On December 7th, 2022 the iReceptor Platform, including all of the repositories used in the platform, moved to iReceptor v4.0. iReceptor v4.0 uses the new v1.4 release of the AIRR Specification and the associated AIRR Data Commons (ADC) query API v1.2. As a result, some of the fields (and their content) stored in the repositories and displayed through the iReceptor Scientific Gateway have changed. These changes apply to all repositories. Data that is downloaded from these repositories directly or through the iReceptor Gateway will also contain these changes, and therefore care should be used when comparing data that was downloaded before and after this change. All deprecated fields in the AIRR specification still exist in the specification but are marked as deprecated. For more information on these changes, please refer to the AIRR Specification v1.4 Release Notes.
A comprehensive list of the data provenance changes of moving from iReceptor v3.0 to iReceptor v4.0 are listed below:
- The controlled vocabulary for keywords_study has been extended to the following set: contains_ig, contains_tr, contains_paired_chain, contains_schema_rearrangement, contains_schema_clone, contains_schema_cell, contains_schema_receptor
- Modified the type of the template_amount field from a string to a number
- Added the required field template_amount_unit defining the units for the input template quantification. This is an ontology field from the Unit Ontology and contains a label and an Ontology ID
- Modified the type of the field collection_time_point_relative from a string to a number
- Added the required field collection_time_point_relative_unit defining the units for the sample collection This is an ontology field from the Unit Ontology and contains a label and an Ontology ID
- Support for the following required (nullable) fields has been added: sequencing_data_id, germline_set_ref, index_filename, index_length
In addition to the above changes to existing data in the AIRR Data Commons, we are please to announce the addition of a range of new data entities in the AIRR Data Commons. This includes the ability to store, search, and analyze Single Cell immune profiling data include paired chain Cell objects and gene expression (e.g. from the 10X cell ranger pipeline), as well as Clones, Immune Receptor Genotype, and MHC Genotype.