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 :ref:`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 Contact information (data collection) collected_by string free text important "Full contact information of the data collector, i.e. the person who is legally responsible for data collection and release. This should include an e-mail address and a persistent identifier such as an ORCID ID. " Dr. P. Stibbons, p.stibbons@unseenu.edu, https://orcid.org/0000-0002-1825-0097 1 study Lab name lab_name string free text important Department of data collector Department for Planar Immunology 1 study Lab address lab_address string free text important Institution and institutional address of data collector School of Medicine, Unseen University, Ankh-Morpork, Disk World 1 study Contact information (data deposition) submitted_by string free text important "Full contact information of the data depositor, i.e., the person submitting the data to a repository. This should include an e-mail address and a persistent identifier such as an ORCID ID. This is supposed to be a short-lived and technical role until the submission is relased. " Adrian Turnipseed, a.turnipseed@unseenu.edu, https://orcid.org/0000-0002-1825-0097 1 study Relevant publications pub_ids string free text important "Publications describing the rationale and/or outcome of the study. Where ever possible, a persistent identifier should be used such as a DOI or a Pubmed ID " PMID:85642 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 :ref:`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 minimum age_min number positive number important Specific age or lower boundary of age range. 60 1 subject Age maximum age_max number positive number important "Upper boundary of age range or equal to age_min for specific age. This field should only be null if age_min is null. " 80 1 subject Age unit age_unit :ref:`Ontology ` Ontology: { top_node: { id: UO:0000003, label: time unit}} important Unit of age range id: UO:0000036, label: year 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 string free text important Broad geographic origin of ancestry (continent) list of continents, mixed or unknown 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 disease_diagnosis :ref:`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 string free text important Time duration between initial diagnosis and current intervention 23 months 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 :ref:`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 number positive number important Time point at which sample was taken, relative to `Collection time event` 14 2 sample Sample collection time unit collection_time_point_relative_unit :ref:`Ontology ` Ontology: { top_node: { id: UO:0000003, label: time unit}} important Unit of Sample collection time id: UO:0000033, label: day 2 sample Collection time event collection_time_point_reference string free text important Event in the study schedule to which `Sample collection time` relates to Primary vaccination 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 :ref:`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 species cell_species :ref:`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 number positive number important Amount of template that went into the process 1000 3 process (nucleic acid) Template amount time unit template_amount_unit :ref:`Ontology ` Ontology: { top_node: { id: UO:0000002, label: physical quantity}} important Unit of template amount 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