https://github.com/waldronlab/ncbitaxon
Hosting the NCBI taxnomy
https://github.com/waldronlab/ncbitaxon
Last synced: 16 days ago
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Hosting the NCBI taxnomy
- Host: GitHub
- URL: https://github.com/waldronlab/ncbitaxon
- Owner: waldronlab
- Created: 2024-08-20T19:11:08.000Z (almost 2 years ago)
- Default Branch: devel
- Last Pushed: 2024-08-21T15:11:13.000Z (almost 2 years ago)
- Last Synced: 2024-09-05T15:59:22.025Z (almost 2 years ago)
- Language: R
- Homepage:
- Size: 7.81 KB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# NCBI ontology
This repo contains the NCBI ontology.
This resource was created because a vignette in the waldronlab/BugSigDBStats repo needed to be run with a GHA. However, there were some memory-related issues when generating the ontology object in R. Documented [here](https://github.com/waldronlab/BugSigDBStats/blob/cded25c9f59ac0a01f5b8442060931070c546773/inst/scripts/semsim.Rmd#L26-L50). To circumvent this, the R object is created and hosted in this repo.
This data is used by the BugSigDBStats::getNcbiTaxonomyObo function and this function
was used for the BugSigDB paper [Figure 2](https://github.com/waldronlab/BugSigDBPaper/blob/3b4c917ebeafe2b02a0fa689cfea5ca03a534b6c/vignettes/Figure2.Rmd#L88-L92).
The onto.R file contains the code used to generate the data (R object).
## Information about the original source
[NCBI Organismal Classification](https://obofoundry.org/ontology/ncbitaxon.html)
[Build for NCBITaxon Ontology](https://github.com/obophenotype/ncbitaxon)