File size: 1,513 Bytes
9ae68e3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | type QuantityKind =
| "observed" | "inferred" | "derived" | "predicted"
| "constrained" | "encoded" | "executed";
type Datum<T> =
| { status: "present"; value: T }
| {
status: "missing";
reason: "not_measured" | "not_reported" | "failed_qc" | "unknown";
detail?: string;
};
type ArtifactRef =
| { status: "available"; artifactId: string; sha256: string }
| { status: "unavailable"; reason: string };
interface SourceLocator {
artifact: ArtifactRef;
recordLocator: string;
}
interface ExpressionObservation {
schemaVersion: "bio-semantics/1.0.0";
observationId: string;
datasetId: string;
sampleId: string;
geneId: string;
condition: Datum<string>;
timepoint: Datum<{ value: string; unit: string }>;
replicate: Datum<string>;
batch: Datum<string>;
cellType: Datum<string>;
measurement:
| {
kind: "raw_read_count";
quantityKind: "observed";
unit: "reads";
value: Datum<string>;
}
| {
kind: "normalized_expression";
quantityKind: "derived";
unit: string;
value: Datum<string>;
transformation: ArtifactRef;
};
quality: Array<{
name: string;
unit: string;
value: Datum<string>;
quantityKind: "observed" | "derived";
source: SourceLocator;
}>;
source: SourceLocator;
origin:
| { kind: "measurement" }
| {
kind: "synthetic_fixture";
fixtureId: string;
excludedFromScientificConclusions: true;
};
}
|