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miairr.yaml
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miairr.yaml
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study_id:
miairr_set: 1
miairr_subset: study
miairr_name: Study
format: free text
example: PRJNA001
study_title:
miairr_set: 1
miairr_subset: study
miairr_name: Study title
format: free text
example: Effects of sun light exposure of the Treg repertoire
study_description:
miairr_set: 1
miairr_subset: study
miairr_name: Study type
format: {"ontology": "NCIT", "top_node": "Study Design", "draft": true}
example: Case-Control Study
inclusion_exclusion_criteria:
miairr_set: 1
miairr_subset: study
miairr_name: Study inclusion/exclusion criteria
format: free text
example: "Include: Clinical P. falciparum infection; Exclude: Seropositive for HIV"
grants:
miairr_set: 1
miairr_subset: study
miairr_name: Grant funding agency
format: free text
example: NIH, award number R01GM987654
collected_by:
miairr_set: 1
miairr_subset: study
miairr_name: Contact information (data collection)
format: free text
example: Dr. P. Stibbons, p.stibbons@unseenu.edu
lab_name:
miairr_set: 1
miairr_subset: study
miairr_name: Lab name
format: free text
example: Department for Planar Immunology
lab_address:
miairr_set: 1
miairr_subset: study
miairr_name: Lab address
format: free text
example: School of Medicine, Unseen University, Ankh-Morpork, Disk World
submitted_by:
miairr_set: 1
miairr_subset: study
miairr_name: Contact information (data deposition)
format: free text
example: Adrian Turnipseed, a.turnipseed@unseenu.edu
pub_ids:
miairr_set: 1
miairr_subset: study
miairr_name: Relevant publications
format: PubMed ID
example: PMID85642
subject_id:
miairr_set: 1
miairr_subset: subject
miairr_name: Subject ID
format: free text
example: SUB856413
synthetic:
miairr_set: 1
miairr_subset: subject
miairr_name: Synthetic library
format: TRUE/FALSE
example: FALSE
organism:
miairr_set: 1
miairr_subset: subject
miairr_name: Organism
format: {"ontology": "NCBITAXON", "top_node": "Gnathostomata", "draft": false}
example: Homo sapiens
sex:
miairr_set: 1
miairr_subset: subject
miairr_name: Sex
format: {"controlled_vocabulary": ["male", "female", "pooled", "hermaphrodite", "intersex", "not collected", "not applicable"]}
example: female
age:
miairr_set: 1
miairr_subset: subject
miairr_name: Age
format: time duration and unit
example: 65 a
age_event:
miairr_set: 1
miairr_subset: subject
miairr_name: Age event
format: free text
example: enrollment
ancestry_population:
miairr_set: 1
miairr_subset: subject
miairr_name: Ancestry population
format: free text
example: list of continents, mixed or unknown
ethnicity:
miairr_set: 1
miairr_subset: subject
miairr_name: Ethnicity
format: free text
example: English, Kurds, Manchu, Yakuts (and other fields from Wikipedia)
race:
miairr_set: 1
miairr_subset: subject
miairr_name: Race
format: free text
example: White, American Indian or Alaska Native, Black, Asian, Native Hawaiian or Other Pacific Islander, Other
strain_name:
miairr_set: 1
miairr_subset: subject
miairr_name: Strain name
format: free text
example: C57BL/6J
linked_subjects:
miairr_set: 1
miairr_subset: subject
miairr_name: Relation to other subjects
format: free text
example: SUB1355648
link_type:
miairr_set: 1
miairr_subset: subject
miairr_name: Relation type
format: free text
example: father, daughter, household
study_group_description:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Study group description
format: free text
example: control
disease_diagnosis:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Diagnosis
format: free text
example: Multiple myeloma
disease_length:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Length of disease
format: time duration and unit
example: 23 months
disease_stage:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Disease stage
format: free text
example: Stage II
prior_therapies:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Prior therapies for primary disease under study
format: free text
example: melphalan/prednisone
immunogen:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Immunogen/agent
format: free text
example: bortezomib
intervention:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Intervention definition
format: free text
example: systemic chemotherapy, 6 cycles, 1.25 mg/m2
medical_history:
miairr_set: 1
miairr_subset: diagnosis and intervention
miairr_name: Other relevant medical history
format: free text
example: MGUS, first diagnosed 5 years prior
sample_id:
miairr_set: 2
miairr_subset: sample
miairr_name: Biological sample ID
format: free text
example: SUP52415
sample_type:
miairr_set: 2
miairr_subset: sample
miairr_name: Sample type
format: free text
example: Biopsy
tissue:
miairr_set: 2
miairr_subset: sample
miairr_name: Tissue
format: free text
example: Bone marrow
anatomic_site:
miairr_set: 2
miairr_subset: sample
miairr_name: Anatomic site
format: free text
example: Iliac crest
disease_state_sample:
miairr_set: 2
miairr_subset: sample
miairr_name: Disease state of sample
format: free text
example: Tumor infiltration
collection_time_point_relative:
miairr_set: 2
miairr_subset: sample
miairr_name: Sample collection time
format: free text
example: 14 d
collection_time_point_reference:
miairr_set: 2
miairr_subset: sample
miairr_name: Collection time event
format: free text
example: Primary vaccination
biomaterial_provider:
miairr_set: 2
miairr_subset: sample
miairr_name: Biomaterial provider
format: free text
example: Tissues-R-Us, Tampa, FL, USA
tissue_processing:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Tissue processing
format: free text
example: Collagenase A/Dnase I digested, followed by Percoll gradient
cell_subset:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Cell subset
format: {"ontology": "CL", "top_node": "lymphocyte", "draft": true}
example: class switched memory B cell
cell_phenotype:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Cell subset phenotype
format: free text
example: CD19+ CD38+ CD27+ IgM- IgD-
single_cell:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Single-cell sort
format: TRUE/FALSE
example: FALSE
cell_number:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Number of cells in experiment
format: number
example: 1000000
cells_per_reaction:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Number of cells per sequencing reaction
format: number
example: 50000
cell_storage:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Cell storage
format: TRUE/FALSE
example: TRUE
cell_quality:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Cell quality
format: free text
example: 90% viability as determined by 7-AAD
cell_isolation:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Cell isolation / enrichment procedure
format: free text
example: Cells were stained with fluorochrome labeled antibodies and then sorted on a FlowMerlin (CE) cytometer
cell_processing_protocol:
miairr_set: 3
miairr_subset: process (cell)
miairr_name: Processing protocol
format: free text
example: Stimulated wih anti-CD3/anti-CD28
template_class:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Target substrate
format: {"controlled_vocabulary": ["DNA", "RNA"]}
example: RNA
template_quality:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Target substrate quality
format: free text
example: RIN 9.2
template_amount:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Template amount
format: free text
example: 1000 ng
library_generation_method:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Library generation method
format: {"controlled_vocabulary": ["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"]}
example: RT(oligo-dT)+TS(UMI)+PCR
library_generation_protocol:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Library generation protocol
format: free text
example: cDNA was generated using
library_generation_kit_version:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Protocol IDs
format: free text
example: v2.1 (2016-09-15)
pcr_target_locus:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Target locus for PCR
format: free text
example: Constant region vs. V region amplification
forward_pcr_primer_target_location:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Forward PCR primer target location
format: free text
example: IGHV, +23
reverse_pcr_primer_target_location:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Reverse PCR primer target location
format: free text
example: IGHG, +57
complete_sequences:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Complete sequences
format: {"controlled_vocabulary": ["partial", "complete", "complete+untemplated"]}
example: partial
physical_linkage:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Physical linkage of different loci
format: {"controlled_vocabulary": ["none", "hetero_head-head"]}
example: hetero_head-head
total_reads_passing_qc_filter:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Total reads passing QC filter
format: number
example: 10365118
sequencing_platform:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Sequencing platform
format: free text
example: Alumina LoSeq 1000
read_length:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Read lengths
format: array of numbers
example: "[300,300]"
sequencing_facility:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Sequencing facility
format: free text
example: Seqs-R-Us, Vancouver, BC, Canada
sequencing_run_id:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Batch number
format: free text
example: 160101_M01234_0201_000000000-D2T7V
sequencing_run_date:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Date of sequencing run
format: ISO8601-compliant date
example: 2016-12-16
sequencing_kit:
miairr_set: 3
miairr_subset: process (nucleic acid)
miairr_name: Sequencing kit
format: free text
example: "FullSeq 600, Alumina, #M123456C0, 789G1HK"
raw_data:
miairr_set: 4
miairr_subset: data (raw reads)
miairr_name: Raw sequence data
format: FASTQ
example: <n/a>
software_versions:
miairr_set: 5
miairr_subset: process (computational)
miairr_name: Software tools and version numbers
format: free text
example: IgBLAST 1.6
paired_reads_assembly:
miairr_set: 5
miairr_subset: process (computational)
miairr_name: Paired read assembly
format: free text
example: PandaSeq (minimal overlap 50, threshold 0.8)
quality_thresholds:
miairr_set: 5
miairr_subset: process (computational)
miairr_name: Quality thresholds
format: free text
example: Average Phred score >=20
primer_match_cutoffs:
miairr_set: 5
miairr_subset: process (computational)
miairr_name: Primer match cutoffs
format: free text
example: Hamming distance <= 2
collapsing_method:
miairr_set: 5
miairr_subset: process (computational)
miairr_name: Collapsing method
format: free text
example: MUSCLE 3.8.31
data_processing_protocols:
miairr_set: 5
miairr_subset: process (computational)
miairr_name: Data processing protocols
format: free text
example: Data was processed using [...]
germline_database:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: V(D)J germline reference database
format: free text
example: ENSEMBL, Homo sapiens build 90, 2017-10-01
cell_id:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: Cell Index
format: free text
example: W06_046_091
v_call:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: V gene
format: free text
example: IGHV1-34*01
d_call:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: D gene
format: free text
example: IGHD2-2*01
j_call:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: J gene
format: free text
example: IGHJ4*01
c_call:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: C region
format: free text
example: IGHG1
junction:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: IMGT-JUNCTION nucleotide sequence
format: free text
example: TGTGCAAGAGCGGGAGTTTACGACGGATATACTATGGACTACTGG
junction_aa:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: IMGT-JUNCTION amino acid sequence
format: free text
example: CARAGVYDGYTMDYW
duplicate_count:
miairr_set: 6
miairr_subset: data (processed sequence)
miairr_name: Read count
format: number
example: 123