Appendix A: Key Terms

The following table provides definitions for terms and abbreviations relevant to this documentation.

Definitions and abbreviation

Term	Abbreviation	Retired synonyms	Definition
Adaptive Immune Receptor Repertoire	AIRR		A collection of vertebrate immune receptors whose loci typically undergo RAG-mediated rearrangement, i.e., immunoglobulins and T cell receptors.
AIRR Community	AIRR-C		The Adaptive Immune Receptor Repertoire Community is a grassroots collaboration for developing and promoting best practices for generating, analyzing, curating, and sharing AIRR-seq data, see [DOI:10.3389/fimmu.2017.01418]. As of 12/2017, AIRR-C became a Committee within The Antibody Society (TAbS) and is therefore also known as “The AIRR Community Committee within The Antibody Society”.
AIRR Community Standards	AIRR-C Standards	AIRR Standards	The collection of all norms, including standards, guidelines, best practices, recommendations and definitions, which have been developed and published by the AIRR Community, in their respective current version.
AIRR Data Commons	ADC		The network of data repositories, which make AIRR-seq data FAIR by implementing the ADC API, adhering to the MiAIRR metadata standard and provide data in an AIRR Format.
AIRR Data Commons Application Program Interface	ADC API		The standard defining how AIRR-seq data located in a repository can be programmatically searched and retrieved.
AIRR Data Schema			The formal definition of all specified properties of an AIRR-seq study. This includes groupings of properties, relations between properties and the permissible representations of property values.
AIRR Formats		AIRR Data Representation	The collection of definitions of on-disk and/or in-transit representation of the entities specified in the AIRR Data Schema and in MiAIRR.
AIRR Sequencing	AIRR-seq		The experimental observation of an Adaptive Immune Receptor Repertoire by means of nucleic acid sequencing.
API			Application Programming Interface
CAIRR			CEDAR AIRR
CEDAR			Center for Expanded Data Annotation and Retrieval
Clone			[biological definition] A group of B or T cells that are all descended from the same naive ancestal cell and carry the same rearrangements. In B cells, the Ig sequence may vary between members of a Clone due to somatic hypermutation. To indicate this fact, the term “clonal linage” is preferred by some researchers. 2) [informatic defintion] The informatic representation of the biological clone.
FAIR			The acronym for “Findable, Accessible, Interoperable, Reusable”, a set of principles to facilitate the reuse of research data, defined by Wilkinson et al. (2016).
HTTP			Hypertext Transfer Protocol
JSON			JavaScript Object Notation
MiAIRR			The acronym for “Minimal Information about an Adaptive Immune Receptor Repertoire study”, the AIRR Community-defined set of properties on which information must or should be provided to allow for the meaningful interpretation of the data. MiAIRR was originally specified in [DOI:10.1038/ni.3873] and continuous to be further developed in AIRR Community Git repository [https://github.com/airr-community/airr-standards]. It should be noted that the current version of MiAIRR is a complete subset of the AIRR Data Schema definitions.
Rearrangement			[biological definition] The physical combination of V and J or V, D, and J genes into a complete IG or TR. 2) [informatic definition] The representation of a biological rearrangement, which is obtained through sequencing and annotated with features, such as gene calls, from data processing.
REST			Representational State Transfer
TSV			Tab Separated Values
URL			Universal Resource Locator
YAML			YAML Ain’t Markup Language