Difference between revisions of "Taxonomy ontology"
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(→Taxonomy ontology content from Catalog of Fishes) |
(→Taxonomy ontology structure) |
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</pre> | </pre> | ||
| − | Here are | + | 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: |
<pre> | <pre> | ||
[Term] | [Term] | ||
| − | id: NCBITaxon: | + | id: NCBITaxon:7996 |
| − | name: | + | name: Ictaluridae |
| − | is_a: NCBITaxon: | + | is_a: NCBITaxon:7995 |
| − | synonym: " | + | 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 | property_value: has_rank NCBITaxon:genus | ||
| − | xref: GC_ID: | + | xref: GC_ID:1 |
[Term] | [Term] | ||
| − | id: NCBITaxon: | + | id: NCBITaxon:7998 |
| − | name: | + | name: Ictalurus punctatus |
| − | is_a: NCBITaxon: | + | is_a: NCBITaxon:7997 |
| − | synonym: " | + | synonym: "channel catfish" EXACT genbank_common_name [] |
| − | |||
property_value: has_rank NCBITaxon:species | property_value: has_rank NCBITaxon:species | ||
| − | xref: GC_ID: | + | xref: GC_ID:1 |
</pre> | </pre> | ||
| − | Other uses for the synonym field can be seen in the OBO file, such as for | + | 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== | ==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? | 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? | ||
Revision as of 20:26, 14 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. - 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?
