Skip to content


Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time
October 19, 2015 21:13
October 6, 2022 01:39
October 7, 2015 15:55
February 15, 2021 11:37
October 7, 2015 12:55
February 15, 2021 11:37
February 21, 2022 23:33


Build for NCBITaxon Ontology

The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl.


For details on using the ontology, see the OBO page:

This README details with technical aspects of the build


Outdated, see end of README for updated instructions

Releases of the obo/owl happen when the Continuous Integration Job is manually triggered. Currently this must be done by an OBO administrator. There is currently no fixed cycle, and this is generally done on demand. The team that informally handles this are:

  • James Overton, IEBD/OBO
  • Heiko Dietze, LBNL/GO
  • Frederic Bastian, BgeeDb/Uberon
  • Chris Mungall, LBNL/GO/Monarch/Uberon/OBO
  • Peter Midford, Phenoscape
  • Bill Duncan (LBNL)
  • Nicolas Matentzoglu (EMBL-EBI)


Currently there is one subset, ncbitaxon/subsets/taxslim - for details, see subsets/


The license for this software is BSD3. See the 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:

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 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
  2. Download all generated files from the Jenkins job (except for env.txt), including the files in the subset directory.
  3. On GitHub, go to Code, and click on 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.