Receptor Schema (Experimental)#
General#
The purpose of the Receptor
object is to represent reactivity data
of actual Receptors, i.e., Ig or TCR, either directly or indirectly.
To this end, the Receptor
object has two main sections:
The
receptor_*
properties: These properties describe the receptor as an abstract and global concept, i.e., the actual Ig/TCR protein complex MAY or MAY NOT have been observed in the current study. However, the Rearrangements encoding the respective chains MUST be present in the studies as well as the information linking them (see below). This allows data curators to provide potential reactivities of a potential receptor by referencing to its entry in an external database (e.g., IEDB).The
reactivity_measurements
array: This structure contains one or more entries, describing reactivities of the receptor that have been observed in the current study.
The Receptor
object explicitly requires full sequence information
of the two associated variable domains. This is considered to be an
acceptable restriction from an AIRR-seq perspective, where sequencing
typically precedes or takes place in combination with the determination
of receptor reactivity.
Identifiers#
The Receptor
objects has two properties that serve as identifiers:
receptor_id
is a local identifier and its uniqueness MUST NOT be assumed beyond the scope of the study the receptor was reported in. This property can be used, e.g., to represent designations for Ig/TCR used in a manuscript.receptor_hash
is the SHA256 hash of the receptors variable domain amino acid sequences, which serves as a globally unique identifier that can be independently calculated by repositories without requiring prior communication. It is calculated as follows, wherebase16
designates the function described in RFC4648 Section 6:lower_case( base16( sha256( concatenate( upper_case(receptor_variable_domain_1_aa), upper_case(receptor_variable_domain_2_aa) ) ) ) )
Relations to other AIRR Schema objects#
The Receptor
object is only directly linked to the Cell
object,
which then in turn contains the references to the records in the
Rearrangements
that encode the respective chains of the receptor.
Therefore a given rearrangement cannot directly reference to a receptor,
which is also not a meaningful thing to do, as the paired chain would
be unclear, but is necessary to determine a receptors reactivity.
Annotation guidelines#
Reactivity information SHOULD be provided if it was either directly
recorded in the current study or is indirectly available in a public
database, where it can be linked. If no information about the receptor,
besides the translated amino acid sequence of the associated chains is
available, the respective object MAY still be created if the curator
considers this information to be beneficial, e.g., if there is some
evidence (surface expression, reaction to superantigens) that the
receptor is functional and present on the surface. In the absence of any
such data, Receptor
objects SHOULD NOT be created.
Note on cells expressing more than a single receptor#
Cells that express more than a single IGH/TRB/TRD or a single
IGK/IGL/TRA/TRG chain are regularly observered as allelic exclusion is
never complete and its efficiency is rather low for loci like TRA.
Such dual-expressing cells can technically be accommodated in the
current AIRR Schema as an individual Cell
object can link to more
than two rearrangemts and to more than a single Receptor
. In the
case of two potential receptors, both MAY be created as an objects, if
the general annotation rules are met (i.e., the direct or indirect
presence of reactivity information) for each of them. Note that the
annotation of cell-based reactivity information is currently not
supported for dual-expressing cells, in this case additional information
confirming the reactivity of one of the receptors would be required.
Representation of bi-specific antibodies#
The goal of the AIRR Standards is primarily to represent naturally
occuring receptors. While bi-specific antibodies may arise in
dual IGK/IGL expressing B cells their individual reactivity is
not measured on a regular basis. Therefore they are currently not
supported in the Receptor
schema.
Receptor Fields#
Name |
Type |
Attributes |
Definition |
---|---|---|---|
|
string |
required |
ID of the current Receptor object, unique within the local repository. |
|
string |
required |
The SHA256 hash of the receptor amino acid sequence, calculated on the concatenated |
|
string |
required |
The top-level receptor type, either Immunoglobulin (Ig) or T Cell Receptor (TCR). |
|
string |
required |
Complete amino acid sequence of the mature variable domain of the Ig heavy, TCR beta or TCR delta chain. The mature variable domain is defined as encompassing all AA from and including first AA after the the signal peptide to and including the last AA that is completely encoded by the J gene. |
|
string |
required |
Locus from which the variable domain in receptor_variable_domain_1_aa originates |
|
string |
required |
Complete amino acid sequence of the mature variable domain of the Ig light, TCR alpha or TCR gamma chain. The mature variable domain is defined as encompassing all AA from and including first AA after the the signal peptide to and including the last AA that is completely encoded by the J gene. |
|
string |
required |
Locus from which the variable domain in receptor_variable_domain_2_aa originates |
|
array of string |
optional, nullable |
Array of receptor identifiers defined for the Receptor object |
|
array of object |
optional, nullable |
Records of reactivity measurement |