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. - possibly somewhat out of date
• 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 three actual taxon terms. The term for the species descends via is_a from the term for the genus, and likewise for the genus and family. The rank is specified in the property_value. Other names are placed in the synonym fields:

[Term]
id: NCBITaxon:7996
name: Ictaluridae
is_a: NCBITaxon:7995
synonym: "North American freshwater catfishes" EXACT common_name []
synonym: "bullhead catfishes" EXACT genbank_common_name []
property_value: has_rank NCBITaxon:family
xref: GC_ID:1

[Term]
id: NCBITaxon:7997
name: Ictalurus
is_a: NCBITaxon:7996
property_value: has_rank NCBITaxon:genus
xref: GC_ID:1

[Term]
id: NCBITaxon:7998
name: Ictalurus punctatus
is_a: NCBITaxon:7997
synonym: "channel catfish" EXACT genbank_common_name []
property_value: has_rank NCBITaxon:species
xref: GC_ID:1

Other uses for the synonym field can be seen in the OBO file, such as for obsolete names. We may want to also provide a definition from the original species description.

Taxonomy ontology content from Catalog of Fishes

Which parts of the CoF schema should be included in the taxonomy ontology? Also, is there information not in the Catalog of Fishes that should be included in the taxonomy ontology?