ISADotNet

ISA compliant experimental metadata toolkit in F#

The library contains types and functionality for creating and working on experimental metadata in ISA format. Additionally, the types can easily be written to and read from Json files in ISAJson format and Microsoft Excel files in ISATab format.

Installation

The ISADotNet nuget package can be found here

The ISADotNet.XLSX nuget package can be found here

Adding a package reference via dotnet: dotnet add package ISADotNet --version 0.1.0

Adding a package reference in F# interactive: #r "nuget: ISADotNet, 0.1.0"

What is ISA?

ISA is a specification for annotation of research data. The metadata in nested in three different layers: Investigation, Study and Assay.

Around these three main entities, the following abstract datamodel is specified:

Source: https://isa-specs.readthedocs.io/en/latest/_images/isa_model_1_ccoded.png

Additional Info: https://isa-specs.readthedocs.io/en/latest/isamodel.html

Usage

Querymodel

The querymodel is used to intuitively retreive information from the ISA metadata.

#r @"nuget: ISADotNet.XLSX"

open ISADotNet


let _,_,persons,a = ISADotNet.XLSX.AssayFile.Assay.fromFile assayPath

let qa = QueryModel.QAssay.fromAssay a

Retreiving values:

let firstValue = qa.Values().First

firstValue.NameText
firstValue.ValueText

->

val it: string = "Sample type"

val it: string = "cell culture"

Retreiving nodes:

qa.Sources().Head
qa.FirstSamples().Head
qa.FirstData().Head
qa.LastData().Head

->

val it: string = "001_uncult_8°"

val it: string = "001-007_uncult_8°_son"

val it: string = "20210913_1558_001.mzml"

val it: string = "20210913_1558_001.mzml"

Nodes as anchors:

let nodeOfInterest = qa.Samples().[5]

qa.FirstProcessedDataOf(nodeOfInterest)

->

val nodeOfInterest: string = "008-014_uncult_22°_ext"

val it: string list =
  ["20210913_1558_021.mzml"; "20210913_1558_022.mzml";
   "20210913_1558_023.mzml"; "20210913_1558_024.mzml";
   "20210913_1558_025.mzml"; "20210913_1558_026.mzml";
   "20210913_1558_027.mzml"; "20210913_1558_028.mzml";
   "20210913_1558_029.mzml"; "20210913_1558_030.mzml";
   "20210913_1558_031.mzml"; "20210913_1558_032.mzml";
   "20210913_1558_033.mzml"; "20210913_1558_034.mzml";
   "20210913_1558_035.mzml"; "20210913_1558_036.mzml";
   "20210913_1558_037.mzml"; "20210913_1558_038.mzml";
   "20210913_1558_039.mzml"; "20210913_1558_040.mzml"]

---

qa.SourcesOf(nodeOfInterest)

->

val it: string list =
  ["008_uncult_22°"; "009_uncult_22°"; "010_uncult_22°"; "011_uncult_22°";
   "012_uncult_22°"; "013_uncult_22°"; "014_uncult_22°"]

---

qa.PreviousCharacteristicsOf(nodeOfInterest)
    .Item("Organism")
    .ValueText

->

val it: string = "Chlamydomonas rheinhardtii"

---

qa.SucceedingParametersOf(nodeOfInterest)
|> Seq.map (fun p -> p.HeaderText,p.ValueText)
|> Seq.take 5
|> Seq.toList

->

val it: (string * string) list =
  [("Parameter [Library strategy]", "Illumina library prep");
   ("Parameter [Library Selection]", "cDNA");
   ("Parameter [Library layout]", "single-end");
   ("Parameter [Library preparation kit]",
    "CleanTag® Small RNA Library Prep Kit");
   ("Parameter [Library preparation kit version]", "3")]