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DataPLANT

Datamap

The Datamap files used to annotate data files are modeled in ARCtrl as Datamap objects.

They can be found in Study, Assay, Workflow and Run folders and therefore in the ArcStudy, ArcAssay, ArcWorkflow and ArcRun classes.

The Datamap itself is a table with fixed columns. Each row in the Datamap represents and annotates a Data Fragment of a data file and is modeled as an DataContext object. The Datamap therefore consists of a collection of DataContext objects.

Basic Usage

Section titled Basic Usage

In this small tutorial we will show how to create a Datamap and integrate it into an ARC. The Datamap will describe a CSV file called sugar_result.csv located in assays/MyAssay/dataset, with two columns, each containing measurements of cellular sugar content:

sugar_result.csv

sug_s1_r1sug_s1_r2
15.514.8
15.215.1
15.914.7

Preparation

Section titled Preparation

First, we will prepare some ontology terms that we will use in the Datamap.

open ARCtrl


let molecule_count = OntologyAnnotation(
    name="molecule count",
    tsr ="UO",
    tan="http://purl.obolibrary.org/obo/UO_0000192"
)


let mmol_p_kg = OntologyAnnotation(
    name="Millimole per Kilogram",
    tsr="NCIT",
    tan="http://purl.obolibrary.org/obo/NCIT_C68892"
)


let float_type = OntologyAnnotation(
    name="float",
    tsr="NCIT",
    tan="http://purl.obolibrary.org/obo/NCIT_C48150"
)

Create a Datamap object

Section titled Create a Datamap object

We create a Datamap that describes two columns of a CSV file.

Here we create two DataContext objects, which represent each a row in the Datamap and annotate one column in the CSV file.

Afterwards, we will initialize a Datamap object with the two DataContext objects.

let col1Entry = DataContext(
    name="assays/MyAssay/dataset/sugar_result.csv#col=1",
    format="text/csv",
    selectorFormat="https://datatracker.ietf.org/doc/html/rfc7111",
    explication=molecule_count,
    unit=mmol_p_kg,
    objectType=float_type,
    label="sug_s1_r1",
    description="Measured sugar concentration in sample 1, replicate 1"
)


let col2Entry = DataContext(
    name="assays/MyAssay/dataset/sugar_result.csv#col=2",
    format="text/csv",
    selectorFormat="https://datatracker.ietf.org/doc/html/rfc7111",
    explication=molecule_count,
    unit=mmol_p_kg,
    objectType=float_type,
    label="sug_s1_r2",
    description="Measured sugar concentration in sample 1, replicate 2"
)


let datamap = DataMap(ResizeArray[col1Entry; col2Entry])

Writing the Datamap

Section titled Writing the Datamap

We have two approaches to write the Datamap to a file:

1. Single File

Using the XlsxController to write the Datamap to a singular Excel file, usable in or out of the ARC context.

open ARCtrl.Spreadsheet


XlsxController.Datamap.toXlsxFile("isa.datamap.xlsx", datamap)

2. As part of an ARC

Include the Datamap in an ARC and write or update the whole ARC, which will include the Datamap as well.

  1. First, we load the ARC from a repository.
  2. Then we set the DataMap of the assay “MyAssay” to our datamap.
  3. Finally, we update the ARC to write the changes back to the repository.
let arc = ARC.load("path_to_my_arc")


arc.ISA.Value.GetAssay("MyAssay").DataMap <- Some datamap


arc.Update("path_to_my_arc")