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

Last synced: 23 days ago
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Host: GitHub
URL: https://github.com/damourchris/ontologymapping.jl
Owner: damourChris
License: mit
Created: 2024-09-20T21:13:15.000Z (4 months ago)
Default Branch: main
Last Pushed: 2024-10-15T16:13:54.000Z (3 months ago)
Last Synced: 2024-11-05T13:26:53.338Z (2 months ago)
Language: Julia
Size: 209 KB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 1
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.bib

Awesome Lists containing this project

README

        # OntologyMapping

[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://damourChris.github.io/OntologyMapping.jl/stable/)

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://damourChris.github.io/OntologyMapping.jl/dev/)

[![Build Status](https://github.com/damourChris/OntologyMapping.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/damourChris/OntologyMapping.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Coverage](https://codecov.io/gh/damourChris/OntologyMapping.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/damourChris/OntologyMapping.jl)

A Julia package for mapping IDs between ontologies. The main entry point is the map_to_ontology 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](https://damourChris.github.io/OntologyMapping.jl/stable/).