Difference between revisions of "Taxonomy ontology"
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− | 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 go in the definition field | + | 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. |
Revision as of 20:44, 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....
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.