OBO.NET

An OBO file format parser, written in F#.

Usage

Basics

Read an OBO file

open OBO.NET

let testOntology = OboOntology.fromFile true filepath

Create OBO terms

OOP style (recommended):

let myOboTerm = 
    OboTerm.Create(
        "TO:00000000", 
        Name = "testTerm", 
        CreatedBy = "myself"
    )

Functional style:

let myOboTerm = 
    OboTerm.create 
        "TO:00000000" 
        (Some "testTerm") 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        None 
        (Some "myself") 
        None

Create an OBO ontology

let myOntology = OboOntology.create [myOboTerm] []

Save an OBO ontology

OboOntology.toFile "myOboOntology.obo" myOntology

Get all is_as of a Term

let termOfInterest = testOntology.Terms[5]

let isAs = OboOntology.getIsAs termOfInterest testOntology
// output is a list of (input OboTerm * is_a OboTerm (if it exists in the given OboOntology))

Get all is_as of a Term recursively

let termOfInterest = testOntology.Terms[5]

let isAs = testOntology.GetParentOntologyAnnotations(termOfInterest.Id)
// output is an ISADotNet.OntologyAnnotation list

let isAsTerms = isAs |> List.map (fun oa -> testOntology.GetTerm(oa.TermAccessionString.ToString()))
// output is an OboTerm list

Get all related Terms of a Term

let termOfInterest = testOntology.Terms[5]

let relatedTerms = OboOntology.getRelatedTerms termOfInterest testOntology
// output is a list of (input OboTerm * relation as string * related OboTerm (if it exists in the given OboOntology))

Get all synonym Terms of a Term

let termOfInterest = testOntology.Terms[5]

let synonyms = OboOntology.tryGetSynonyms termOfInterest testOntology
// output is a seq of (TermSynonymScope * synonymous OboTerm (if it exists in the given OboOntology))

Working with TermRelations

TermRelations are abstractions of all relations that an OboTerm can have with another one. Such TermRelations can be

• Empty of SourceTerm (if there is no TermRelation between a SourceTerm and a TargetTerm),
• TargetMissing of Relation * SourceTerm (if there is a TermRelation between a SourceTerm and a TargetTerm but the TargetTerm is missing),
• and Target of Relation * SourceTerm * TargetTerm. Relation is of generic type 'a and can therefore be of any type that you prefer (e.g. string or a custom-made Record or Union).

Create a TermRelation

let termOfInterest = testOntology.Terms[5]
let targetOfInterest = testOntology.Terms[7]

let emptyTermRelation = Empty termOfInterest
let targetMissingTermRelation = TargetMissing ("unconnected_to", termOfInterest)
let targetTermRelation = Target ("connected_to", termOfInterest, targetOfInterest)

// exemplary
type MyRelation =
    | IsA
    | HasA
    | PartOf
    | ConnectedTo
    | Unknown of string

let targetTermRelation' = Target (ConnectedTo, termOfInterest, targetOfInterest)

Get all TermRelations of a Term

let termOfInterest = testOntology.Terms[5]

let relations = OboOntology.getRelations termOfInterest testOntology
// output is a list of TermRelations<string> (includes all relationships and is_as)

Develop

Build (QuickStart)

If not already done, install .NET SDK >= 6.

In any shell, run build.cmd <target> where <target> may be

• if <target> is empty, it just runs dotnet build after cleaning everything
• RunTests to run unit tests
  • RunTestsWithCodeCov to run unit tests with code coverage
• ReleaseNotes semver:<version> where <version> may be major, minor, or patch to update RELEASE_NOTES.md
• Pack to create a NuGet release
  • PackPrelease to create a NuGet prerelease
• BuildDocs to create docs
  • BuildDocsPrerelease to create prerelease docs
• WatchDocs to create docs and run them locally
• WatchDocsPrelease to create prerelease docs and run them locally
• PublishNuget to create a NuGet release and publish it
  • PublishNugetPrelease to create a NuGet prerelease and publish it