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AIRR Community Terminology

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Definitions

AIRR Community

  • Adaptive Immune Receptor Repertoire (AIRR) [restricted]: A collection of vertebrate immune receptors whose loci typically undergo RAG-mediated rearrangement, i.e., immunoglobulins and T cell receptors.
  • AIRR Community (AIRR-C) [restricted]: 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 Leadership (AIRR-C Leadership): The group of persons who serve as either members of the AIRR Community Executive SC and/or co-leads of any other AIRR Community WG or SC.
  • AIRR Community Meeting (AIRR-C Meeting): The official meeting of the AIRR Community at which the General Assembly convenes. These meetings are held approximately every 18 months.
  • AIRR Community Member (AIRR-C Member): An individual whose AIRR Community membership application has been approved and has not been terminated and who is not in arrears with his/her annual membership fee.
  • AIRR Community Standards (AIRR-C Standards) (previously: AIRR Standards) [restricted]: 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) [restricted]: 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) [restricted]: The standard defining how AIRR-seq data located in a repository can be programmatically searched and retrieved.
  • AIRR Data Schema [restricted]: 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 (previously: AIRR Data Representation) [restricted]: 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.
  • Interval: The period between two consecutive AIRR Community Meetings.
  • MiAIRR [restricted]: 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 continues 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.
  • Sub-committee (SC): A formally established group within the AIRR Community to address continuous or repetitive duties of high organizational relevance to the AIRR Community. Sub-committees consist of one or more Co-Leaders and additional individuals, all of whom are required to be AIRR Community Members.
  • Working Group (WG): A formally established group within the AIRR Community, which has received a mandate from the General Assembly to work on a specified topic on behalf of the AIRR Community. Participation in working groups is open to all interested individuals, an AIRR Community membership is not required. Working groups are chaired by one or more (Co)-leaders, at least one of which is required to be an AIRR Community Member. Working groups focus on a set of specified goals and will be disbanded when these goals are accomplished.
  • Working Group Participant (WG Participant): An individual who regularly attends WG conference calls, contributes ideas or other information to the WG and takes part in the generation of working group products. Participant status is independent of AIRR Community Membership. The determination of which individuals of a WG are considered to be Participants is made by the WG (Co-)leads in consultation with other Participants of the WG. Subscription to a WG's mailing list is typically not a sufficient criterion to be considered as a Participant.

Biology

  • Antibody (Ab): A soluble protein consisting of n Ig heavy / Ig light heterotetramers (with n typically being 1, 2 or 5, depending on the isotype) plus the optional J chain (IgM & IgA) and the secretory component (IgA).
  • B cell receptor (BCR): A protein complex on the cell surface encompassing Ig heavy / Ig light heterotetramers and the associated signal transduction components (e.g., Igα and Igβ).
  • Clonal expansion: The proliferation of an individual T or B cell that gives rise to a Clone.
  • Clonal lineage: See Clone.
  • Complementarity determining region (CDR): The complementarity determining regions of an Ig or TCR are the protein loops that are mainly responsible for the interaction with an antigen. There are three CDRs in total (CDR1-3) of which CDR3 is encoded by the junction of the V(D)J rearrangement.
  • Constant region (C region): The constant region of IG or TR genes. For IGH, multiple C regions exist, which encode different isotypes, e.g., IgD, IgG1, IgA2.
  • Framework region (FWR, FR): The framework regions of an Ig or TCR, which generally correspond to the beta strands forming the core of the variable domain.
  • Immunoglobulin (Ig, IG): Can refer to the locus, rearranged gene, transcript, polypeptide or as an umbrella term also to BCRs and antibodies. Note that while "Ig" is a general abbreviation, "IG" specifically refers to the nucleic acids that encode any of the Ig chains.
  • Public clone: A set of rearrangements from multiple individuals all using the same V and J genes and having high sequence identity in CDR3. Technically they are convergent rearrangements rather than a true clone. Suggestive of functional selection.
  • T cell receptor (TCR): A protein complex on the cell surface encompassing the TCRα/β or TCRγ/δ heterodimers and the CD3 signal transduction components.
  • TR: The nucleic acids that encode any of the TCR chains.
  • Unique molecular identifier (UMI): A stretch of random or semi-random nucleotides used to uniquely label each original molecule input into a PCR reaction. Sequences with the same UMI can be collapsed to allow sequencing error correction and quantification.
  • V(D)J: The genetic makeup of a rearranged IG or TR. All loci include variable (V) and joining (J) genes; in addition, the IGH, TRB, and TRD loci also include diversity (D) genes.

mixed (Bio/IT)

  • Clone: Multiple definitions:
    1. [biology] 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. [data] The informatic representation of the biological clone.
  • Repertoire: Multiple definitions:
    1. [biology] Currently undefined due to lack of consensus.
    2. [data] The informatic representation of the biological repertoire.
  • Rearrangement: Multiple definitions:
    1. [biology] The physical combination of V and J or V, D, and J genes into a complete IG or TR.
    2. [data] The representation of a biological rearrangement, which is obtained through sequencing and annotated with features, such as gene calls, from data processing.

Abbreviations

IT-related

  • API: Application Programming Interface
  • HTTP: Hypertext Transfer Protocol
  • JSON: JavaScript Object Notation
  • REST: Representational State Transfer
  • TSV: Tab Separated Values
  • URL: Universal Resource Locator
  • YAML: YAML Ain't Markup Language

other

  • CAIRR: CEDAR AIRR
  • CEDAR: Center for Expanded Data Annotation and Retrieval
  • 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).
  • TAbS: The Antibody Society is an international, non-profit association representing individuals and organizations involved in antibody-related research and development.

Footnotes

[restricted](1, 2, 3, 4, 5, 6, 7, 8)

There is a small but important set of terms that either designate AIRR-C WG products or are obviously linked to the identity of the ai. Consistent use of these terms both within AIRR-C as well as to the larger community is important to facilitate clear and unambiguous communication. Therefore, the terms marked as restricted in this document, shall be used if and only if they reference an entity that matches the terms definition. Conversely,

  1. terms that are synonymous to restricted terms, or
  2. terms that are obvious derivatives of a restricted term, or
  3. changes to the meaning of a restricted term, including the narrowing or broadening of its meaning,

shall be avoided. Authors that seek AIRR-C endorsement for any kind of document must confirm that they acknowledge and comply with these conditions. They can include a waiver for specific terms from the responsible WG/SC a priori. Specific complaints about potential non-compliance that arise during the endorsement process will be heard by Exec and will halt the endorsement process until Exec considers them to be resolved.