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airr-schema.yaml
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airr-schema.yaml
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#
# Schema definitions for AIRR standards objects
#
Info:
title: AIRR Schema
description: Schema definitions for AIRR standards objects
version: 1.3
contact:
name: AIRR Community
url: https://github.com/airr-community
license:
name: Creative Commons Attribution 4.0 International
url: https://creativecommons.org/licenses/by/4.0/
# Properties that are based upon an ontology use this
# standard schema definition
Ontology:
discriminator: AIRR
type: object
properties:
id:
type: string
description: Identifier for the ontology term
value:
type: string
description: Value for the ontology term
# AIRR specification extensions
#
# The schema definitions for AIRR standards objects is extended to
# provide a number of AIRR specific attributes. This schema definition
# specifies the structure, property names and data types. These
# attributes are attached to an AIRR field with the x-airr property.
Attributes:
discriminator: AIRR
type: object
required:
- miairr
properties:
miairr:
type: boolean
description: True if a MiAIRR field
default: false
required:
type: boolean
description: Indicates if field is required by MiAIRR and/or ADC API
nullable:
type: boolean
description: Indicates if field can have null value
adc-api-optional:
type: boolean
description: True if query support is optional for ADC API implementations. If False or undefined, an ADC API implementation must support queries upon this field.
deprecated:
type: boolean
description: True if the field is being deprecated from the schema.
set:
type: integer
description: MiAIRR set
subset:
type: string
description: MiAIRR subset
name:
type: string
description: MiAIRR name
format:
type: string
description: Field format. If null then assume the full range of the field data type
enum:
- ontology
- controlled vocabulary
- physical quantity
ontology:
type: object
description: Ontology definition for field
properties:
draft:
type: boolean
description: Indicates if ontology definition is a draft
name:
type: string
description: Ontology name
url:
type: string
description: >
Ontology URL. If the ontology is included in the EMBL-EBI Ontology Lookup Service (OLS) set of
ontologies, the OLS URL should be used (e.g., https://www.ebi.ac.uk/ols/ontologies/ncbitaxon).
top_node:
type: object
description: Term to use as top node for ontology
properties:
id:
type: string
description: Ontology identifer for the top node term
value:
type: string
description: Ontology value for the top node term
# The overall study with a globally unique study_id
Study:
discriminator: AIRR
type: object
properties:
study_id:
type: string
description: Unique ID assigned by study registry
example: PRJNA001
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Study ID
study_title:
type: string
description: Descriptive study title
example: Effects of sun light exposure of the Treg repertoire
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Study title
study_type:
$ref: '#/Ontology'
description: Type of study design
example:
id: C15197
value: Case-Control Study
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Study type
format: ontology
ontology:
draft: true
name: NCIT
url: https://www.ebi.ac.uk/ols/ontologies/ncit
top_node:
id: C63536
value: Study
study_description:
type: string
description: Generic study description
example: Longer description
inclusion_exclusion_criteria:
type: string
description: List of criteria for inclusion/exclusion for the study
example: "Include: Clinical P. falciparum infection; Exclude: Seropositive for HIV"
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Study inclusion/exclusion criteria
grants:
type: string
description: Funding agencies and grant numbers
example: NIH, award number R01GM987654
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Grant funding agency
collected_by:
type: string
description: 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.
example: Dr. P. Stibbons, p.stibbons@unseenu.edu
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Contact information (data collection)
lab_name:
type: string
description: Department of data collector
example: Department for Planar Immunology
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Lab name
lab_address:
type: string
description: Institution and institutional address of data collector
example: School of Medicine, Unseen University, Ankh-Morpork, Disk World
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Lab address
submitted_by:
type: string
description: Full contact information of the data depositor, i.e. the person submitting the data to a repository. This is supposed to be a short-lived and technical role until the submission is relased.
example: Adrian Turnipseed, a.turnipseed@unseenu.edu
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Contact information (data deposition)
pub_ids:
type: string
description: Publications describing the rationale and/or outcome of the study
example: "PMID:85642"
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Relevant publications
keywords_study:
type: array
items:
type: string
enum:
- contains_ig
- contains_tcr
- contains_single_cell
- contains_paired_chain
description: Keywords describing properties of one or more data sets in a study
example:
- contains_ig
- contains_paired_chain
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: study
name: Keywords for study
# 1-to-n relationship between a study and its subjects
# subject_id is unique within a study
Subject:
discriminator: AIRR
type: object
properties:
subject_id:
type: string
description: Subject ID assigned by submitter, unique within study
example: SUB856413
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Subject ID
synthetic:
type: boolean
description: TRUE for libraries in which the diversity has been synthetically generated (e.g. phage display)
x-airr:
miairr: true
required: true
nullable: false
set: 1
subset: subject
name: Synthetic library
organism:
$ref: '#/Ontology'
description: Binomial designation of subject's species
example:
id: 9096
value: Homo sapiens
x-airr:
miairr: true
required: true
nullable: false
set: 1
subset: subject
name: Organism
format: ontology
ontology:
draft: false
name: NCBITAXON
url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node:
id: 7776
value: Gnathostomata
sex:
type: string
enum:
- male
- female
- pooled
- hermaphrodite
- intersex
- "not collected"
- "not applicable"
description: Biological sex of subject
example: female
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Sex
format: controlled vocabulary
age:
type: string
x-airr:
deprecated: true
age_min:
type: number
description: Specific age or lower boundary of age range.
example: 60
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Age minimum
age_max:
type: number
description: Upper boundary of age range or equal to age_min for specific age. This field should only be null if age_min is null.
example: 80
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Age maximum
age_unit:
$ref: '#/Ontology'
description: Unit of age range
example:
id: UO_0000036
value: year
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Age unit
format: ontology
ontology:
draft: true
name: Units of measurement ontology
url: https://www.ebi.ac.uk/ols/ontologies/UO
top_node:
id: UO_0000003
value: time unit
age_event:
type: string
description: 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.
example: enrollment
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Age event
ancestry_population:
type: string
description: Broad geographic origin of ancestry (continent)
example: list of continents, mixed or unknown
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Ancestry population
ethnicity:
type: string
description: Ethnic group of subject (defined as cultural/language-based membership)
example: English, Kurds, Manchu, Yakuts (and other fields from Wikipedia)
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Ethnicity
race:
type: string
description: Racial group of subject (as defined by NIH)
example: White, American Indian or Alaska Native, Black, Asian, Native Hawaiian or Other Pacific Islander, Other
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Race
strain_name:
type: string
description: Non-human designation of the strain or breed of animal used
example: C57BL/6J
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Strain name
linked_subjects:
type: string
description: Subject ID to which `Relation type` refers
example: SUB1355648
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Relation to other subjects
link_type:
type: string
description: Relation between subject and `linked_subjects`, can be genetic or environmental (e.g.exposure)
example: father, daughter, household
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: subject
name: Relation type
diagnosis:
type: array
description: Diagnosis information for subject
items:
$ref: '#/Diagnosis'
# 1-to-n relationship between a subject and its diagnoses
Diagnosis:
discriminator: AIRR
type: object
properties:
study_group_description:
type: string
description: Designation of study arm to which the subject is assigned to
example: control
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Study group description
disease_diagnosis:
type: string
description: Diagnosis of subject
example: Multiple myeloma
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Diagnosis
disease_length:
type: string
description: Time duration between initial diagnosis and current intervention
example: 23 months
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Length of disease
format: physical quantity
disease_stage:
type: string
description: Stage of disease at current intervention
example: Stage II
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Disease stage
prior_therapies:
type: string
description: List of all relevant previous therapies applied to subject for treatment of `Diagnosis`
example: melphalan/prednisone
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Prior therapies for primary disease under study
immunogen:
type: string
description: Antigen, vaccine or drug applied to subject at this intervention
example: bortezomib
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Immunogen/agent
intervention:
type: string
description: Description of intervention
example: systemic chemotherapy, 6 cycles, 1.25 mg/m2
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Intervention definition
medical_history:
type: string
description: Medical history of subject that is relevant to assess the course of disease and/or treatment
example: MGUS, first diagnosed 5 years prior
x-airr:
miairr: true
required: true
nullable: true
set: 1
subset: diagnosis and intervention
name: Other relevant medical history
# 1-to-n relationship between a subject and its samples
# sample_id is unique within a study
Sample:
discriminator: AIRR
type: object
properties:
sample_id:
type: string
description: Sample ID assigned by submitter, unique within study
example: SUP52415
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Biological sample ID
sample_type:
type: string
description: The way the sample was obtained, e.g. fine-needle aspirate, organ harvest, peripheral venous puncture
example: Biopsy
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Sample type
tissue:
type: string
description: The actual tissue sampled, e.g. lymph node, liver, peripheral blood
example: Bone marrow
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Tissue
anatomic_site:
type: string
description: The anatomic location of the tissue, e.g. Inguinal, femur
example: Iliac crest
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Anatomic site
disease_state_sample:
type: string
description: Histopathologic evaluation of the sample
example: Tumor infiltration
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Disease state of sample
collection_time_point_relative:
type: string
description: Time point at which sample was taken, relative to `Collection time event`
example: "14 d"
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Sample collection time
format: physical quantity
collection_time_point_reference:
type: string
description: Event in the study schedule to which `Sample collection time` relates to
example: Primary vaccination
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Collection time event
biomaterial_provider:
type: string
description: Name and address of the entity providing the sample
example: Tissues-R-Us, Tampa, FL, USA
x-airr:
miairr: true
required: true
nullable: true
set: 2
subset: sample
name: Biomaterial provider
# 1-to-n relationship between a sample and processing of its cells
CellProcessing:
discriminator: AIRR
type: object
properties:
tissue_processing:
type: string
description: Enzymatic digestion and/or physical methods used to isolate cells from sample
example: Collagenase A/Dnase I digested, followed by Percoll gradient
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Tissue processing
cell_subset:
$ref: '#/Ontology'
description: Commonly-used designation of isolated cell population
example:
id: CL_0000972
value: class switched memory B cell
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Cell subset
format: ontology
ontology:
draft: true
name: CL
url: https://www.ebi.ac.uk/ols/ontologies/cl
top_node:
id: CL_0000542
value: lymphocyte
cell_phenotype:
type: string
description: List of cellular markers and their expression levels used to isolate the cell population
example: CD19+ CD38+ CD27+ IgM- IgD-
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Cell subset phenotype
cell_species:
$ref: '#/Ontology'
description: >
Binomial designation of the species from which the analyzed cells originate. Typically, this value
should be identical to `organism`, if which case it SHOULD NOT be set explicitly. Howver, there are
valid experimental setups in which the two might differ, e.g. chimeric animal models. If set, this
key will overwrite the `organism` information for all lower layers of the schema.
example:
id: 9096
value: Homo sapiens
x-airr:
miairr: false
required: false
nullable: true
format: ontology
ontology:
draft: false
name: NCBITAXON
url: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon
top_node:
id: 7776
value: Gnathostomata
single_cell:
type: boolean
description: TRUE if single cells were isolated into separate compartments
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Single-cell sort
cell_number:
type: integer
description: Total number of cells that went into the experiment
example: 1000000
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Number of cells in experiment
cells_per_reaction:
type: integer
description: Number of cells for each biological replicate
example: 50000
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Number of cells per sequencing reaction
cell_storage:
type: boolean
description: TRUE if cells were cryo-preserved between isolation and further processing
example: TRUE
x-airr:
miairr: true
required: true
nullable: false
set: 3
subset: process (cell)
name: Cell storage
cell_quality:
type: string
description: Relative amount of viable cells after preparation and (if applicable) thawing
example: 90% viability as determined by 7-AAD
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Cell quality
cell_isolation:
type: string
description: Description of the procedure used for marker-based isolation or enrich cells
example: Cells were stained with fluorochrome labeled antibodies and then sorted on a FlowMerlin (CE) cytometer
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Cell isolation / enrichment procedure
cell_processing_protocol:
type: string
description: 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
example: Stimulated wih anti-CD3/anti-CD28
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (cell)
name: Processing protocol
# object for PCR primer targets
PCRTarget:
discriminator: AIRR
type: object
properties:
pcr_target_locus:
type: string
enum:
- IGH
- IGI
- IGK
- IGL
- TRA
- TRB
- TRD
- TRG
description: >
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.
example: IGK
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (nucleic acid [pcr])
name: Target locus for PCR
format: controlled vocabulary
forward_pcr_primer_target_location:
type: string
description: Position of the most distal nucleotide templated by the forward primer or primer mix
example: IGHV, +23
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (nucleic acid [pcr])
name: Forward PCR primer target location
reverse_pcr_primer_target_location:
type: string
description: Position of the most proximal nucleotide templated by the reverse primer or primer mix
example: IGHG, +57
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (nucleic acid [pcr])
name: Reverse PCR primer target location
# generally, a 1-to-1 relationship between a CellProcessing and processing of its nucleic acid
# but may be 1-to-n for technical replicates.
NucleicAcidProcessing:
discriminator: AIRR
type: object
properties:
template_class:
type: string
enum:
- DNA
- RNA
description: The class of nucleic acid that was used as primary starting material for the following procedures
example: RNA
x-airr:
miairr: true
required: true
nullable: false
set: 3
subset: process (nucleic acid)
name: Target substrate
format: controlled vocabulary
template_quality:
type: string
description: Description and results of the quality control performed on the template material
example: RIN 9.2
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (nucleic acid)
name: Target substrate quality
template_amount:
type: string
description: Amount of template that went into the process
example: 1000 ng
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (nucleic acid)
name: Template amount
format: physical quantity
library_generation_method:
type: string
enum:
- "PCR"
- "RT(RHP)+PCR"
- "RT(oligo-dT)+PCR"
- "RT(oligo-dT)+TS+PCR"
- "RT(oligo-dT)+TS(UMI)+PCR"
- "RT(specific)+PCR"
- "RT(specific)+TS+PCR"
- "RT(specific)+TS(UMI)+PCR"
- "RT(specific+UMI)+PCR"
- "RT(specific+UMI)+TS+PCR"
- "RT(specific)+TS"
- "other"
description: Generic type of library generation
example: RT(oligo-dT)+TS(UMI)+PCR
x-airr:
miairr: true
required: true
nullable: false
set: 3
subset: process (nucleic acid)
name: Library generation method
format: controlled vocabulary
library_generation_protocol:
type: string
description: Description of processes applied to substrate to obtain a library that is ready for sequencing
example: cDNA was generated using
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (nucleic acid)
name: Library generation protocol
library_generation_kit_version:
type: string
description: When using a library generation protocol from a commercial provider, provide the protocol version number
example: v2.1 (2016-09-15)
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (nucleic acid)
name: Protocol IDs
pcr_target:
type: array
description: >
If a PCR step was performed that specifically targets the IG/TR loci, the target and primer locations
need to be provided here. This field holds an array of PCRTarget objects, so that multiplex PCR setups
amplifying multiple loci at the same time can be annotated using one record per locus. PCR setups not
targeting any specific locus must not annotate this field but select the appropriate
library_generation_method instead.
items:
$ref: '#/PCRTarget'
complete_sequences:
type: string
enum:
- partial
- complete
- "complete+untemplated"
description: >
To be considered `complete`, the procedure used for library construction MUST generate sequences that
1) include the first V segment codon that encodes the mature polypeptide chain (i.e. after the
leader sequence) and 2) include the last complete codon of the J segment (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.
example: partial
x-airr:
miairr: true
required: true
nullable: false
set: 3
subset: process (nucleic acid)
name: Complete sequences
format: controlled vocabulary
physical_linkage:
type: string
enum:
- none
- "hetero_head-head"
description: >
Describes the mode of linkage if a method was used which physically links nucleic acids derived from
distinct loci in a single-cell context.
example: hetero_head-head
x-airr:
miairr: true
required: true
nullable: false
set: 3
subset: process (nucleic acid)
name: Physical linkage of different loci
format: controlled vocabulary
# 1-to-n relationship between a NucleicAcidProcessing and SequencingRun with resultant raw sequence file(s)
SequencingRun:
discriminator: AIRR
type: object
properties:
sequencing_run_id:
type: string
description: ID of sequencing run assigned by the sequencing facility
example: 160101_M01234_0201_000000000-D2T7V
x-airr:
miairr: true
required: true
nullable: true
set: 3
subset: process (sequencing)
name: Batch number
total_reads_passing_qc_filter:
type: integer
description: Number of usable reads for analysis
example: 10365118