OBO.NET

An OBO file format parser, written in F#.

Usage

Basics

Read an OBO file

openOBO.NETlettestOntology= OboOntology.fromFile true filepath

Create OBO terms

OOP style (recommended):

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

Functional style:

letmyOboTerm= 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

letmyOntology= OboOntology.create [myOboTerm][]

Save an OBO ontology

OboOntology.toFile "myOboOntology.obo" myOntology

Get all is_as of a Term

lettermOfInterest= testOntology.Terms[5]letisAs= 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

lettermOfInterest= testOntology.Terms[5]letisAs= testOntology.GetParentOntologyAnnotations(termOfInterest.Id)// output is an ISADotNet.OntologyAnnotation listletisAsTerms= isAs |> List.map (fun oa -> testOntology.GetTerm(oa.TermAccessionString.ToString()))// output is an OboTerm list

Get all related Terms of a Term

lettermOfInterest= testOntology.Terms[5]letrelatedTerms= 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

lettermOfInterest= testOntology.Terms[5]letsynonyms= 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

lettermOfInterest= testOntology.Terms[5]lettargetOfInterest= testOntology.Terms[7]letemptyTermRelation= Empty termOfInterest
lettargetMissingTermRelation= TargetMissing ("unconnected_to", termOfInterest)lettargetTermRelation= Target ("connected_to", termOfInterest, targetOfInterest)// exemplarytypeMyRelation=| IsA
| HasA
| PartOf
| ConnectedTo
| Unknown ofstringlettargetTermRelation' = Target (ConnectedTo, termOfInterest, targetOfInterest)

Get all TermRelations of a Term

lettermOfInterest= testOntology.Terms[5]letrelations= 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