Appendix A: Key Terms#
The following table provides definitions for terms and abbreviations relevant to this documentation.
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 |
|
||
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. |
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Rearrangement |
|
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REST |
Representational State Transfer |
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TSV |
Tab Separated Values |
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URL |
Universal Resource Locator |
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YAML |
YAML Ain’t Markup Language |