.. this Changelog is based on the merged pull requests involving the ````airr-schema.yaml```` file since Jan 9 2018 Schema Release Notes ================================================================================ Version 1.3.1: October 13, 2020 -------------------------------------------------------------------------------- **Version 1.3 documentation patch release.** Alignment Schema: 1. Added the deprecation tags for ``rearrangement_id``, which were accidentally left out of the v1.3.0 release. 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. .. 2. #296 by bussec was merged on Jan 4, 2020 3. #155 by bussec was merged on Oct 16, 2018 • Approved 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. .. 8. #257 by bcorrie was merged on Oct 7 • Approved 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``. .. 3. #254 by franasa was merged on Oct 11 • Approved 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. .. 2. #260 by bussec was merged on Nov 8, 2019; #281 Reverted ``locus_species`` by bcorrie was merged on Nov 27, 2019 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. .. 4. #288 by bussec was merged on Dec 10, 2019 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 .. 1. #153 by javh was merged on Sep 13 • Approved 2. #150 by schristley was merged on Aug 28 3. #221 by bussec was merged on Aug 7 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 .. 2. #134 by schristley was merged on Jul 12 3. #200 by bussec was merged on Jun 13 • Approved 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. .. 1. #182 by bussec was merged on Apr 1 • Approved 2. #182 by bussec was merged on Apr 1 • Approved 3. #182 by bussec was merged on Apr 1 • Approved 4. #182 by bussec was merged on Apr 1 • Approved 5. #182 by bussec was merged on Apr 1 • Approved 6. #182 by bussec was merged on Apr 1 • Approved 7. #182 by bussec was merged on Apr 1 • Approved 8. #182 by bussec was merged on Apr 1 • Approved 9. #156 by schristley was merged on Mar 4 • Approved 10. #156 by schristley was merged on Mar 4 • Approved 11. #156 by schristley was merged on Mar 4 • Approved 12. #156 by schristley was merged on Mar 4 • Approved 13. by schristley was merged on Mar 4 • Approved 14. in progress.. #124 by javh was merged on Apr 20 15. #106 by javh was merged on Apr 18, 2018 16. #106 by javh was merged on Apr 18, 2018 17. #94 on Mar 22, 2018 18. #94 on Mar 22, 2018 19. #94 on Mar 22, 2018 20. #78 on Jan 26, 2018 #53 21. #78 on Jan 26, 2018 #67 22. #75 on Jan 9, 2018. also: #84, #85, #89 23. #75 on Jan 9, 2018. also: #84,. #85,. #89 Version 1.0.1: Jan 9, 2018 -------------------------------------------------------------------------------- **MiAIRR v1 official release and initial draft of Rearrangement and Alignment schemas.**