Annotation Tables

The Tables shown in xlsx files in ISA files are modelled in ARCtrl as ArcTable object. These objects are assigned as ArcTables interface in both ArcAssay and ArcStudy.

ArcTables are column-major objects, with the columns being typed as CompositeColumn. Each CompositeColumn consists of a CompositeHeader and a collection of CompositeCells, which make up the values of the table.

Note

As the prefix Composite suggests, these types do not represent a list of singular values.

Instead, each CompositeColumn may translate to 1, 3 or 4 xlsx columns, depending on the column type.

Building an ArcTable

Section titled Building an ArcTable

FSharp

open ARCtrl


let growth = ArcTable.init("Growth")

// create ontology annotation for "species"
let oa_species =
    OntologyAnnotation(
        "species", "NCIT", "NCIT:C45293"
    )
// create ontology annotation for "chlamy"
let oa_chlamy =
    OntologyAnnotation(
        "Chlamydomonas reinhardtii", "NCBITaxon", "NCBITaxon_3055"
    )

let oa_time =
    OntologyAnnotation(
        "time", "EFO", "EFO:0000721"
    )

let oa_day =
    OntologyAnnotation(
        "day", "UO", "UO:0000033"
    )

// This will create an input column with one row cell.
// In xlsx this will be exactly 1 column.
growth.AddColumn(
    CompositeHeader.Input IOType.Source,
    [|CompositeCell.createFreeText "Input1"|]
)

// this will create an Characteristic [species] column with one row cell.
// in xlsx this will be exactly 3 columns.
growth.AddColumn(
    CompositeHeader.Characteristic oa_species,
    [|CompositeCell.createTerm oa_chlamy|]
)

// this will create an Parameter [time] column with one row cell.
// in xlsx this will be exactly 4 columns.
growth.AddColumn(
    CompositeHeader.Parameter oa_species,
    [|CompositeCell.createUnitized("5", oa_day)|]
)

growth.AddColumn(
    CompositeHeader.Output IOType.Sample,
    [|CompositeCell.createFreeText "Output1"|]
)

JavaScript

import {ArcTable, OntologyAnnotation, CompositeHeader, CompositeCell, IOType} from "@nfdi4plants/arctrl";


let growth = ArcTable.init("Growth")

let oa_species = new OntologyAnnotation("species", "NCIT", "NCIT:C45293")

let oa_chlamy = new OntologyAnnotation("Chlamydomonas reinhardtii", "NCBITaxon", "NCBITaxon_3055")

let oa_time = new OntologyAnnotation("time", "EFO", "EFO:0000721")

let oa_day = new OntologyAnnotation("day", "UO", "UO:0000033")


// This will create an input column with one row cell.
// In xlsx this will be exactly 1 column.
growth.AddColumn(CompositeHeader.input(IOType.source()), [CompositeCell.createFreeText("Input1")])

// This will create an Characteristic [species] column with one row cell.
// In xlsx this will be exactly 3 columns.
growth.AddColumn(CompositeHeader.characteristic(oa_species), [CompositeCell.createTerm(oa_chlamy)])

// This will create an Parameter [time] column with one row cell.
// In xlsx this will be exactly 4 columns.
growth.AddColumn(CompositeHeader.parameter(oa_time), [CompositeCell.createUnitized("5", oa_day)])

// This will create an Output column with one row cell.
// In xlsx this will be exactly 1 columns.
growth.AddColumn(CompositeHeader.output(IOType.sample()), [CompositeCell.createFreeText("Output1")])

Python

from arctrl.arctrl import ArcTable, OntologyAnnotation, CompositeHeader, CompositeCell, IOType

growth = ArcTable.init("Growth")

oa_species = OntologyAnnotation("species", "NCIT", "NCIT:C45293")

oa_chlamy = OntologyAnnotation("Chlamydomonas reinhardtii", "NCBITaxon", "NCBITaxon_3055")

oa_time = OntologyAnnotation("time", "EFO", "EFO:0000721")

oa_day = OntologyAnnotation("day", "UO", "UO:0000033")


# This will create an input column with one row cell.
# In xlsx this will be exactly 1 column.
growth.AddColumn(CompositeHeader.input(IOType.source()), [CompositeCell.create_free_text("Input1")])

# This will create an Characteristic [species] column with one row cell.
# In xlsx this will be exactly 3 columns.
growth.AddColumn(CompositeHeader.characteristic(oa_species), [CompositeCell.create_term(oa_chlamy)])

# This will create an Parameter [time] column with one row cell.
# In xlsx this will be exactly 4 columns.
growth.AddColumn(CompositeHeader.parameter(oa_time), [CompositeCell.create_unitized("5", oa_day)])

# This will create an Output column with one row cell.
# In xlsx this will be exactly 1 columns.
growth.AddColumn(CompositeHeader.output(IOType.sample()), [CompositeCell.create_free_text("Output1")])