Taxonomy ontology

The taxonomy ontology will be based on the Catalog of Fishes.

Resources

Here are some useful resources for creating the taxonomy ontology:

• Chris Mungall's NCBI Taxonomy in OBO format - this file is huge!
• Catalog of Fishes database schema documentation.
• OBO Flat File Format Specification
• OBO Identifier Lifecycle

Taxonomy ontology structure

The NCBI taxonomy ontology has some special terms and relations which are probably relevant to the fish taxonomy ontology. One of these is the "has_rank" typedef, which is used as a property value on the taxon terms:

[Typedef]
id: has_rank
name: has_rank
def: "A metadata relation between a class and its taxonomic rank (eg species, family)" []
comment: This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored
is_metadata_tag: true

Some special terms are included which represent taxonomic ranks. They descend from the term "taxonomic_rank":

[Term]
id: NCBITaxon:taxonomic_rank
name: taxonomic_rank
def: "A level of depth within a species taxonomic tree" []
comment: This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored

[Term]
id: NCBITaxon:superkingdom
name: superkingdom
is_a: NCBITaxon:taxonomic_rank

[Term]
id: NCBITaxon:genus
name: genus
is_a: NCBITaxon:taxonomic_rank

[Term]
id: NCBITaxon:species
name: species
is_a: NCBITaxon:taxonomic_rank

etc....

Here are two actual taxon terms. The term for the species descends via is_a from the term for the genus. The rank is specified in the property_value. Other names are placed in the synonym fields:

[Term]
id: NCBITaxon:22
name: Shewanella
is_a: NCBITaxon:267890
synonym: "Shewanella MacDonell and Colwell 1986" RELATED synonym []
property_value: has_rank NCBITaxon:genus
xref: GC_ID:11

[Term]
id: NCBITaxon:23
name: Shewanella colwelliana
is_a: NCBITaxon:22
synonym: "Alteromonas colwelliana" RELATED synonym []
synonym: "Shewanella colwelliana (Weiner et al. 1988) Coyne et al. 1990" RELATED synonym []
property_value: has_rank NCBITaxon:species
xref: GC_ID:11

Other uses for the synonym field can be seen in the OBO file, such as for a common name. It seems like a common name could alternatively go in the definition field, but this doesn't seem to be the case in the NCBI taxonomy ontology.