Taxonomy ontology

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Revision as of 20:39, 9 August 2007 by Jpb15 (talk | contribs) (Taxonomy ontology structure)

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

Resources

Here are some useful resources for creating the taxonomy ontology:

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:16
name: Methylophilus
is_a: NCBITaxon:32011
synonym: "Methylophilus Jenkins et al. 1987" RELATED synonym []
synonym: "Methylotrophus" RELATED misspelling []
synonym: "Methyliphilus" EXACT equivalent_name []
property_value: has_rank NCBITaxon:genus
xref: GC_ID:11

[Term]
id: NCBITaxon:17
name: Methylophilus methylotrophus
is_a: NCBITaxon:16
synonym: "Methylophilus methylotrophus Jenkins et al. 1987" RELATED synonym []
synonym: "Methylotrophus methylophilus" RELATED synonym []
synonym: "Methylophilus methylitrophus" EXACT equivalent_name []
synonym: "Methyliphilus methylotrophus" EXACT equivalent_name []
synonym: "Methyliphilus methylitrophus" EXACT equivalent_name []
property_value: has_rank NCBITaxon:species
xref: GC_ID:11