AIRR Knowledge Schema
Common data model schema for the AIRR Knowledge Commons
URI: https://github.com/airr-knowledge/ak-schema
Name: ak-schema
Classes
Slots
| Slot | Description |
|---|---|
| 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) |
| antibody | B cell receptor, immunoglobulin antibody |
| antigen | A material entity with antigen role |
| 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 | |
| author | Corresponding author |
| authors | The authors of a reference |
| bcell_receptors | |
| 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 |
| 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_item_types | semantic types of the data |
| data_items | set of data items |
| 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 |
| data_transformation | a process that transforms input data into output data |
| data_transformation_types | semantic types of the data transformation |
| 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_format | Format and organization of the data in the file |
| 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 |
| has_specified_input | input data item |
| has_specified_output | output data item |
| 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 |
| measurement_category | The measurement result category |
| measurement_unit | The measurement result value unit |
| measurement_value | The measurement result value |
| medical_history | Medical history of subject that is relevant to assess the course of disease a... |
| mhc | Major histocompatibility complex |
| 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 |
| 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 `... |
| 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_data | |
| 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 | |
| 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 |
| target_entity_type | The type of the entity being measured |
| tcell_chains | The T cell receptor chains being measured |
| tcell_receptor | T cell receptor |
| 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... |
| 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... |
| virtual_pairing | boolean to indicate if pairing was inferred |
| vj_in_frame | True if the V and J gene alignments are in-frame |
| was_generated_by | direct provenance link of one entity (input) to another (output) for a data t... |
| year | The year of the issue of the journal in which a reference was published |
Enumerations
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| Double | A real number that conforms to the xsd:double specification |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|