| aa_hash |
|
| ab_tcell_receptors |
|
| acknowledgement_id |
unique identifier of this Acknowledgement within the file |
| acknowledgements |
|
| adc_publish_date |
Date the study was first published in the AIRR Data Commons |
| adc_update_date |
Date the study data was updated in the AIRR Data Commons |
| age |
The age of a participant relative to age_event |
| age_event |
Event in the study schedule to which Age refers |
| age_max |
Upper boundary of age range or equal to age_min for specific age |
| age_min |
Specific age or lower boundary of age range |
| age_unit |
Unit of age range |
| akc_id |
A unique identifier for a thing in the AKC |
| aliases |
Alternative names for this sequence |
| aligned_sequence |
Aligned sequence if this delineation provides an alignment |
| alignment_labels |
One string for each codon in the aligned_sequence indicating the label of tha... |
| allele_description_id |
Unique identifier of this AlleleDescription within the file |
| allele_description_ref |
Unique reference to the allele description, in standardized form (Repo:Label:... |
| allele_descriptions |
list of allele_descriptions in the germline set |
| allele_designation |
|
| allele_name |
Allele name as allocated by the inference pipeline |
| allele_similarity_cluster_designation |
ID of the similarity cluster used in this germline set, if designated |
| allele_similarity_cluster_member_id |
Membership ID of the allele within the similarity cluster, if a cluster is de... |
| analysis_provenance_id |
Identifier for machine-readable PROV model of analysis provenance |
| anatomic_site |
The anatomic location of the tissue, e |
| ancestry_population |
Broad geographic origin of ancestry (continent) |
| antigen |
The substance against which the receptor was tested |
| antigen_source_species |
The species from which the antigen was isolated |
| antigen_type |
The type of antigen before processing by the immune system |
| archival_id |
Identifier for external archival resource for the investigation, e |
| assay_type |
The specific type of an assay |
| assays |
The assays performed by the investigation |
| assessment_type |
The specific type of an assessment |
| assessments |
The assessment that a dataset is about |
| author |
Corresponding author |
| authors |
The authors of a reference |
| bcell_receptors |
|
| biological_sex |
The biological sex of a participant |
| biomaterial_provider |
Name and address of the entity providing the sample |
| c_alignment_end |
End position of the C gene alignment in both the sequence_alignment and germl... |
| c_alignment_start |
Start position of the C gene alignment in both the sequence_alignment and ger... |
| c_call |
Constant region gene with allele |
| c_cigar |
CIGAR string for the C gene alignment |
| c_germline_alignment |
Aligned constant region germline sequence spanning the same region as the c_s... |
| c_germline_alignment_aa |
Amino acid translation of the c_germline_aligment field |
| c_germline_end |
Alignment end position in the C gene reference sequence (1-based closed inter... |
| c_germline_start |
Alignment start position in the C gene reference sequence (1-based closed int... |
| c_identity |
Fractional identity for the C gene alignment |
| c_score |
Alignment score for the C gene alignment |
| c_sequence_alignment |
Aligned portion of query sequence assigned to the constant region, including ... |
| c_sequence_alignment_aa |
Amino acid translation of the c_sequence_alignment field |
| c_sequence_end |
End position of the C gene in the query sequence (1-based closed interval) |
| c_sequence_start |
Start position of the C gene in the query sequence (1-based closed interval) |
| c_support |
C gene alignment E-value, p-value, likelihood, probability or other similar m... |
| call |
Gene assignment with allele |
| cdr1 |
Nucleotide sequence of the aligned CDR1 region |
| cdr1_aa |
Amino acid translation of the cdr1 field |
| cdr1_end |
|
| cdr1_start |
|
| cdr2 |
Nucleotide sequence of the aligned CDR2 region |
| cdr2_aa |
Amino acid translation of the cdr2 field |
| cdr2_end |
|
| cdr2_start |
|
| cdr3 |
Nucleotide sequence of the aligned CDR3 region |
| cdr3_aa |
Amino acid translation of the cdr3 field |
| cdr3_end |
CDR3 end position in the query sequence (1-based closed interval) |
| cdr3_start |
|
| cell_id |
|
| cell_isolation |
Description of the procedure used for marker-based isolation or enrich cells |
| cell_number |
Total number of cells that went into the experiment |
| cell_phenotype |
List of cellular markers and their expression levels used to isolate the cell... |
| cell_processing_protocol |
Description of the methods applied to the sample including cell preparation/ ... |
| cell_quality |
Relative amount of viable cells after preparation and (if applicable) thawing |
| cell_species |
Binomial designation of the species from which the analyzed cells originate |
| cell_storage |
TRUE if cells were cryo-preserved between isolation and further processing |
| cell_subset |
Commonly-used designation of isolated cell population |
| cells_per_reaction |
Number of cells for each biological replicate |
| chain_codomain |
Immune receptor chain element in binary relation codomain |
| chain_domain |
Immune receptor chain element in binary relation domain |
| chain_similarity_type |
Type of similarity calculation between two immune receptor chains |
| chain_type |
Gene locus (chain type) |
| chains |
|
| chromosome |
chromosome on which the gene is located |
| cigar |
Alignment CIGAR string |
| clone_count |
Absolute count of the size (number of members) of this clone in the repertoir... |
| clone_id |
|
| coding_sequence |
Nucleotide sequence of the core coding region, such as the coding region of a... |
| collapsing_method |
The method used for combining multiple sequences from (4) into a single seque... |
| collected_by |
Full contact information of the data collector, i |
| collection_time_point_reference |
Event in the study schedule to which Sample collection time relates to |
| collection_time_point_relative |
Time point at which sample was taken, relative to Collection time event |
| collection_time_point_relative_unit |
Unit of Sample collection time |
| complete_sequences |
To be considered complete, the procedure used for library construction MUST... |
| complete_vdj |
Complete VDJ flag |
| conclusions |
The conclusions from the investigation |
| consensus_count |
Number of reads contributing to the UMI consensus or contig assembly for this... |
| curation |
|
| curational_tags |
Controlled-vocabulary tags applied to this description |
| d2_alignment_end |
End position of the second D gene alignment in both the sequence_alignment an... |
| d2_alignment_start |
Start position of the second D gene alignment in both the sequence_alignment ... |
| d2_call |
Second D gene with allele |
| d2_cigar |
CIGAR string for the second D gene alignment |
| d2_frame |
Numerical reading frame (1, 2, 3) of the second D gene in the query nucleotid... |
| d2_germline_alignment |
Aligned D gene germline sequence spanning the same region as the d2_sequence_... |
| d2_germline_alignment_aa |
Amino acid translation of the d2_germline_alignment field |
| d2_germline_end |
Alignment end position in the second D gene reference sequence (1-based close... |
| d2_germline_start |
Alignment start position in the second D gene reference sequence (1-based clo... |
| d2_identity |
Fractional identity for the second D gene alignment |
| d2_score |
Alignment score for the second D gene alignment |
| d2_sequence_alignment |
Aligned portion of query sequence assigned to the second D gene, including an... |
| d2_sequence_alignment_aa |
Amino acid translation of the d2_sequence_alignment field |
| d2_sequence_end |
End position of the second D gene in the query sequence (1-based closed inter... |
| d2_sequence_start |
Start position of the second D gene in the query sequence (1-based closed int... |
| d2_support |
D gene alignment E-value, p-value, likelihood, probability or other similar m... |
| d_alignment_end |
|
| d_alignment_start |
|
| d_call |
|
| d_cigar |
CIGAR string for the first or only D gene alignment |
| d_frame |
Numerical reading frame (1, 2, 3) of the first or only D gene in the query nu... |
| d_germline_alignment |
Aligned D gene germline sequence spanning the same region as the d_sequence_a... |
| d_germline_alignment_aa |
Amino acid translation of the d_germline_alignment field |
| d_germline_end |
Alignment end position in the D gene reference sequence for the first or only... |
| d_germline_start |
Alignment start position in the D gene reference sequence for the first or on... |
| d_identity |
Fractional identity for the first or only D gene alignment |
| d_rs_3_prime_end |
End co-ordinate in the sequence field of the 3 prime D recombination site (D-... |
| d_rs_3_prime_start |
Start co-ordinate in the sequence field of the 3 prime D recombination site (... |
| d_rs_5_prime_end |
End co-ordinate in the sequence field of 5 the prime D recombination site (D-... |
| d_rs_5_prime_start |
Start co-ordinate in the sequence field of the 5 prime D recombination site (... |
| d_score |
Alignment score for the first or only D gene alignment |
| d_sequence_alignment |
Aligned portion of query sequence assigned to the first or only D gene, inclu... |
| d_sequence_alignment_aa |
Amino acid translation of the d_sequence_alignment field |
| d_sequence_end |
End position of the first or only D gene in the query sequence |
| d_sequence_start |
Start position of the first or only D gene in the query sequence |
| d_support |
D gene alignment E-value, p-value, likelihood, probability or other similar m... |
| data_location_type |
The type of location where data was found, e |
| data_location_value |
An identifier for the location of the data, e |
| data_processing |
List of Data Processing objects |
| data_processing_files |
Array of file names for data produced by this data processing |
| data_processing_id |
|
| data_processing_protocols |
General description of how QC is performed |
| datasets |
The datasets that support a conclusion |
| deleted_genes |
Array of genes identified as being deleted in this genotype |
| delineation_scheme |
Name of the delineation scheme |
| deposited_version |
Version number of the sequence within the repository |
| derivation |
The class of nucleic acid that was used as primary starting material |
| description |
A human-readable description for a thing |
| diagnosis |
Diagnosis information for subject |
| disease |
The disease relevant to an immune exposure |
| disease_diagnosis |
Diagnosis of subject |
| disease_length |
Time duration between initial diagnosis and current intervention |
| disease_severity |
The severity of the disease relevant to an immune exposure |
| disease_stage |
Stage of disease at current intervention |
| disease_state_sample |
Histopathologic evaluation of the sample |
| documented_alleles |
List of alleles documented in reference set(s) |
| documents |
The documents produced by the investigation |
| duplicate_count |
Copy number or number of duplicate observations for the query sequence |
| duration |
The duration of this life event |
| epitope |
The epitope being measured |
| epitopes |
|
| ethnicity |
Ethnic group of subject (defined as cultural/language-based membership) |
| exclusion_criteria |
Participants are excluded from an investigation if they meet this criteria |
| experiment_type |
The type of experiment that supports the conclusion |
| exposure_material |
The material relevant to an immune exposure |
| expression_id |
Identifier of this expression property measurement |
| expression_index |
Index addressing the current event within the raw data set |
| expression_raw_doi |
DOI of raw data set containing the current event |
| expression_study_method |
Keyword describing the methodology used to assess expression |
| file_type |
File format for the raw reads or sequences |
| filename |
File name for the raw reads or sequences |
| forward_pcr_primer_target_location |
Position of the most distal nucleotide templated by the forward primer or pri... |
| functional |
True if the gene is functional, false if it is a pseudogene |
| fwr1 |
Nucleotide sequence of the aligned FWR1 region |
| fwr1_aa |
Amino acid translation of the fwr1 field |
| fwr1_end |
|
| fwr1_start |
|
| fwr2 |
Nucleotide sequence of the aligned FWR2 region |
| fwr2_aa |
Amino acid translation of the fwr2 field |
| fwr2_end |
|
| fwr2_start |
|
| fwr3 |
Nucleotide sequence of the aligned FWR3 region |
| fwr3_aa |
Amino acid translation of the fwr3 field |
| fwr3_end |
|
| fwr3_start |
|
| fwr4 |
Nucleotide sequence of the aligned FWR4 region |
| fwr4_aa |
Amino acid translation of the fwr4 field |
| fwr4_end |
FWR4 end position in the query sequence (1-based closed interval) |
| fwr4_start |
FWR4 start position in the query sequence (1-based closed interval) |
| gd_tcell_receptors |
|
| gene |
The MHC gene to which the described allele belongs |
| gene_designation |
Gene number or other identifier, as (and if) defined |
| gene_end |
Co-ordinate in the sequence field of the last gene-coding nucleotide in the c... |
| gene_start |
Co-ordinate in the sequence field of the first nucleotide in the coding_seque... |
| genotype |
|
| genotype_class_list |
List of Genotypes included in this Receptor Genotype Set |
| geolocation |
The geolocation of a participant at birth |
| germline_alignment |
|
| germline_alignment_aa |
|
| germline_database |
Source of germline V(D)J genes with version number or date accessed |
| germline_end |
Alignment end position in the reference sequence (1-based closed interval) |
| germline_set_id |
Unique identifier of the GermlineSet within this file |
| germline_set_name |
descriptive name of this germline set |
| germline_set_ref |
|
| germline_start |
Alignment start position in the reference sequence (1-based closed interval) |
| gff_end |
Genomic co-ordinates of the end of the sequence of interest described in this... |
| gff_seqid |
Sequence (from the assembly) of a window including the gene and preferably al... |
| gff_start |
Genomic co-ordinates of the start of the sequence of interest described in th... |
| grants |
Funding agencies and grant numbers |
| identity |
Alignment fractional identity |
| igh_chain |
IG heavy chain |
| igk_chain |
IG kappa light chain |
| igl_chain |
IG lambda light chain |
| immune_exposures |
|
| immunogen |
Antigen, vaccine or drug applied to subject at this intervention |
| inclusion_criteria |
Participants in an investigation must meet this criteria |
| inclusion_exclusion_criteria |
List of criteria for inclusion/exclusion for the study |
| index_filename |
File name for the index file |
| index_length |
Read length in bases for the index file |
| individual_full_name |
Full name of individual |
| inference_process |
Information on how the genotype was acquired |
| inference_type |
Type of inference(s) from which this gene sequence was inferred |
| institution_name |
Individual's department and institution name |
| intervention |
Description of intervention |
| investigation |
An investigation in which the study arm participates |
| investigation_type |
Type of study design |
| investigations |
The investigations that a reference or conclusion are about |
| isotype |
The isotype of the chain |
| issue |
The issue of the journal in which a reference was published |
| j_alignment_end |
End position of the J gene alignment in both the sequence_alignment and germl... |
| j_alignment_start |
Start position of the J gene alignment in both the sequence_alignment and ger... |
| j_call |
|
| j_cdr3_end |
In the case of a J-gene, the co-ordinate in the sequence field of the first n... |
| j_cigar |
CIGAR string for the J gene alignment |
| j_codon_frame |
Codon position of the first nucleotide in the 'coding_sequence' field |
| j_donor_splice |
Co-ordinate in the sequence field of the final 3' nucleotide of the J-REGION ... |
| j_frameshift |
True if the J gene in the query nucleotide sequence contains a translational ... |
| j_germline_alignment |
Aligned J gene germline sequence spanning the same region as the j_sequence_a... |
| j_germline_alignment_aa |
Amino acid translation of the j_germline_alignment field |
| j_germline_end |
Alignment end position in the J gene reference sequence (1-based closed inter... |
| j_germline_start |
Alignment start position in the J gene reference sequence (1-based closed int... |
| j_identity |
Fractional identity for the J gene alignment |
| j_rs_end |
End co-ordinate in the sequence field of J recombination site (J-genes only) |
| j_rs_start |
Start co-ordinate in the sequence field of J recombination site (J-genes only... |
| j_score |
Alignment score for the J gene alignment |
| j_sequence_alignment |
Aligned portion of query sequence assigned to the J gene, including any indel... |
| j_sequence_alignment_aa |
Amino acid translation of the j_sequence_alignment field |
| j_sequence_end |
End position of the J gene in the query sequence (1-based closed interval) |
| j_sequence_start |
Start position of the J gene in the query sequence (1-based closed interval) |
| j_support |
J gene alignment E-value, p-value, likelihood, probability or other similar m... |
| journal |
The journal in which a reference was published |
| junction |
|
| junction_aa |
Amino acid translation of the junction |
| junction_aa_length |
|
| junction_aa_vj_allele_hash |
|
| junction_aa_vj_gene_hash |
|
| junction_end |
Junction region end position in the alignment (1-based closed interval) |
| junction_length |
|
| junction_start |
Junction region start position in the alignment (1-based closed interval) |
| keywords_study |
Keywords describing properties of one or more data sets in a study |
| lab_address |
|
| lab_name |
|
| label |
|
| leader_1_end |
End co-ordinate in the sequence field of L-PART1 (V-genes only) |
| leader_1_start |
Start co-ordinate in the sequence field of L-PART1 (V-genes only) |
| leader_2_end |
End co-ordinate in the sequence field of L-PART2 (V-genes only) |
| leader_2_start |
Start co-ordinate in the sequence field of L-PART2 (V-genes only) |
| library_generation_kit_version |
When using a library generation protocol from a commercial provider, provide ... |
| library_generation_method |
Generic type of library generation |
| library_generation_protocol |
Description of processes applied to substrate to obtain a library that is rea... |
| life_event |
The life event corresponding to an immune exposure |
| life_event_type |
The specific type of a life event |
| life_events |
|
| ligand_type |
Classification of ligand binding to receptor |
| link_type |
Relation between subject and linked_subjects, can be genetic or environment... |
| linked_subjects |
Subject ID to which Relation type refers |
| locus |
|
| maintainer |
Maintainer of this sequence record |
| medical_history |
Medical history of subject that is relevant to assess the course of disease a... |
| mhc_allele_1 |
Allele designation of the MHC alpha chain |
| mhc_allele_2 |
Allele designation of the MHC class II beta chain or the invariant beta2-micr... |
| mhc_alleles |
List of MHC alleles of the indicated mhc_class identified in an individual |
| mhc_class |
|
| mhc_gene_1 |
The MHC gene to which the mhc_allele_1 belongs |
| mhc_gene_2 |
The MHC gene to which the mhc_allele_2 belongs |
| mhc_genotype_id |
A unique identifier for this MHCGenotype, assumed to be unique in the context... |
| mhc_genotype_list |
List of MHCGenotypes included in this set |
| mhc_genotype_set |
MHC genotype set for this subject |
| mhc_genotype_set_id |
A unique identifier for this MHCGenotypeSet |
| mhc_genotyping_method |
Information on how the genotype was determined |
| month |
The month of the issue of the journal in which a reference was published |
| n1_length |
Number of untemplated nucleotides 5' of the first or only D gene alignment |
| n2_length |
Number of untemplated nucleotides 3' of the first or only D gene alignment |
| n3_length |
Number of untemplated nucleotides 3' of the second D gene alignment |
| name |
A human-readable name for a thing |
| newick |
Newick string of the tree edges |
| nodes |
Dictionary of nodes in the tree, keyed by sequence_id string |
| np1 |
Nucleotide sequence of the combined N/P region between the V gene and first D... |
| np1_aa |
Amino acid translation of the np1 field |
| np1_length |
Number of nucleotides between the V gene and first D gene alignments or betwe... |
| np2 |
Nucleotide sequence of the combined N/P region between either the first D gen... |
| np2_aa |
Amino acid translation of the np2 field |
| np2_length |
Number of nucleotides between either the first D gene and J gene alignments o... |
| np3 |
Nucleotide sequence of the combined N/P region between the second D gene and ... |
| np3_aa |
Amino acid translation of the np3 field |
| np3_length |
Number of nucleotides between the second D gene and J gene alignments |
| observation_type |
The type of observation from which this sequence was drawn, such as direct se... |
| orcid_id |
Individual's ORCID identifier |
| organism |
The type of organism that the conclusion is about |
| p3d2_length |
Number of palindromic nucleotides 3' of the second D gene alignment |
| p3d_length |
Number of palindromic nucleotides 3' of the first or only D gene alignment |
| p3v_length |
Number of palindromic nucleotides 3' of the V gene alignment |
| p5d2_length |
Number of palindromic nucleotides 5' of the second D gene alignment |
| p5d_length |
Number of palindromic nucleotides 5' of the first or only D gene alignment |
| p5j_length |
Number of palindromic nucleotides 5' of the J gene alignment |
| pages |
The pages of the issue of the journal in which a reference was published |
| paired_filename |
File name for the second file in paired-read sequencing |
| paired_read_direction |
Read direction for the second file in paired-read sequencing |
| paired_read_length |
Read length in bases for the second file in paired-read sequencing |
| paired_reads_assembly |
How paired end reads were assembled into a single receptor sequence |
| paralogs |
Gene symbols of any paralogs |
| participant |
The participant of a life event |
| participants |
The participants involved with the investigation |
| patch_no |
Genome assembly patch number in which this gene was determined |
| pcr_target |
If a PCR step was performed that specifically targets the IG/TR loci, the tar... |
| pcr_target_locus |
Designation of the target locus |
| peptide_end |
End position of the peptide within the reference protein sequence |
| peptide_start |
Start position of the peptide within the reference protein sequence |
| phasing |
Chromosomal phasing indicator |
| phenotypic_sex |
The phenotypic sex of a participant |
| physical_linkage |
In case an experimental setup is used that physically links nucleic acids der... |
| primary_annotation |
If true, indicates this is the primary or default data processing for the rep... |
| primer_match_cutoffs |
How primers were identified in the sequences, were they removed/masked/etc? |
| prior_therapies |
List of all relevant previous therapies applied to subject for treatment of `... |
| process |
The type of specimen collection process that resulted in this specimen |
| productive |
True if the V(D)J sequence is predicted to be productive |
| property |
Name of the property observed, typically a gene or antibody identifier (and l... |
| property_type |
Keyword describing the property type and detection method used to measure the... |
| property_value |
Level at which the property was observed in the experiment (non-normalized) |
| pub_ids |
|
| quality |
The Sanger/Phred quality scores for assessment of sequence quality |
| quality_alignment |
Sanger/Phred quality scores for assessment of sequence_alignment quality |
| quality_thresholds |
How/if sequences were removed from (4) based on base quality scores |
| race |
Racial group of subject (as defined by NIH) |
| rank |
Alignment rank |
| reactivity_measurements |
Records of reactivity measurement |
| reactivity_method |
The methodology used to assess expression (assay implemented in experiment) |
| reactivity_readout |
Reactivity measurement read-out |
| reactivity_unit |
The unit of the measurement |
| reactivity_value |
The absolute (processed) value of the measurement |
| read_direction |
Read direction for the raw reads or sequences |
| read_length |
Read length in bases for the first file in paired-read sequencing |
| rearranged_support |
|
| rearrangements |
Array of sequence identifiers defined for the Rearrangement object |
| receptor_genotype_id |
A unique identifier within the file for this Receptor Genotype, typically gen... |
| receptor_genotype_set |
Immune receptor genotype set for this subject |
| receptor_genotype_set_id |
A unique identifier for this Receptor Genotype Set, typically generated by th... |
| receptor_hash |
The SHA256 hash of the receptor amino acid sequence, calculated on the concat... |
| receptor_id |
ID of the current Receptor object, unique within the local repository |
| receptor_ref |
Array of receptor identifiers defined for the Receptor object |
| receptor_type |
The top-level receptor type, either Immunoglobulin (Ig) or T Cell Receptor (T... |
| receptor_variable_domain_1_aa |
Complete amino acid sequence of the mature variable domain of the Ig heavy, T... |
| receptor_variable_domain_1_locus |
Locus from which the variable domain in receptor_variable_domain_1_aa origina... |
| receptor_variable_domain_2_aa |
Complete amino acid sequence of the mature variable domain of the Ig light, T... |
| receptor_variable_domain_2_locus |
Locus from which the variable domain in receptor_variable_domain_2_aa origina... |
| receptors |
Array of receptor identifiers defined for the Receptor object |
| reference_set_ref |
Repository and list from which it was taken (issuer/name/version) |
| references |
|
| release_date |
Date of this release |
| release_description |
Brief descriptive notes of the reason for this release and the changes embodi... |
| release_version |
|
| repertoire_description |
|
| repertoire_group_description |
Repertoire collection description |
| repertoire_group_id |
Identifier for this repertoire collection |
| repertoire_group_name |
Short display name for this repertoire collection |
| repertoire_id |
|
| repertoire_name |
Short generic display name for the repertoire |
| repertoires |
List of repertoires in this collection with an associated description and tim... |
| repository_name |
|
| repository_ref |
Queryable id or accession number of the sequence published by the repository |
| result |
The content of the conclusion |
| rev_comp |
|
| reverse_pcr_primer_target_location |
Position of the most proximal nucleotide templated by the reverse primer or p... |
| sample |
List of Sample Processing objects |
| sample_id |
Sample ID assigned by submitter, unique within study |
| sample_processing_id |
|
| sample_type |
The way the sample was obtained, e |
| score |
Alignment score |
| seed_id |
sequence_id of the seed sequence |
| segment |
The segment for this alignment |
| sequence |
Nucleotide sequence |
| sequence_aa |
Amino acid translation of the query nucleotide sequence |
| sequence_alignment |
|
| sequence_alignment_aa |
Amino acid translation of the aligned query sequence |
| sequence_delineation_id |
Unique identifier of this SequenceDelineationV within the file |
| sequence_end |
|
| sequence_id |
|
| sequence_start |
|
| sequence_type |
Sequence type (V, D, J, C) |
| sequences |
List sequence_id strings that act as keys to the Rearrangement records for me... |
| sequencing_data_id |
Persistent identifier of raw data stored in an archive (e |
| sequencing_facility |
Name and address of sequencing facility |
| sequencing_files |
Set of sequencing files produced by the sequencing run |
| sequencing_kit |
Name, manufacturer, order and lot numbers of sequencing kit |
| sequencing_platform |
Designation of sequencing instrument used |
| sequencing_run_date |
Date of sequencing run |
| sequencing_run_id |
ID of sequencing run assigned by the sequencing facility |
| sex |
Biological sex of subject |
| simulations |
The simulations performed by the investigation |
| single_cell |
TRUE if single cells were isolated into separate compartments |
| software_versions |
Version number and / or date, include company pipelines |
| source_organism |
The organism that the source protein comes from |
| source_protein |
The protein that this epitope comes from |
| source_uri |
AKC reference to a foreign thing |
| sources |
The source URLs for a reference |
| species |
Binomial designation of subject's species |
| species_subgroup |
Race, strain or other species subgroup to which this subject belongs |
| species_subgroup_type |
|
| specimen |
The specimen that was input for an assay |
| specimen_collections |
|
| specimen_processing |
A series of zero or more specimen processing steps that precede an assay |
| specimen_processings |
|
| specimen_type |
The type of this specimen |
| specimens |
|
| start |
The start time of this life event, relative to the T0 event |
| status |
Status of record, assumed active if the field is not present |
| stop_codon |
True if the aligned sequence contains a stop codon |
| strain |
The strain of the participant (non-human study participants) |
| strain_name |
Non-human designation of the strain or breed of animal used |
| strand |
sense (+ or -) |
| study |
Study object |
| study_arm |
The study arm that a participant is a member of |
| study_arms |
The study arms that are relevant for a study event |
| study_contact |
Full contact information of the contact persons for this study This should in... |
| study_description |
Generic study description |
| study_event |
The study event corresponding to a life event |
| study_events |
|
| study_group_description |
Designation of study arm to which the subject is assigned to |
| study_id |
Unique ID assigned by study registry such as one of the International Nucleot... |
| study_title |
Descriptive study title |
| study_type |
Type of study design |
| subgroup_designation |
Identifier of the gene subgroup or clade, as (and if) defined |
| subject |
Subject object |
| subject_id |
Subject ID assigned by submitter, unique within study |
| submitted_by |
Full contact information of the data depositor, i |
| support |
Alignment E-value, p-value, likelihood, probability or other similar measure ... |
| synthetic |
TRUE for libraries in which the diversity has been synthetically generated (e |
| t0_event |
The T0 event used to specify the time of this life event |
| t0_event_type |
The type of the T0 event used to specify the time of this life event |
| target_entity_type |
The type of the entity being measured |
| tcell_chains |
The T cell receptor chains being measured |
| tcell_receptors |
The T cell receptors being measured |
| template_amount |
Amount of template that went into the process |
| template_amount_unit |
Unit of template amount |
| template_class |
The class of nucleic acid that was used as primary starting material for the ... |
| template_quality |
Description and results of the quality control performed on the template mate... |
| time_point |
Time point designation for this repertoire within the group |
| time_point_label |
Informative label for the time point |
| time_point_unit |
Unit of the time point |
| time_point_value |
Value of the time point |
| time_unit |
The time unit used to measure the start and duration of this life event |
| tissue |
The actual tissue sampled, e |
| tissue_processing |
Enzymatic digestion and/or physical methods used to isolate cells from sample |
| title |
The title of a reference |
| total_reads_passing_qc_filter |
Number of usable reads for analysis |
| tra_chain |
T cell receptor alpha chain |
| trb_chain |
T cell receptor beta chain |
| trd_chain |
T cell receptor delta chain |
| tree_id |
Identifier for the tree |
| trg_chain |
T cell receptor gamma chain |
| type |
|
| umi_count |
|
| unaligned_sequence |
entire V-sequence covered by this delineation |
| undocumented_alleles |
List of alleles inferred to be present and not documented in an identified Ge... |
| unit |
The measurement result value unit |
| unrearranged_support |
|
| update_date |
Subsequence updates to the investigation or its data |
| utr_5_prime_end |
End co-ordinate in the sequence field of the 5 prime UTR (V-genes only) |
| utr_5_prime_start |
Start co-ordinate in the sequence field of the 5 prime UTR (V-genes only) |
| v_alignment_end |
|
| v_alignment_start |
|
| v_call |
|
| v_cigar |
CIGAR string for the V gene alignment |
| v_frameshift |
True if the V gene in the query nucleotide sequence contains a translational ... |
| v_gene_delineations |
|
| v_germline_alignment |
Aligned V gene germline sequence spanning the same region as the v_sequence_a... |
| v_germline_alignment_aa |
Amino acid translation of the v_germline_alignment field |
| v_germline_end |
Alignment end position in the V gene reference sequence (1-based closed inter... |
| v_germline_start |
Alignment start position in the V gene reference sequence (1-based closed int... |
| v_identity |
Fractional identity for the V gene alignment |
| v_rs_end |
End co-ordinate in the sequence field of the V recombination site (V-genes on... |
| v_rs_start |
Start co-ordinate in the sequence field of the V recombination site (V-genes ... |
| v_score |
Alignment score for the V gene |
| v_sequence_alignment |
Aligned portion of query sequence assigned to the V gene, including any indel... |
| v_sequence_alignment_aa |
Amino acid translation of the v_sequence_alignment field |
| v_sequence_end |
End position of the V gene in the query sequence (1-based closed interval) |
| v_sequence_start |
Start position of the V gene in the query sequence (1-based closed interval) |
| v_support |
V gene alignment E-value, p-value, likelihood, probability or other similar m... |
| value |
The measurement result value |
| virtual_pairing |
boolean to indicate if pairing was inferred |
| vj_in_frame |
True if the V and J gene alignments are in-frame |
| year |
The year of the issue of the journal in which a reference was published |