MiAIRR Data Elements

The AIRR Community has agreed to six high-level data sets that will guide the publication, curation and sharing of AIRR-Seq data and metadata: Study and subject, sample collection, sample processing and sequencing, raw sequences, processing of sequence data, and processed AIRR sequences.

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Set / Subset	Designation / Field	Type / Format	Level	Definition	Example
1 / study	Study ID study_id	string free text	important	Unique ID assigned by study registry such as one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.	PRJNA001
1 / study	Study title study_title	string free text	important	Descriptive study title	Effects of sun light exposure of the Treg repertoire
1 / study	Study type study_type	Ontology Ontology: { top_node: { id: NCIT:C63536, label: Study}}	important	Type of study design	id: NCIT:C15197, label: Case-Control Study
1 / study	Study inclusion/exclusion criteria inclusion_exclusion_criteria	string free text	important	List of criteria for inclusion/exclusion for the study	Include: Clinical P. falciparum infection; Exclude: Seropositive for HIV
1 / study	Grant funding agency grants	string free text	important	Funding agencies and grant numbers	NIH, award number R01GM987654
1 / study	Contributors contributors	array of Contributor **	essential	List of individuals who contributed to the study. Note that these are not necessarily identical with the authors on an associated manuscript or other scholarly communication. Further note that typically at least the three CRediT contributor roles “supervision”, “investigation” and “data curation” should be assigned. The coresponding author should be listed last.
1 / study	Relevant publications pub_ids	array of string **	important	Array of publications describing the rationale and/or outcome of the study as an array of CURIE objects such as a DOI or Pubmed ID. Where more than one publication is given, if there is a primary publication for the study it should come first.	[‘PMID:29144493’, ‘DOI:10.1038/ni.3873’]
1 / study	Keywords for study keywords_study	array of string **	important	Keywords describing properties of one or more data sets in a study. “contains_schema” keywords indicate that the study contains data objects from the AIRR Schema of that type (Rearrangement, Clone, Cell, Receptor) while the other keywords indicate that the study design considers the type of data indicated (e.g. it is possible to have a study that “contains_paired_chain” but does not “contains_schema_cell”).	[‘contains_ig’, ‘contains_schema_rearrangement’, ‘contains_schema_clone’, ‘contains_schema_cell’]
1 / subject	Subject ID subject_id	string free text	important	Subject ID assigned by submitter, unique within study. If possible, a persistent subject ID linked to an INSDC or similar repository study should be used.	SUB856413
1 / subject	Synthetic library synthetic	boolean true | false	essential	TRUE for libraries in which the diversity has been synthetically generated (e.g. phage display)
1 / subject	Organism species	Ontology Ontology: { top_node: { id: NCBITAXON:7776, label: Gnathostomata}}	essential	Binomial designation of subject’s species	id: NCBITAXON:9606, label: Homo sapiens
1 / subject	Sex sex	string free text	important	Biological sex of subject	female
1 / subject	age	TimeInterval **	important	Age of subject expressed as a time interval. If singular time point then min == max in the time interval.
1 / subject	Age event age_event	string free text	important	Event in the study schedule to which Age refers. For NCBI BioSample this MUST be sampling. For other implementations submitters need to be aware that there is currently no mechanism to encode to potential delta between Age event and Sample collection time, hence the chosen events should be in temporal proximity.	enrollment
1 / subject	Ancestry population ancestry_population	Ontology Ontology: { top_node: { id: GAZ:00000448, label: geographic location}}	important	Broad geographic origin of ancestry (continent)	id: GAZ:00000459, label: South America
1 / subject	location_birth	Ontology Ontology: { top_node: { id: GAZ:00000448, label: geographic location}}	important	Self-reported location of birth of the subject, preferred granularity is country-level	id: GAZ:00002939, label: Poland
1 / subject	Ethnicity ethnicity	string free text	important	Ethnic group of subject (defined as cultural/language-based membership)	English, Kurds, Manchu, Yakuts (and other fields from Wikipedia)
1 / subject	Race race	string free text	important	Racial group of subject (as defined by NIH)	White, American Indian or Alaska Native, Black, Asian, Native Hawaiian or Other Pacific Islander, Other
1 / subject	Strain name strain_name	string free text	important	Non-human designation of the strain or breed of animal used	C57BL/6J
1 / subject	Relation to other subjects linked_subjects	string free text	important	Subject ID to which Relation type refers	SUB1355648
1 / subject	Relation type link_type	string free text	important	Relation between subject and linked_subjects, can be genetic or environmental (e.g.exposure)	father, daughter, household
1 / diagnosis and intervention	Study group description study_group_description	string free text	important	Designation of study arm to which the subject is assigned to	control
1 / diagnosis and intervention	Diagnosis timepoint diagnosis_timepoint	TimePoint **	important	Time point for the diagnosis	OrderedDict([(‘label’, ‘Study enrollment’), (‘value’, 60), (‘unit’, OrderedDict([(‘id’, ‘UO:0000033’), (‘label’, ‘day’)]))])
1 / diagnosis and intervention	Diagnosis disease_diagnosis	Ontology Ontology: { top_node: { id: DOID:4, label: disease}}	important	Diagnosis of subject	id: DOID:9538, label: multiple myeloma
1 / diagnosis and intervention	Length of disease disease_length	TimeQuantity **	important	Time duration between initial diagnosis and current intervention	OrderedDict([(‘quantity’, 23), (‘unit’, OrderedDict([(‘id’, ‘UO:0000035’), (‘label’, ‘month’)]))])
1 / diagnosis and intervention	Disease stage disease_stage	string free text	important	Stage of disease at current intervention	Stage II
1 / diagnosis and intervention	Prior therapies for primary disease under study prior_therapies	string free text	important	List of all relevant previous therapies applied to subject for treatment of Diagnosis	melphalan/prednisone
1 / diagnosis and intervention	Immunogen/agent immunogen	string free text	important	Antigen, vaccine or drug applied to subject at this intervention	bortezomib
1 / diagnosis and intervention	Intervention definition intervention	string free text	important	Description of intervention	systemic chemotherapy, 6 cycles, 1.25 mg/m2
1 / diagnosis and intervention	Other relevant medical history medical_history	string free text	important	Medical history of subject that is relevant to assess the course of disease and/or treatment	MGUS, first diagnosed 5 years prior
2 / sample	Biological sample ID sample_id	string free text	important	Sample ID assigned by submitter, unique within study. If possible, a persistent sample ID linked to INSDC or similar repository study should be used.	SUP52415
2 / sample	Sample type sample_type	string free text	important	The way the sample was obtained, e.g. fine-needle aspirate, organ harvest, peripheral venous puncture	Biopsy
2 / sample	Tissue tissue	Ontology Ontology: { top_node: { id: UBERON:0010000, label: multicellular anatomical structure}}	important	The actual tissue sampled, e.g. lymph node, liver, peripheral blood	id: UBERON:0002371, label: bone marrow
2 / sample	Anatomic site anatomic_site	string free text	important	The anatomic location of the tissue, e.g. Inguinal, femur	Iliac crest
2 / sample	Disease state of sample disease_state_sample	string free text	important	Histopathologic evaluation of the sample	Tumor infiltration
2 / sample	Sample collection time collection_time_point_relative	TimePoint **	important	Time point at which sample was taken, relative to label event	OrderedDict([(‘label’, ‘Primary vaccination’), (‘value’, 14), (‘unit’, OrderedDict([(‘id’, ‘UO:0000033’), (‘label’, ‘day’)]))])
2 / sample	Sample collection location collection_location	Ontology Ontology: { top_node: { id: GAZ:00000448, label: geographic location}}	important	Location where the sample was taken, preferred granularity is country-level	id: GAZ:00002939, label: Poland
2 / sample	Biomaterial provider biomaterial_provider	string free text	important	Name and address of the entity providing the sample	Tissues-R-Us, Tampa, FL, USA
3 / process (cell)	Tissue processing tissue_processing	string free text	important	Enzymatic digestion and/or physical methods used to isolate cells from sample	Collagenase A/Dnase I digested, followed by Percoll gradient
3 / process (cell)	Cell subset cell_subset	Ontology Ontology: { top_node: { id: CL:0000542, label: lymphocyte}}	important	Commonly-used designation of isolated cell population	id: CL:0000972, label: class switched memory B cell
3 / process (cell)	Cell subset phenotype cell_phenotype	string free text	important	List of cellular markers and their expression levels used to isolate the cell population.	CD19+ CD38+ CD27+ IgM- IgD-
3 / process (cell)	Cell annotation cell_label	string free text	defined	Free text cell type annotation. Primarily used for annotating cell types that are not provided in the Cell Ontology.	age-associated B cell
3 / process (cell)	Cell species cell_species	Ontology Ontology: { top_node: { id: NCBITAXON:7776, label: Gnathostomata}}	defined	Binomial designation of the species from which the analyzed cells originate. Typically, this value should be identical to species, in which case it SHOULD NOT be set explicitly. However, there are valid experimental setups in which the two might differ, e.g., chimeric animal models. If set, this key will overwrite the species information for all lower layers of the schema.	id: NCBITAXON:9606, label: Homo sapiens
3 / process (cell)	Single-cell sort single_cell	boolean true | false	important	TRUE if single cells were isolated into separate compartments
3 / process (cell)	Number of cells in experiment cell_number	integer positive integer	important	Total number of cells that went into the experiment	1000000
3 / process (cell)	Number of cells per sequencing reaction cells_per_reaction	integer positive integer	important	Number of cells for each biological replicate	50000
3 / process (cell)	Cell storage cell_storage	boolean true | false	important	TRUE if cells were cryo-preserved between isolation and further processing	True
3 / process (cell)	Cell quality cell_quality	string free text	important	Relative amount of viable cells after preparation and (if applicable) thawing	90% viability as determined by 7-AAD
3 / process (cell)	Cell isolation / enrichment procedure cell_isolation	string free text	important	Description of the procedure used for marker-based isolation or enrich cells	Cells were stained with fluorochrome labeled antibodies and then sorted on a FlowMerlin (CE) cytometer.
3 / process (cell)	Processing protocol cell_processing_protocol	string free text	important	Description of the methods applied to the sample including cell preparation/ isolation/enrichment and nucleic acid extraction. This should closely mirror the Materials and methods section in the manuscript.	Stimulated wih anti-CD3/anti-CD28
3 / process (nucleic acid)	Target substrate template_class	string free text	essential	The class of nucleic acid that was used as primary starting material for the following procedures	RNA
3 / process (nucleic acid)	Target substrate quality template_quality	string free text	important	Description and results of the quality control performed on the template material	RIN 9.2
3 / process (nucleic acid)	Template amount template_amount	PhysicalQuantity **	important	Amount of template that went into the process	OrderedDict([(‘quantity’, 1000), (‘unit’, OrderedDict([(‘id’, ‘UO:0000024’), (‘label’, ‘nanogram’)]))])
3 / process (nucleic acid)	Library generation method library_generation_method	string free text	essential	Generic type of library generation	RT(oligo-dT)+TS(UMI)+PCR
3 / process (nucleic acid)	Library generation protocol library_generation_protocol	string free text	important	Description of processes applied to substrate to obtain a library that is ready for sequencing	cDNA was generated using
3 / process (nucleic acid)	Protocol IDs library_generation_kit_version	string free text	important	When using a library generation protocol from a commercial provider, provide the protocol version number	v2.1 (2016-09-15)
3 / process (nucleic acid)	Complete sequences complete_sequences	string free text	essential	To be considered complete, the procedure used for library construction MUST generate sequences that 1) include the first V gene codon that encodes the mature polypeptide chain (i.e. after the leader sequence) and 2) include the last complete codon of the J gene (i.e. 1 bp 5’ of the J->C splice site) and 3) provide sequence information for all positions between 1) and 2). To be considered complete & untemplated, the sections of the sequences defined in points 1) to 3) of the previous sentence MUST be untemplated, i.e. MUST NOT overlap with the primers used in library preparation. mixed should only be used if the procedure used for library construction will likely produce multiple categories of sequences in the given experiment. It SHOULD NOT be used as a replacement of a NULL value.	partial
3 / process (nucleic acid)	Physical linkage of different rearrangements physical_linkage	string free text	essential	In case an experimental setup is used that physically links nucleic acids derived from distinct Rearrangements before library preparation, this field describes the mode of that linkage. All hetero_* terms indicate that in case of paired-read sequencing, the two reads should be expected to map to distinct IG/TR loci. *_head-head refers to techniques that link the 5’ ends of transcripts in a single-cell context. *_tail-head refers to techniques that link the 3’ end of one transcript to the 5’ end of another one in a single-cell context. This term does not provide any information whether a continuous reading-frame between the two is generated. *_prelinked refers to constructs in which the linkage was already present on the DNA level (e.g. scFv).	hetero_head-head
3 / process (nucleic acid [pcr])	Target locus for PCR pcr_target_locus	string free text	important	Designation of the target locus. Note that this field uses a controlled vocubulary that is meant to provide a generic classification of the locus, not necessarily the correct designation according to a specific nomenclature.	IGK
3 / process (nucleic acid [pcr])	Forward PCR primer target location forward_pcr_primer_target_location	string free text	important	Position of the most distal nucleotide templated by the forward primer or primer mix	IGHV, +23
3 / process (nucleic acid [pcr])	Reverse PCR primer target location reverse_pcr_primer_target_location	string free text	important	Position of the most proximal nucleotide templated by the reverse primer or primer mix	IGHG, +57
3 / process (sequencing)	Batch number sequencing_run_id	string free text	important	ID of sequencing run assigned by the sequencing facility	160101_M01234
3 / process (sequencing)	Total reads passing QC filter total_reads_passing_qc_filter	integer positive integer	important	Number of usable reads for analysis	10365118
3 / process (sequencing)	Sequencing platform sequencing_platform	string free text	important	Designation of sequencing instrument used	Alumina LoSeq 1000
3 / process (sequencing)	Sequencing facility sequencing_facility	string free text	important	Name and address of sequencing facility	Seqs-R-Us, Vancouver, BC, Canada
3 / process (sequencing)	Date of sequencing run sequencing_run_date	string free text	important	Date of sequencing run	2016-12-16
3 / process (sequencing)	Sequencing kit sequencing_kit	string free text	important	Name, manufacturer, order and lot numbers of sequencing kit	FullSeq 600, Alumina, #M123456C0, 789G1HK
4 / data (raw reads)	Raw sequencing data persistent identifier sequencing_data_id	string free text	important	Persistent identifier of raw data stored in an archive (e.g. INSDC run ID). Data archive should be identified in the CURIE prefix.	SRA:SRR11610494
4 / data (raw reads)	Raw sequencing data file type file_type	string free text	important	File format for the raw reads or sequences
4 / data (raw reads)	Raw sequencing data file name filename	string free text	important	File name for the raw reads or sequences. The first file in paired-read sequencing.	MS10R-NMonson-C7JR9_S1_R1_001.fastq
4 / data (raw reads)	Read direction read_direction	string free text	important	Read direction for the raw reads or sequences. The first file in paired-read sequencing.	forward
4 / data (raw reads)	Forward read length read_length	integer positive integer	important	Read length in bases for the first file in paired-read sequencing	300
4 / data (raw reads)	Paired raw sequencing data file name paired_filename	string free text	important	File name for the second file in paired-read sequencing	MS10R-NMonson-C7JR9_S1_R2_001.fastq
4 / data (raw reads)	Paired read direction paired_read_direction	string free text	important	Read direction for the second file in paired-read sequencing	reverse
4 / data (raw reads)	Paired read length paired_read_length	integer positive integer	important	Read length in bases for the second file in paired-read sequencing	300
5 / process (computational)	Software tools and version numbers software_versions	string free text	important	Version number and / or date, include company pipelines	IgBLAST 1.6
5 / process (computational)	Paired read assembly paired_reads_assembly	string free text	important	How paired end reads were assembled into a single receptor sequence	PandaSeq (minimal overlap 50, threshold 0.8)
5 / process (computational)	Quality thresholds quality_thresholds	string free text	important	How/if sequences were removed from (4) based on base quality scores	Average Phred score >=20
5 / process (computational)	Primer match cutoffs primer_match_cutoffs	string free text	important	How primers were identified in the sequences, were they removed/masked/etc?	Hamming distance <= 2
5 / process (computational)	Collapsing method collapsing_method	string free text	important	The method used for combining multiple sequences from (4) into a single sequence in (5)	MUSCLE 3.8.31
5 / process (computational)	Data processing protocols data_processing_protocols	string free text	important	General description of how QC is performed	Data was processed using […]
5 / data (processed sequence)	V(D)J germline reference database germline_database	string free text	important	Source of germline V(D)J genes with version number or date accessed.	ENSEMBL, Homo sapiens build 90, 2017-10-01