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ontologymapping.jl

https://github.com/damourchris/ontologymapping.jl

Science Score: 31.0%

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Last synced: 9 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: damourChris
  • License: mit
  • Language: Julia
  • Default Branch: main
  • Size: 212 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

OntologyMapping

Stable Dev Build Status Coverage

A Julia package for mapping IDs between ontologies. The main entry point is the maptoontology function, which maps a list of IDs to a ontology.

For now, it intends to map human annotation to a ontology. Namely, the original purpose was to map cell type annotation to the Cell Line Ontology (CLO). However, it can (remains to be tested) be used to map any annotation to any ontology.

Installation

!!! note This package is part of the SysBioRegistry. If this is your first time instaling a package from this registry make sure to first run the following command in the Julia REPL: julia using Pkg Pkg.Registry.add(RegistrySpec(url = "https://github.com/damourChris/SysBioRegistry.jl")) This is not required if you wish to install the package from the GitHub repository.

You can install the package by running the following command in the Julia REPL: julia using Pkg Pkg.add("OntologyMapping")

Or alternatively, you can install the package from the GitHub repository by running the following command in the Julia REPL: julia using Pkg Pkg.add(url="https://github.com/damourChris/OntologyMapping.jl")

Usage

julia julia> using ExpressionData julia> using OntologyMapping julia> julia> ids_to_map = ["T cell", "B cells", "NK cell"] julia> replacements = ("cells" => "cell") julia> rand_eset = rand(ExpressionSet, 10, 3) julia> rand_eset.phenotype_data[!, :cell_types] = ids_to_map julia> julia> mapped_eset = map_to_ontology(rand_eset, "cl"; ontology_col="cell_types", replacements=replacements, target_col="mapped_cell_types") julia> phenotype_data(mapped_eset) 3×3 DataFrame Row │ sample_names cell_types mapped_cell_types │ String String String ─────┼───────────────────────────────────────────── 1 │ sample_1 T cell CL_0000084 2 │ sample_2 B cell CL_0000236 3 │ sample_3 NK cell CL_0000623

Documentation

For more information, check the documentation.

Owner

  • Name: Christopher Damour
  • Login: damourChris
  • Kind: user
  • Location: Maastricht

My public student profile

Citation (CITATION.bib) 

@misc{OntologyMapping.jl,
	author  = {Chris Damour},
	title   = {OntologyMapping.jl},
	url     = {https://github.com/damourChris/OntologyMapping.jl},
	version = {v1.0.0},
	year    = {2024},
	month   = {9}
}

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.github/workflows/CompatHelper.yml actions
.github/workflows/TagBot.yml actions
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