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Schema Release Notes

Version 1.3.0: May 28, 2020

Version 1.3 schema release.

New Schema:

  1. Introduced the Repertoire Schema for describing study meta data.

  2. Introduced the PCRTarget Schema for describing primer target locations.

  3. Introduced the SampleProcessing Schema for describing experimental processing steps for a sample.

  4. Replaced the SoftwareProcessing schema with the DataProcessing schema.

  5. Introduced experimental schema for clonal clusters, lineage trees, tree nodes, and cells as Clone, Tree, Node, and Cell objects, respectively.

General Updates:

  1. Added multiple additional attributes to a large number of schema propertes as AIRR extension attributes in the x-airr field. The new Attributes object contains definitions for these x-airr field attributes.

  2. Added the top level required property to all relevant schema objects.

  3. Added the title attribute containing the short, descriptive name to all relevant schema object fields.

  4. Added an example attribute containing an example data value to multiple schema object fields.

AIRR Data Commons API:

  1. Added OpenAPI V2 specification (specs/adc-api.yaml) for AIRR Data Commons API major version 1.

Ontology Support:

  1. Added Ontology and CURIEResolution objects to support ontologies.

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

Rearrangement Schema:

  1. Added the complete_vdj field to annotate whether a V(D)J alignment was full length.

  2. Added the junction_length_aa field defining the length of the junction amino acid sequence.

  3. Added the repertoire_id, sample_processing_id, and data_processing_id fields to serve as linkers to the appropriate metadata objects.

  4. Added a controlled vocabulary to the locus field: IGH, IGI, IGK, IGL, TRA, TRB, TRD, TRG.

  5. Deprecated the rearrangement_set_id and germline_database fields.

  6. Deprecated rearrangement_id field and made the sequence_id field be the primary unique identifer for a rearrangement record, both in files and data repositories.

  7. Added support secondary D gene rearrangement through the additional fields: d2_call, d2_score, d2_identity, d2_support, d2_cigar np3, np3_aa, np3_length, n3_length, p5d2_length, p3d2_length, d2_sequence_start, d2_sequence_end, d2_germline_start, d2_germline_start, d2_alignment_start, d2_alignment_end, d2_sequence_alignment, d2_sequence_alignment_aa, d2_germline_alignment, d2_germline_alignment_aa.

  8. Updated field definitions with more concise V(D)J call descriptions.

Alignment Schema:

  1. Deprecated the rearrangement_set_id and germline_database fields.

  2. Added the data_processing_id field.

Study Schema:

  1. Added the study_type field containing an ontology defined term for the study design.

Subject Schema:

  1. Deprecated the organism field in favor of the new species field.

  2. Deprecated the age field.

  3. Introduced age ranges: age_min, age_max, and age_unit.

Diagnosis Schema:

  1. Changed the type of the disease_diagnosis field from string to Ontology.

Sample Schema:

  1. Changed the type of the tissue field from string to Ontology.

CellProcessing Schema:

  1. Changed the type of the cell_subset field from string to Ontology.

  2. Introduced the cell_species field which denotes the species from which the analyzed cells originate.

NucleicAcidProcessing Schema:

  1. Defined the template_class field as type string.

  2. Added a controlled vocabulary the library_generation_method field.

  3. Changed the controlled vocabulary terms of complete_sequences. Replacing complete & untemplated with complete+untemplated and adding mixed.

  4. Added the pcr_target field referencing the new PCRTarget schema object.

SequencingRun Schema:

  1. Added the sequencing_run_id field which serves as the object identifer field.

  2. Added the sequencing_files field which links to the RawSequenceData schema objects defining the raw read data.

RawSequenceData Schema:

  1. Added the file_type field defining the sequence file type. This field is a controlled vocabulary restricted to: fasta, fastq.

  2. Added the paired_read_length field defining mate-pair read lengths.

  3. Defined the read_direction and paired_read_direction fields as type string.

DataProcessing Schema:

  1. Replaces the SoftwareProcessing object.

  2. Added data_processing_id, primary_annotation, data_processing_files, germline_database and analysis_provenance_id fields.

Version 1.2.1: Oct 5, 2018

Minor patch release.

  1. Schema gene vs segment terminology corrections

  2. Added Info object

  3. Updated cell_subset URL in AIRR schema

Version 1.2.0: Aug 18, 2018

Peer reviewed released of the Rearrangement schema.

  1. 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).

  2. Removed foreign study_id fields

  3. Introduced keywords_study field

Version 1.1.0: May 3, 2018

Initial public released of the Rearrangement and Alignment schemas.

  1. Added required and nullable constrains to AIRR schema.

  2. Schema definitions for MiAIRR attributes and ontology.

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

  4. Rename rearrangement_set_id to data_processing_id.

  5. Rename study_description to study_type.

  6. Added physical_quantity format.

  7. Raw sequencing files into separate schema object.

  8. Rename Attributes object.

  9. Added primary_annotation and repertoire_id.

  10. Added diagnosis to repertoire object.

  11. Added ontology for organism.

  12. Added more detailed specification of sequencing_run, repertoire and rearrangement.

  13. Added repertoire schema.

  14. Rename definitions.yaml to airr-schema.yaml.

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

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

  17. Added missing c_identity and c_evalue fields to Rearrangement spec.

  18. Swapped order of N and S operators in CIGAR string.

  19. Some description clean up for consistency in Rearrangement spec.

  20. Remove repeated objects in definitions.yaml.

  21. Added Alignment object to definitions.yaml.

  22. Updated MiARR format consistency check TSV with junction change.

  23. 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.

OntoVoc Report - Sprint 04/2020 Data Submission and Query