VALIDATIONS.md

Validations performed by pret

This document summarizes all the validations that are performed by pret

Validation of scalar attributes

Attribute	Validation
:measurement/cell-count	>= 0
:measurement/tpm	>= 0
:measurement/fpkm	>= 0
:measurement/rpkm	>= 0
:measurement/rsem-raw-count	>= 0
:measurement/rsem-normalized-count	>= 0
:measurement/rsem-scaled-estimate	>= 0
:measurement/nanostring-count	>= 0
:measurement/vaf	[0, 1]
:measurement/percent-of-total-cells	[0, 1]
:measurement/percent-of-parent	[0, 1]
:measurement/percent-of-nuclei	[0, 1]
:measurement/percent-of-lymphocytes	[0, 1]
:measurement/percent-of-leukocytes	[0, 1]
:measurement/percent-of-live	[0, 1]
:measurement/live-percent	[0, 1]
:measurement/percent-of-singlets	[0, 1]
:measurement/a-allele-cn	[-2, 50]
:measurement/b-allele-cn	[-2, 50]
:measurement/baf-n	[0, 1]
:measurement/baf	[0, 1]
:measurement/t-alt-count	>= 0
:measurement/t-ref-count	>= 0
:measurement/t-depth	>= 0
:measurement/n-alt-count	>= 0
:measurement/n-ref-count	>= 0
:measurement/n-depth	>= 0
:measurement/cell-count	>= 0
:measurement/singlets-count	>= 0
:measurement/live-count	>= 0
:measurement/lymphocyte-count	>= 0
:measurement/leukocyte-count	>= 0
:measurement/nuclei-count	>= 0
:measurement/average-depth	>= 0
:measurement/fraction-aligned-reads	[0, 1]
:measurement/read-count	>= 0
:measurement/read-count-otu	>= 0
:measurement/read-count-otu-rarefied	>= 0
:measurement/tumor-purity	[0, 1]
:measurement/contamination	[0, 1]
:measurement/tss-score	>= 0
:measurement/fraction-reads-in-peaks	[0, 1]
:measurement/reads-count	>= 0
:measurement/total-reads	>= 0
:measurement/cfdna-ng-mL	>= 0
:measurement/pg-mL	>= 0
:measurement/ng-mL	>= 0
:measurement/U-L	>= 0
:measurement/nanostring-signature-score	>= 0
:measurement/chromvar-tf-binding-score	>= 0
:measurement/absolute-cn	>= 0
:measurement/tmb-indel	>= 0
:measurement/tmb-snv	>= 0
:measurement/tmb-total	>= 0
:measurement/tcr-count	>= 0
:measurement/tcr-clonality	[0, 1]
:measurement/tcr-frequency	[0, 1]
:clinical-observation/pfs	>= 0
:clinical-observation/dfi	>= 0
:clinical-observation/os	>= 0
:clinical-observation/ttf	>= 0
:clinical-observation/bmi	>= 0
:clinical-observation/ldh	>= 0
:clinical-observation/absolute-leukocyte-count	>= 0
:clinical-observation/absolute-monocyte-count	>= 0
:timepoint/relative-order	> 0
:timepoint/offset	> 0
:study-day/day	>= 0
:therapy/line	> 0
:therapy/order	> 0
:atac-peak/-log10pvalue	>= 0
:atac-peak/-log10qvalue	>= 0
:atac-peak/quality-score	>= 0
:atac-peak/summit-offset	>= 0
:subject/age	>= 0

Validation of required attributes for entity kinds

kind	required attributes
sample	:sample/id :sample/subject
dataset	:dataset/name :dataset/samples :dataset/assays :dataset/timepoints :dataset/subjects
assay	:assay/name :assay/measurement-sets :assay/technology
measurement-set	:measurement-set/name :measurement-set/measurements
clinical-observation-set	:clinical-observation-set/name :clinical-observation-set/clinical-observations
clinical-observation	:clinical-observation/subject :clinical-observation/timepoint
timepoint	:timepoint/id :timepoint/type If, and only if, part of a treatment regimen: :timepoint/relative-order :timepoint/treatment-regimen
genomic-coordinate	:genomic-coordinate/id :genomic-coordinate/assembly :genomic-coordinate/contig :genomic-coordinate/start :genomic-coordinate/end :genomic-coordinate/strand
variant	:variant/id :variant/genomic-coordinates :variant/ref-allele :variant/alt-allele
subject	:subject/id
treatment-regimen	:treatment-regimen/name
cell-population	:cell-population/name :cell-population/from-clustering If from-clusteringis false: :cell-population/cell-type
therapy	:therapy/treatment-regimen :therapy/order
cnv	:cnv/genomic-coordinates
tcr	:tcr/id At least one of the following: :tcr/alhpa-1 :tcr/beta
measurement	:measurement/sample (see below for more details)
drug-regimen	:drug-regimen/drug
clinical-trial	:clinical-trial/nct-number
atac-peak	:atac-peak/name :atac-peak/genomic-coordinates :atac-peak/jointly-called :atac-peak/fixed-width
otu	:otu/id :otu/kingdom
meddra-disease	:meddra-disease/preferred-name :meddra-disease/synonyms
gdc-anatomic-site	:gdc-anatomic-site/name
ctcae-adverse-event	:ctcae-adverse-event/name :ctcae-adverse-event/meddra-code
gene-product	:gene-product/id :gene-product/gene
nanostring-signature	:nanostring-signature/name :nanostring-signature/genes
study-day	:study-day/id :study-day/day :study-day/reference-event

Validation of measurements

Additionally measurements are further validated based on their kind (which is determined by their target)

measurement kind	required attributes	allowed optional attributes
cell population	:measurement/sample :measurement/cell-population	:measurement/region-of-interest :measurement/epitope :measurement/percent-of-total-cells :measurement/median-channel-value :measurement/cell-count :measurement/percent-of-nuclei :measurement/percent-of-lymphocytes :measurement/percent-of-leukocytes :measurement/percent-of-live :measurement/percent-of-parent :measurement/percent-of-singlets
variant	:measurement/sample :measurement/variant	:measurement/t-alt-count :measurement/t-ref-count :measurement/t-depth :measurement/n-alt-count :measurement/n-ref-count :measurement/n-depth :measurement/vaf
cnv	:measurement/sample :measurement/cnv	:measurement/a-allele-cn :measurement/b-allele-cn :measurement/segment-mean-lrr :measurement/loh :measurement/baf :measurement/baf-n :measurement/absolute-cn
gene-product	:measurement/sample :measurement/gene-product	:measurement/tpm :measurement/fpkm :measurement/rsem-raw-count :measurement/rsem-normalized-count :measurement/rsem-scaled-estimate :measurement/rpkm :measurement/nanostring-count :measurement/read-count
epitope	:measurement/sample :measurement/epitope	:measurement/median-channel-value :measurement/ng-mL :measurement/U-L :measurement/nanostring-count
nanostring-signature	:measurement/sample :measurement/nanostring-signature :measurement/nanostring-signature-score
atac-peak	:measurement/sample :measurement/atac-peak :measurement/reads-count
tcr	:measurement/sample :measurement/tcr-frequency :measurement/tcr-count :measurement/tcr-v :measurement/tcr-d :measurement/tcr-j
otu	:measurement/sample :measurement/otu	:measurement/read-count-otu :measurement/read-count-otu-rarefied
measurement witout target	:measurement/sample	:measurement/tcr-clonality :measurement/cell-count :measurement/singlets-count :measurement/live-count :measurement/lymphocyte-count :measurement/leukocyte-count :measurement/nuclei-count :measurement/live-percent :measurement/average-depth :measurement/fraction-aligned-reads :measurement/total-reads :measurement/tumor-purity :measurement/contamination :measurement/tss-score :measurement/fraction-reads-in-peaks :measurement/cfdna-ng-mL :measurement/tmb-indel :measurement/tmb-snv :measurement/tmb-total

Additionally every measurement, irrespective of kind, must have at least one of these attributes

:measurement/percent-of-total-cells
:measurement/median-channel-value
:measurement/cell-count
:measurement/percent-of-parent
:measurement/percent-of-nuclei
:measurement/percent-of-lymphocytes
:measurement/percent-of-leukocytes
:measurement/percent-of-live
:measurement/percent-of-singlets
:measurement/live-percent
:measurement/t-alt-count
:measurement/t-ref-count
:measurement/t-depth
:measurement/n-alt-count
:measurement/n-ref-count
:measurement/n-depth
:measurement/vaf
:measurement/a-allele-cn
:measurement/b-allele-cn
:measurement/segment-mean-lrr
:measurement/loh
:measurement/baf
:measurement/baf-n
:measurement/tpm
:measurement/fpkm
:measurement/rsem-raw-count
:measurement/rsem-normalized-count
:measurement/rsem-scaled-estimate
:measurement/rpkm
:measurement/nanostring-count
:measurement/median-channel-value
:measurement/ng-mL
:measurement/U-L
:measurement/tcr-clonality
:measurement/tcr-count
:measurement/tcr-frequency
:measurement/cell-count
:measurement/singlets-count
:measurement/live-count
:measurement/lymphocyte-count
:measurement/leukocyte-count
:measurement/nuclei-count
:measurement/average-depth
:measurement/fraction-aligned-reads
:measurement/read-count
:measurement/tumor-purity
:measurement/contamination
:measurement/tss-score
:measurement/fraction-reads-in-peaks
:measurement/chromvar-tf-binding-score
:measurement/nanostring-signature-score
:measurement/cfdna-ng-mL
:measurement/tmb-indel
:measurement/tmb-snv
:measurement/tmb-total
:measurement/variant
:measurement/absolute-cn
:measurement/protein-array-log-intensity
:measurement/luminex-mfi
:measurement/total-reads
:measurement/read-count
:measurement/read-count-otu
:measurement/read-count-otu-rarefied

Composite id validations

pret also validates that certain ids are obtained by concatenating other entity attributes with a specific separator

id	attributes	separator
:genomic-coordinate/id	:genomic-coordinate/assembly :genomic-coordinate/contig :genomic-coordinate/strand :genomic-coordinate/start :genomic-coordinate/end	:
:variant/id	:variant/genomic-coordinates :variant/ref-allele :variant/alt-allele	/