https://github.com/obophenotype/ncbitaxon
Build for NCBITaxon
https://github.com/obophenotype/ncbitaxon
ncbi-taxonomy obofoundry ontology taxonomy
Last synced: 2 months ago
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Build for NCBITaxon
- Host: GitHub
- URL: https://github.com/obophenotype/ncbitaxon
- Owner: obophenotype
- License: bsd-3-clause
- Created: 2015-10-07T19:51:40.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2025-12-14T13:43:56.000Z (6 months ago)
- Last Synced: 2025-12-16T20:22:02.306Z (6 months ago)
- Topics: ncbi-taxonomy, obofoundry, ontology, taxonomy
- Language: Python
- Homepage:
- Size: 5.64 MB
- Stars: 30
- Watchers: 11
- Forks: 8
- Open Issues: 28
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Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://zenodo.org/badge/latestdoi/13996/obophenotype/ncbitaxon)
# Build for NCBITaxon Ontology
The NCBITaxon ontology is an automatic translation of the [NCBI taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy) into obo/owl.
# Details
For details on using the ontology, see the OBO page:
http://obofoundry.org/ontology/ncbitaxon.html
This README details with technical aspects of the build
## Subsets
Currently there is one subset, ncbitaxon/subsets/taxslim - for details, see [subsets/README.md](subsets/README.md)
## Licensing
The license for this software is BSD3. See the [LICENSE](LICENSE) file.
Note that the *content* of the ontology is not covered by this software license. The content comes from NCBI.
## Citing the NCBITaxon ontology
before citing, ask yourself what the artefact you wish to cite is:
* The NCBI taxonomy **database**
* The OBO/OWL rendering of the NCBI taxonomy database
The latter is a fairly trivial translation of the former. If you are in any way citing the *contents* then **you should cite the database**. Currently the most up to date reference is:
* Federhen, Scott. **The NCBI taxonomy database.** *Nucleic acids research 40.D1 (2012): D136-D143.* [http://nar.oxfordjournals.org/content/40/D1/D136.short](http://nar.oxfordjournals.org/content/40/D1/D136.short)
If you specifically wish to cite the OBO/OWL translation, use the URL for this page
## Editors guide for running releases
### Using gh for releases
1. `sh odk.sh bash` (to enter ODK container)
1. `make clean all -B`
2. `cd subsets`
3. `make all -B`
4. `cd ..`
2. gh release create v2021-06-10
3. gh release upload v2021-06-10 ncbitaxon.json ncbitaxon.json.gz ncbitaxon.obo ncbitaxon.obo.gz ncbitaxon.owl ncbitaxon.owl.gz subsets/taxslim-disjoint-over-in-taxon.owl subsets/taxslim.obo subsets/taxslim.owl subsets/taxslim.json
### Using Monarch Jenkins
1. Trigger the Jenkins Job on [ci.monarchinitiative.org](https://ci.monarchinitiative.org/view/pipelines/job/ncbi_taxon/)
2. Download all generated files from the Jenkins job (except for env.txt), including the files in the [subset](https://ci.monarchinitiative.org/view/pipelines/job/ncbi_taxon/lastSuccessfulBuild/artifact/subsets/) directory.
3. On GitHub, go to [Code](https://github.com/obophenotype/ncbitaxon), and click on [releases](https://github.com/obophenotype/ncbitaxon/releases).
4. Click "Draft a new release". The tag is something like `v2020-02-28`. Provide a title and a meaningful description, and upload all the files downloaded from the Jenkins job above. Hit `Publish release`.