Clone Schema#

A Clone object groups a set of Rearrangements or Cells that are inferred to be related by common descent from a single naive ancestor. The member Rearrangements and Cells are referenced from Clone as an array of Nodes and can include inferred ancestors that were not directly observed. All members of a Clone must be from either a single RepertoireGroup or from a single Repertoire if a RepertoireGroup was not created.

A Node links members of a Clone to their original metadata and annotations.

File Format Specification#

Files are YAML/JSON with an AIRR Data File structure. Files should be encoded as UTF-8. Identifiers are case-sensitive. Files should have the extension .yaml, .yml, or .json.

File Structure#

The DataFile is a dictionary (key/value pair) structure with the keys Clone and Node.
The file can (optionally) contain an Info object, at the beginning of the file, based upon the Info schema in the OpenAPI V2 specification. If provided, version in Info should reference the version of the AIRR schema for the file.
The file should correspond to a list of Clone objects, using Clone as the key to the list.
The file should correspond to a list of Node objects, using Node as the key to the list.
Each Clone object should contain a top-level key/value pair for clone_id that uniquely identifies the clone and a top-level key/value pair for either repertoire_group_id or repertoire_id that identifies the source of the clone’s members.
Each Node object should contain top-level key/value pairs for node_id (uniquely identifies the node) and repertoire_id (identifies the source repertoire).
Some fields require the use of a particular ontology or controlled vocabulary.
The structure is the same regardless of whether the data is stored in a file or a data repository.

Schema Field Definitions#

Clone Fields#

Download as TSV

Name	Type	Attributes	Definition
`clone_id`	string	required, identifier	Identifier for the clone.
`repertoire_group_id`	string	required, nullable	Identifier of the RepertoireGroup that this Clone is derived from. If the Clone is derived from a single Repertoire, repertoire_id may be used instead.
`repertoire_id`	string	required, nullable	Identifier of the Repertoire that this Clone is derived from. Should only be used if Clones are calculated from a single Repertoire without defining a RepertoireGroup. Otherwise use repertoire_group_id instead.
`clone_class`	string	optional, nullable	Is this a single-chain clone or a cell-based clone?
`data_processing_id`	string	optional, nullable	Identifier of the data processing object in the repertoire metadata for this clone.
`nodes`	array of Node	required, nullable	List of Nodes that are members of this clone.
`inferred_ancestor`	string	optional, nullable	Node_id string that acts as a key to the Node record for the inferred naive Rearrangement or Cell for this clone.
`clone_count`	integer	optional, nullable	Absolute count of the size (number of members) of this clone in the repertoire. This could simply be the number of sequences (Rearrangement records) observed in this clone, the number of distinct cell barcodes (unique cell_id values), or a more sophisticated calculation appropriate to the experimental protocol. Absolute count is provided versus a frequency so that downstream analysis tools can perform their own normalization.
`seed_id`	string	optional, nullable	sequence_id or cell_id of the seed sequence/cell. Empty string (or null) if there is no seed sequence.
`tree`	string	optional, nullable	Newick string describing the tree.

Node Fields#