Questions
  • Modifications to the AIRR schema
  • Clarifications
  • Annotation guidance

Approved Ontologies

• Cell ontology (CL)

  • used in:

    • Cell subset (cell_subset, Tissue and Cell Processing)

  • 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:

    • Diagnosis (disease_diagnosis, Diagnosis)

  • 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:

    • Species (species, Subject)

    • Cell species (cell_species, Tissue and Cell Processing)

  • 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)

  • 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:

    • Age unit (age_unit, Subject)

  • 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:

    • Tissue (tissue, Sample)

  • 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