Difference between revisions of "Taxonomy ontology"
From phenoscape
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The taxonomy ontology will be based on the Catalog of Fishes. | The taxonomy ontology will be based on the Catalog of Fishes. | ||
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| + | ==Resources== | ||
Here are some useful resources for creating the taxonomy ontology: | Here are some useful resources for creating the taxonomy ontology: | ||
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* [http://www.obofoundry.org/wiki/index.php/Identifiers OBO Identifier Lifecycle] | * [http://www.obofoundry.org/wiki/index.php/Identifiers OBO Identifier Lifecycle] | ||
| − | The NCBI taxonomy ontology has some special terms and relations which are probably relevant to the fish taxonomy ontology. One of these is the | + | ==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: | ||
| + | |||
| + | <pre> | ||
| + | [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 th | ||
| + | e rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored | ||
| + | is_metadata_tag: true | ||
| + | </pre> | ||
Revision as of 20:32, 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 th e rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored is_metadata_tag: true
