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https://github.com/csbiology/obo.net
An OBO file format parser, written in F#.
https://github.com/csbiology/obo.net
Last synced: 30 days ago
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An OBO file format parser, written in F#.
- Host: GitHub
- URL: https://github.com/csbiology/obo.net
- Owner: CSBiology
- License: mit
- Created: 2023-07-21T07:50:52.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-10-30T09:11:33.000Z (2 months ago)
- Last Synced: 2024-11-29T02:49:28.530Z (about 1 month ago)
- Language: F#
- Size: 167 KB
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# OBO.NET
An OBO file format parser, written in F#.
## Usage
### Basics
#### Read an OBO file
```fsharp
open OBO.NET
let testOntology = OboOntology.fromFile true filepath
```
#### Create OBO terms
OOP style (recommended):
```fsharp
let myOboTerm =
OboTerm.Create(
"TO:00000000",
Name = "testTerm",
CreatedBy = "myself"
)
```
Functional style:
```fsharp
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
```fsharp
let myOntology = OboOntology.create [myOboTerm] []
```
#### Save an OBO ontology
```fsharp
OboOntology.toFile "myOboOntology.obo" myOntology
```
#### Get all `is_a`s of a Term
```fsharp
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_a`s of a Term recursively
```fsharp
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
```fsharp
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
```fsharp
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
```fsharp
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
```fsharp
let termOfInterest = testOntology.Terms[5]
let relations = OboOntology.getRelations termOfInterest testOntology
// output is a list of TermRelations (includes all relationships and is_as)
```
## Develop
### Build (QuickStart)
If not already done, install .NET SDK >= 6.
In any shell, run `build.cmd ` where `` may be
- if `` 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:` where `` 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