Release Notes

Under development (Version 1.3.0)

Current changes in the development branch.

  • 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.