Difference between revisions of "Taxonomy ontology"
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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 | 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 | is_metadata_tag: true | ||
| + | </pre> | ||
| + | |||
| + | Some special terms are included which represent taxonomic ranks. They descend from the term "taxonomic_rank": | ||
| + | |||
| + | <pre> | ||
| + | [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.... | ||
</pre> | </pre> | ||
Revision as of 20:36, 9 August 2007
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....
