https://github.com/a-r-j/drugtranslator

R package for translating between drug identifiers using the Chemical Translation Service (CTS)
https://github.com/a-r-j/drugtranslator

biomedical-data-science biomedical-informatics chemical chemical-identifiers chemical-translation-service cheminformatics chemistry drug-development drug-discovery drug-repurposing identifiers r r-package

Last synced: 2 months ago
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R package for translating between drug identifiers using the Chemical Translation Service (CTS)

• Host: GitHub
• URL: https://github.com/a-r-j/drugtranslator
• Owner: a-r-j
• License: mit
• Created: 2019-02-18T17:10:18.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-01-11T00:32:14.000Z (almost 2 years ago)
• Last Synced: 2024-10-10T22:16:49.679Z (3 months ago)
• Topics: biomedical-data-science, biomedical-informatics, chemical, chemical-identifiers, chemical-translation-service, cheminformatics, chemistry, drug-development, drug-discovery, drug-repurposing, identifiers, r, r-package
• Language: R
• Size: 6.84 KB
• Stars: 3
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
 # DrugTranslatoR

R package for translating between drug identifiers using the [Chemical Translation Service (CTS)](https://cts.fiehnlab.ucdavis.edu/)

# Details

Simple R wrapper to send HTTP requests to the CTS server.

# Installation

```

# install devtools if required

if (!requireNamespace("devtools")) install.packages("devtools")

# then install DrugTranslatoR

devtools::install_github("a-r-j/DrugTranslatoR")

```

# Usage

`translateDrugID(from, to, query)` - Translate between different drug/chemical identifiers  

`sourceIDs()` - Fetch list of valid identifies that can be translated from   

`targetIDs()` - Fetch list of valid identifiers that can be translated to    

`expandChemicalFormula(formula)` - Expands a compact chemical formula  

`InChIKey2MolDef(inchikey)` - Converts InChIKey to molecule definition (MDL/SDF)  

`countBiologicalIDs(inchikey)` - Counts biological IDs for InChIKey  

`scoredInChiKeys(from, query, algorithm)` - Gets a list of scored InChIKeys

# Reference:

> The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports. Gert Wohlgemuth, Pradeep Kumar Haldiya, Egon Willighagen, Tobias Kind, Oliver Fiehn. Bioinformatics, Volume 26, Issue 20, 15 October 2010, Pages 2647–2648, https://doi.org/10.1093/bioinformatics/btq476