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Outdated, see end of README for updated instructions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/README.md
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:
- Federhen, Scott. The NCBI taxonomy database. Nucleic acids research 40.D1 (2012): D136-D143. 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
sh odk.sh bash(to enter ODK container)
make clean all -B
make all -B
- gh release create v2021-06-10
- 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
- Trigger the Jenkins Job on ci.monarchinitiative.org
- Download all generated files from the Jenkins job (except for env.txt), including the files in the subset directory.
- On GitHub, go to Code, and click on releases.
- 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