BioFSharp/docs/03_05_obo.fsx at developer · vLeidel/BioFSharp · GitHub

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(**
---
title: Obo
category: BioParsers
categoryindex: 3
index: 4
---
*)

(*** hide ***)

(*** condition: prepare ***)
#r "nuget: FSharpAux, 1.1.0"
#r "nuget: FSharpAux.IO, 1.1.0"
#r "nuget: FSharp.Stats, 0.4.3"
#r "nuget: Plotly.NET, 2.0.0-preview.18"
#r "../src/BioFSharp/bin/Release/netstandard2.0/BioFSharp.dll"
#r "../src/BioFSharp.IO/bin/Release/netstandard2.0/BioFSharp.IO.dll"
#r "../src/BioFSharp.BioContainers/bin/Release/netstandard2.0/BioFSharp.BioContainers.dll"
#r "../src/BioFSharp.ML/bin/Release/netstandard2.0/BioFSharp.ML.dll"
#r "../src/BioFSharp.Stats/bin/Release/netstandard2.0/BioFSharp.Stats.dll"

(*** condition: ipynb ***)
#if IPYNB
#r "nuget: FSharpAux, 1.1.0"
#r "nuget: FSharpAux.IO, 1.1.0"
#r "nuget: FSharp.Stats, 0.4.3"
#r "nuget: Plotly.NET, 2.0.0-preview.18"
#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.18"
#r "nuget: BioFSharp, {{fsdocs-package-version}}"
#r "nuget: BioFSharp.IO, {{fsdocs-package-version}}"
#r "nuget: BioFSharp.BioContainers, {{fsdocs-package-version}}"
#r "nuget: BioFSharp.ML, {{fsdocs-package-version}}"
#r "nuget: BioFSharp.Stats, {{fsdocs-package-version}}"
#endif // IPYNB

(**
# Obo parsing

[![Binder]({{root}}img/badge-binder.svg)](https://mybinder.org/v2/gh/CSBiology/BioFSharp/gh-pages?filepath={{fsdocs-source-basename}}.ipynb)&emsp;
[![Script]({{root}}img/badge-script.svg)]({{root}}{{fsdocs-source-basename}}.fsx)&emsp;
[![Notebook]({{root}}img/badge-notebook.svg)]({{root}}{{fsdocs-source-basename}}.ipynb)

*Summary:* This example shows how to parse obo formatted files with BioFSharp

OBO format is a popular ontology file format. It can express a subset of the description logic language
OWL-DL 2.0 but in addition has standard syntax for representing important classes of meta-data including
as synonyms, references to publications and deprecated IDs. It is designed to be human readable and
editable.

Reading Obo files
-------------------
*)

open FSharpAux.IO
open BioFSharp.IO

let fileDir = __SOURCE_DIRECTORY__ + "/data/"

let psiMs =
    Seq.fromFile (fileDir + "Psi-MS.obo")
    |> Obo.parseOboTerms true
    |> Seq.toArray

psiMs.[0]
(***include-it***)