Creating A Dataset

This walkthrough builds a small process graph from F# objects. The goal is to show the model shape rather than every field in the specification.

Dataset

Start with a dataset. Administrative metadata is optional, but an identifier is the stable handle for the dataset.

let dataset = Dataset("demo-dataset")
dataset.Name <- Some "Minimal ProcessCore example"
dataset.Description <- Some "One extraction process with nested quality control."

LabProtocol

A protocol describes the method. Formal parameters define expected knobs, for which values should be provided when the protocol is executed.

let protocol = LabProtocol()
let temperature = FormalParameter("temperature")
protocol.Name <- Some "Extraction"
protocol.IntendedUse <- Some (DefinedTerm("sample extraction"))
protocol.AddParameter(temperature)

Components are non-transformed entities in a protocol, such as machines or reagents.

let centrifuge = PropertyValue(name = "centrifuge", value = "Eppendorf 5420")
let buffer = PropertyValue(name = "buffer", value = "PBS")

protocol.AddLabEquipment(centrifuge)
protocol.AddLabEquipment(buffer)

LabProcess

LabProcesses are the core of the process graph. They are concrete executions of a protocol, with specific parameter values, and input and output entities.

First, we define input and output, i.e. Material or Data nodes.

let leaf = Material("Leaf tissue")

let extractData = Data("raw/extract.csv")
extractData.EncodingFormat <- Some "text/csv"

A LabProcess connects those inputs to outputs. We also attach parameter values to the process, which should correspond to the protocol's formal parameters.

let extraction = LabProcess("Extraction")
let degrees25 = PropertyValue(name = "temperature", value = "25", unit = "degree Celsius", instanceOf = temperature)
extraction.ExecutesProtocol <- Some protocol
extraction.AddInputMaterial(leaf)
extraction.AddOutputData(extractData)
extraction.AddParameterValue(degrees25)

dataset.AddProcess(extraction)

Nested Datasets

Datasets can contain child datasets. When a child dataset is added, its process nodes are re-canonicalized against the root dataset.

let child = Dataset("qc-dataset")
child.Name <- Some "Quality control"

let qcReport = Data("qc/extract-report.tsv")

let qc = LabProcess("Quality Control")
qc.AddInputData(extractData)
qc.AddOutputData(qcReport)
let threshold = FormalParameter("threshold")
let threshold95 = PropertyValue(name = "threshold", value = "0.95", instanceOf = threshold)
qc.AddParameterValue(threshold95)

child.AddProcess(qc)
dataset.AddPart(child)

The parent process output and the child process input are the same logical Data node: same path, no selector. After AddPart, they are also the same object instance in the root dataset.

let qcInputAfterAttach =
    match qc.Inputs.[0] with
    | DataNode d -> d
    | MaterialNode _ -> failwith "Expected data input"

let sharedDataIdentity =
    obj.ReferenceEquals(extractData, qcInputAfterAttach)

sharedDataIdentity

true

The graph is now queryable from either the dataset or any node.

let finalNodes =
    dataset.FinalNodes()
    |> Seq.map (fun n -> n.Key())
    |> Seq.toList

finalNodes

["D:qc/extract-report.tsv"]

What To Use When