NCBI organismal classification
An ontology representation of the NCBI organismal taxonomy
The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl.
The translation treats each taxon as an obo/owl class whose instances (for most branches of the ontology) would be individual organisms. For example:
'Craig Venter' instance_of NCBITaxon_9606 (Homo sapiens)
The translation faithfully reproduces all of the content of the source database, even where this contravenes OBO guidelines. For example:
- The root class is called ‘root’, rather than something like ‘organism’
- Plural names are used (both Linnaean and common names). E.g. “mammals”
- The organismhood of certain classes might be contested - either biologically (“viruses”) or ontologically (“environmental samples”)
- Synonyms may include quotation marks as part of the text
The purls for this ontology are:
- http://purl.obolibrary.org/obo/ncbitaxon.owl (official purl for ontology)
- http://purl.obolibrary.org/obo/ncbitaxon.obo (obo-format version)
The PURLs should be resolvable in OntoBee. E.g.
- http://purl.obolibrary.org/obo/NCBITaxon_9606 (Homo sapiens)
- http://purl.obolibrary.org/obo/NCBITaxon_7711 (Chordates)
- http://purl.obolibrary.org/obo/NCBITaxon_7955 (Danio rerio)
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
- Frederic Bastian, BgeeDb/Uberon
- Chris Mungall, LBNL/GO/Monarch/Uberon/OBO
- Peter Midford, Phenoscape
Contact the mail list (see below) for comments on this.
The GO uses an extension of NCBITaxon for grouping purposes. See:
this ontology includes new classes in the NCBITaxon_Union namespace. These classes are all defined using unions - for example Prokaryote = Eubacteria OR Archae
One of the main uses for the NCBITaxon ontology is to define taxon constraints in a multi-species ontology. For details, see:
- Waclaw Kusnierczyk (2008) Taxonomy-based partitioning of the Gene Ontology, Journal of Biomedical Informatics
- Deegan Née Clark, J. I., Dimmer, E. C., and Mungall, C. J. (2010). Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. *BMC Bioinformatics 11, 530**
- Taxon constraints in OWL (blog post)
- Taxon constraints in Uberon
- A Taxonomy for Immunologists ICBO 2013
Note that this differs from other OBO ontologies in that it is a translation of a database produced external to OBO. If you wish to suggest actual taxonomy changes to the database, contact NCBI.
The NCBI staff are very responsive and helpful, as this post from the Bgee team shows
If you wish to suggest changes to the translation then contact the maintainer or the mail list above.
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