Cell Reactivity Schema (Experimental)

The CellReactivity object contains information that describes the binding of a compound resembling an Ig or TCR antigen by a single, intact cell. It is critical to note that while such experimental measurements are related to the antigen reactivity of individual Receptors expressed by the cell, the relation is rather complex as multiple Receptor species, different expression levels and background binding of the compound would need to be taken into account. Therefore the AIRR Schema provides a separate record for this information, which is only indirectly linked (via Cell) to the Receptor object.

File Format Specification

The file format has not been specified yet.

Cell Reactivity Fields

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Name	Type	Attributes	Definition
cell_reactivity_id	string	required, identifier	Identifier for the CellReactivity object. This identifier must be unique within a given study, but it is recommended that it be a universally unique record locator to enable database applications.
cell_id	string	required	Identifier of the Cell in the context of which the reactivity measurement was conducted.
repertoire_id	string	optional, nullable	Identifier for the associated repertoire in study metadata.
data_processing_id	string	optional, nullable	Identifier of the data processing object in the repertoire metadata for this cell.
ligand_type	string	required	Classification of ligand binding to the cell
antigen_type	string	required	The type of antigen before processing by the immune system.
antigen	Ontology	required	The substance against which the receptor was tested. This can be any substance that stimulates an adaptive immune response in the host, either through antibody production or by T cell activation after presentation via an MHC molecule.
antigen_source_species	Ontology	optional, nullable	The species from which the antigen was isolated
peptide_start	integer	optional, nullable	Start position of the peptide within the reference protein sequence
peptide_end	integer	optional, nullable	End position of the peptide within the reference protein sequence
peptide_sequence_aa	string	optional, nullable	The actual peptide sequence against which the receptor reactivity was measured. This field should be used as a convenience for antigens of antigen_type protein or peptide.
mhc_class	string	optional, nullable	Class of MHC molecule, only present for MHC:x ligand types
mhc_gene_1	Ontology	optional, nullable	The MHC gene to which the mhc_allele_1 belongs
mhc_allele_1	string	optional, nullable	Allele designation of the MHC alpha chain
mhc_gene_2	Ontology	optional, nullable	The MHC gene to which the mhc_allele_2 belongs
mhc_allele_2	string	optional, nullable	Allele designation of the MHC class II beta chain or the invariant beta2-microglobin chain
reactivity_method	string	required	The methodology used to assess expression (assay implemented in experiment)
reactivity_readout	string	required	Reactivity measurement read-out
reactivity_value	number	required	The absolute (processed) value of the measurement
reactivity_unit	string	required	The unit of the measurement

Within the CellReactivity object, it is expected that the properties antigen_source_species, peptide_start, peptide_end and peptide_sequence_aa have an inseparable relationship with antigen_type. They only present a valid value when antigen_type is protein or peptide, otherwise they MUST contain a NULL value. In the former case, peptide_sequence_aa SHOULD present the actual peptide sequence of the protein used experimentally, while the antigen field SHOULD reference to a database entry of the protein from which the peptide was derived from. Both peptide_start and peptide_end indicate the (1-based) start and end location of peptide_sequence_aa in the reference sequence. Note that highly- repetitive proteins might contain the same peptide at multiple locations of their full-length sequence. While it is generally recommended to always use the position of the first occurence for the peptide_start and peptide_end annotation, this also stresses the importance to compare actual peptide sequences, not only coordinates.

The five MHC properties (mhc_*), which are specifically required for records in which ligand_type is MHC:peptide or MHC:non-peptide should be NULL for all other ligand_types.