Build for NCBITaxon Ontology

The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database 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

Releases

Outdated, see end of README for updated instructions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)

Subsets

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

Licensing

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

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
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.