Release Notes

Version 1.3.0: May 28, 2020

Version 1.3 schema release.

  • Added EBI OLS as default source for ontologies

  • Expanded description for pcr_target

  • Fix capitalization of age_unit description

  • Fix name of age fields

  • Introduced cell_species

  • Added sample_processing_id

  • Added vocabularies/ontologies as JSON string for: Cell subset, Target substrate, Library generation method, Complete sequences, Physical linkage of different loci

  • Include format JSON string

  • Introduced age ranges, age_min, age_max, and age_unit

  • Updated schema with more concise VDJ call descriptions

Version 1.2.1: Oct 5, 2018

Minor patch release.

  • Schema gene vs segment terminology corrections

  • Added Info object

  • Updated cell_subset URL in AIRR schema

Version 1.2.0: Aug 18, 2018

Peer reviewed released of the Rearrangement schema.

  • Definition change for the coordinate fields of the Rearrangement and Alignment schema. Coordinates are now defined as 1-based closed intervals, instead of 0-based half-open intervals (as previously defined in v1.1 of the schema).

  • Removed foreign study_id fields

  • Introduced keywords_study field

Version 1.1.0: May 3, 2018

Initial public released of the Rearrangement and Alignment schemas.

  • Added required and nullable constrains to AIRR schema.

  • Schema definitions for MiAIRR attributes and ontology.

  • Introduction of an x-airr object indicating if field is required by MiAIRR

  • Rename rearrangement_set_id to data_processing_id

  • Rename study_description to study_type

  • Added physical_quantity format

  • Raw sequencing files into separate schema object

  • Rename Attributes object

  • Added primary_annotation and repertoire_id

  • Added diagnosis to repertoire object

  • Added ontology for organism

  • Added more detailed specification of sequencing_run, repertoire and rearrangement

  • Added repertoire schema

  • Rename definitions.yaml to airr-schema.yaml

  • Removed c_call, c_score and c_cigar from required as this is not typical reference aligner output

  • Renamed vdj_score, vdj_identity, vdj_evalue, and vdj_cigar to score, identity, evalue, and cigar

  • Added missing c_identity and c_evalue fields to Rearrangement spec

  • Swapped order of N and S operators in CIGAR string

  • Some description clean up for consistency in Rearrangement spec

  • Remove repeated objects in definitions.yaml

  • Added Alignment object to definitions.yaml

  • Updated MiARR format consistency check TSV with junction change

  • Changed definition from functional to productive

Version 1.0.1: Jan 9, 2018

MiAIRR v1 official release and initial draft of Rearrangement and Alignment schemas.