Taxonomy ontology

The Teleost Taxonomy Ontology (TTO) is based on the Catalog of Fishes and will be updated as CoF updates appear as well as from input from area experts. The reminder of this page will discuss how the TTO is currently implemented. See the Taxonomic Rank Ontology, an alternative implementation based on phylogenetic principles.

Organization

The current organization is derived from the ontology generated from the NCBI taxonomy. There is a hierarchy of taxon names, each of which is a class.

       Cyprinidae   -------------------->  Family
            ^             has_rank
            |
       is_a |
            |
         Davario    -------------------->  Genus
            ^             has_rank
            |
       is_a |
            |
 Davario aequipinnatus ---------------->  Species
                         has_rank

Resources

Here are some useful resources related to the taxonomy ontology (TTO)

• Change list (relative to November 2007 CoF update) for TTO. This list is current for recent changes - older changes will be added.
• Suggested ideas for taxonomy browser and other tools
• Summary of a discussion of TTO issues at the second data jamboree (September 2008)

This is a list of resources related to the development of the TTO.

• 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 - possibly somewhat out of date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

There is now a page devoted to discussion of Taxonomic Ranks.

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?

There is now a rough draft Taxonomy ontology directly from (somewhat dated) dump files from the Catalog of Fishes. A draft version with synonyms is here. The actual top of the tree is still Craniata, other species appearing at the root represent problems - usually related to synonyms that we need to resolve. Also note that I have tagged all synonyms as "RELATED", the weakest category of synonymy. Given the complexities of taxonomic synonymy, this seems to be the appropriate place to start. With the most recent version, most synonyms also include database references (dbxrefs) back to the original genus and species id's from the CoF tables.

Here is a preliminary taxonomy ontology, using data from a somewhat dated CoF dump. The taxa represented here are mentioned in
Fink, S.V., and W. L. Fink. 1981. Interrelationships of the ostariophysan fishes (Teleostei). Zoological Journal of the Linnean Society 72: 297–353.

Craniata is included as a root for the entire taxonomy, even though it does not correspond to any taxonomic level defined in the ontology. Note also that the term ids are not generated by OBO edit, we are basing them on catalog numbers from CoF.
Craniata: 1 Our root
Class: 10 + the class number from CoF (are these subject to splits?)
Order: 1000 + 10 * the order number from CoF - these numbers are sometimes formatted XX.X (to indicate splits?)
Family: 10000 + 10 * the family number from CoF - these numbers are sometimes formatted XX.X (to indicate splits?)
Genus: 100000 + the CAS_GEN value from CoF
Species: 1000000 + the CAS_SPC value from CoF
Unnamed entities: 10000000+ (e.g., sp., spp., etc.)

We should probably discuss whether this id scheme is really what we want to do - it means we can't add taxa from OBOEdit, though that isn't necessarily a problem.

format-version: 1.2
date: 02:10:2007 15:27
saved-by: peter
auto-generated-by: OBO-Edit 1.101
default-namespace: teleost-taxonomy

[Term]
id: TTO: 1029899
name: Prochilodus vimboides
is_a: TTO:101208 ! Prochilodus
property_value: has_rank TTO:species

[Term]
id: TTO:1
name: Craniata

[Term]
id: TTO:10000001
name: Eigenmannia sp.
is_a: TTO:104678 ! Eigenmannia
property_value: has_rank TTO:Unknown_species

[Term]
id: TTO:10000002
name: Sternopygus sp.
is_a: TTO:102060 ! Sternopygus
property_value: has_rank TTO:Unknown_species

[Term]
id: TTO:1003114
name: Notemigonus crysoleucus
is_a: TTO:100967 ! Notemigonus
property_value: has_rank TTO:species

[Term]
id: TTO:1003239
name: Opsariichthys uncirostris
is_a: TTO:103159 ! Opsariichthys
property_value: has_rank TTO:species

[Term]
id: TTO:1004143
name: Chalceus macrolepidotus
is_a: TTO:100825 ! Chalceus
property_value: has_rank TTO:species

[Term]
id: TTO:1004205
name: Hepsetus odoe
is_a: TTO:109162 ! Hepsetus
property_value: has_rank TTO:species

[Term]
id: TTO:1004213
name: Xenocharax spilurus
is_a: TTO:103438 ! Xenocharax
property_value: has_rank TTO:species

[Term]
id: TTO:1004343
name: Rhoadsia altipinna
is_a: TTO:105589 ! Rhoadsia
property_value: has_rank TTO:species

[Term]
id: TTO:100558
name: Chanos
is_a: TTO:10720 ! Chanidae
property_value: has_rank TTO:genus

[Term]
id: TTO:1006103
name: Rhabdolichops troscheli
is_a: TTO:107098 ! Rhabdolichops
property_value: has_rank TTO:species

[Term]
id: TTO:100825
name: Chalceus
is_a: TTO:10910 ! Characidae
property_value: has_rank TTO:genus

[Term]
id: TTO:100967
name: Notemigonus
is_a: TTO:10760 ! Cyprinidae
property_value: has_rank TTO:genus

[Term]
id: TTO:101208
name: Prochilodus
is_a: TTO:10855 ! Prochilodontidae
property_value: has_rank TTO:genus

[Term]
id: TTO:101842
name: Brycon
is_a: TTO:10910 ! Characidae
property_value: has_rank TTO:genus

[Term]
id: TTO:102060
name: Sternopygus
is_a: TTO:11231 ! Sternopygidae
property_value: has_rank TTO:genus

[Term]
id: TTO:1027661
name: Chanos chanos
is_a: TTO:100558 ! Chanos
property_value: has_rank TTO:species

[Term]
id: TTO:1028504
name: Bryconamericus brevirostris
is_a: TTO:105385 ! Bryconamericus
property_value: has_rank TTO:species

[Term]
id: TTO:102915
name: Diplomystes
is_a: TTO:10920 ! Diplomystidae
property_value: has_rank TTO:genus

[Term]
id: TTO:1029536
name: Brycon dentex
is_a: TTO:101842 ! Brycon
property_value: has_rank TTO:species

[Term]
id: TTO:1030110
name: Platyurosternarchus macrostomus
synonym: "Sternarchus macrostoma" EXACT []
is_a: TTO:110391 ! Platyurosternarchus
property_value: has_rank TTO:species

[Term]
id: TTO:103159
name: Opsariichthys
is_a: TTO:10760 ! Cyprinidae
property_value: has_rank TTO:genus

[Term]
id: TTO:103339
name: Auchenoglanis
is_a: TTO:10940 ! Bagridae
property_value: has_rank TTO:genus

[Term]
id: TTO:103438
name: Xenocharax
is_a: TTO:10820 ! Citharinidae
property_value: has_rank TTO:genus

[Term]
id: TTO:1046341
name: Diplomystes chilensis
synonym: "Diplomystes papillosus" EXACT []
is_a: TTO:102915 ! Diplomystes
property_value: has_rank TTO:species

[Term]
id: TTO:104678
name: Eigenmannia
is_a: TTO:11231 ! Sternopygidae
property_value: has_rank TTO:genus

[Term]
id: TTO:105055
name: Zacco
is_a: TTO:10760 ! Cyprinidae
property_value: has_rank TTO:genus

[Term]
id: TTO:1051779
name: Zacco temminckii
is_a: TTO:105055 ! Zacco
property_value: has_rank TTO:species

[Term]
id: TTO:105268
name: Sternarchorhamphus
is_a: TTO:11232 ! Apteronotidae
property_value: has_rank TTO:genus

[Term]
id: TTO:105385
name: Bryconamericus
is_a: TTO:10910 ! Characidae
property_value: has_rank TTO:genus

[Term]
id: TTO:105589
name: Rhoadsia
is_a: TTO:10910 ! Characidae
property_value: has_rank TTO:genus

[Term]
id: TTO:1056213
name: Auchenoglanis monkei
synonym: "Parauchenoglanis guttatus" EXACT []
is_a: TTO:103339 ! Auchenoglanis
property_value: has_rank TTO:species

[Term]
id: TTO:1062171
name: Sternopygus macrurus
is_a: TTO:102060 ! Sternopygus
property_value: has_rank TTO:species

[Term]
id: TTO:107098
name: Rhabdolichops
is_a: TTO:11231 ! Sternopygidae
property_value: has_rank TTO:genus

[Term]
id: TTO:10720
name: Chanidae
is_a: TTO:1350 ! Gonorynchiformes
property_value: has_rank TTO:family

[Term]
id: TTO:10760
name: Cyprinidae
is_a: TTO:1360 ! Cypriniformes
property_value: has_rank TTO:family

[Term]
id: TTO:10820
name: Citharinidae
is_a: TTO:1370 ! Characiformes
property_value: has_rank TTO:family

[Term]
id: TTO:10827
name: Hepsetidae
is_a: TTO:1370 ! Characiformes
property_value: has_rank TTO:family

[Term]
id: TTO:10855
name: Prochilodontidae
is_a: TTO:1370 ! Characiformes
property_value: has_rank TTO:family

[Term]
id: TTO:10910
name: Characidae
is_a: TTO:1370 ! Characiformes
property_value: has_rank TTO:family

[Term]
id: TTO:109162
name: Hepsetus
is_a: TTO:10827 ! Hepsetidae
property_value: has_rank TTO:genus

[Term]
id: TTO:10920
name: Diplomystidae
is_a: TTO:1380 ! Siluriformes
property_value: has_rank TTO:family

[Term]
id: TTO:10940
name: Bagridae
is_a: TTO:1380 ! Siluriformes
property_value: has_rank TTO:family

[Term]
id: TTO:110391
name: Platyurosternarchus
is_a: TTO:11232 ! Apteronotidae
property_value: has_rank TTO:genus

[Term]
id: TTO:11231
name: Sternopygidae
is_a: TTO:1390 ! Gymnotiformes
property_value: has_rank TTO:family

[Term]
id: TTO:11232
name: Apteronotidae
is_a: TTO:1390 ! Gymnotiformes
property_value: has_rank TTO:family

[Term]
id: TTO:1350
name: Gonorynchiformes
is_a: TTO:18 ! Actinopterygii
property_value: has_rank TTO:order

[Term]
id: TTO:1360
name: Cypriniformes
is_a: TTO:18 ! Actinopterygii
property_value: has_rank TTO:order

[Term]
id: TTO:1370
name: Characiformes
is_a: TTO:18 ! Actinopterygii
property_value: has_rank TTO:order

[Term]
id: TTO:1380
name: Siluriformes
is_a: TTO:18 ! Actinopterygii
property_value: has_rank TTO:order

[Term]
id: TTO:1390
name: Gymnotiformes
is_a: TTO:18 ! Actinopterygii
property_value: has_rank TTO:order

[Term]
id: TTO:18
name: Actinopterygii
is_a: TTO:1 ! Craniata
property_value: has_rank TTO:class

[Term]
id: TTO:class
name: class
xref: NCBITaxon:class
is_a: TTO:taxonomic_rank ! taxonomic_rank

[Term]
id: TTO:family
name: family
xref: NCBITaxon:family
is_a: TTO:taxonomic_rank ! taxonomic_rank

[Term]
id: TTO:genus
name: genus
xref: NCBITaxon:genus
is_a: TTO:taxonomic_rank ! taxonomic_rank

[Term]
id: TTO:order
name: order
xref: NCBITaxon:order
is_a: TTO:taxonomic_rank ! taxonomic_rank

[Term]
id: TTO:species
name: species
xref: NCBITaxon:species
is_a: TTO:taxonomic_rank ! taxonomic_rank

[Term]
id: TTO:taxonomic_rank
name: taxonomic_rank
xref: NCBITaxon:taxonomic_rank

[Term]
id: TTO:Unknown_species
name: Unknown species
is_a: TTO:taxonomic_rank ! taxonomic_rank

[Term]
id: TTO:Unknown_species_group
name: Unknown species group
is_a: TTO:taxonomic_rank ! taxonomic_rank

[Term]
id: TTO:Unnamed_species
name: Unnamed species
is_a: TTO:taxonomic_rank ! taxonomic_rank

Note: This page describes some design alternatives for taxonomic ontologies that refer to or include terms for ranks. If you are looking documentation for the Vocabulary of Ranks developed by Phenoscape, you will find it here.

A taxonomic rank ontology allows particular taxa to be treated as historical individuals instead of as universal types.

Taxonomic rank ontology and sample instance data. The ontology terms are surrounded by a grey background. The "Continuant" term would reside in an upper ontology such as BFO. The instance data constitute a particular taxonomy.

Previous attempts to represent taxonomy using ontology usually include taxonomic groups as classes in the ontology. Individual organisms are seen as instances of those universal types. There could be an ontology term Mammal, such that Primates and Rodents are more particular types of Mammals (is_a descendants). Taxonomies are even often used as examples to help explain ontology inheritance to new users. This scheme fails to represent reality in several ways and, as this page will demonstrate, is even misleading.

The "traditional" view

Inference with traditional taxonomy

One of the attractions of a traditional taxonomy for ontology builders that it can support the most common sort of reasoning for Description Logic ontologies. Although neither the TTO nor the NCBI taxonomy ontology attach character values to their classes, in principle such characters could be extracted from keys or from the taxonomic literature. With the addition of such properties, individuals can be classified by starting at the root of the taxonomy and traversing down the tree until either a terminal taxon (species) is reached or a node is reached where no descendant has the combination of characters displayed by the individual. For biologists, this operation is identical to use of an identification key. Such an operation is generally only defined for is_a links.

Problems with the "traditional" view

• The only criterion for inclusion within a taxonomic group is physical descent from a member of that group (we are assuming a taxonomy consistent with phylogeny). There are no universal properties one could ascribe to members of "Mammalia", besides things the members happen to share at this moment. "Hair" is often used an example of a Mammalian property; but of course its commonality is the result of its presence in the common ancestor of all mammals, and many mammals lack hair almost entirely. A mammal species that had no hair at all would nevertheless still be a mammal. Such reversals are common in phylogenies and can occur for both morphological properties (e.g., loss of legs in snakes) and molecular characters (e.g., inferred origin of pseudogenes).
• Descendant terms do not inherit (ontologically) all of the characteristics of their parents. For example, Rodentia has a different age and geographic range from Mammalia.
• Properties of a taxonomic group change through time: its geographic range, genetic and morphological diversity, etc. It can go extinct. These properties inhere in the group, not any one individual.
• Treating taxonomic groups as "classes" or "types" reinforces essentialist ideas of life forms, which evolutionary biology has completely overturned. Essentialist thought is a hindrance to understanding of the evolutionary process.
• Most contemporary treatments of the species concept (refs) treat them, and in many cases higher taxa, as individuals, possessing a history.

Instead of treating taxa as types in an ontology, we can treat individual taxa as instances of the type Taxon, or more specifically as instances of some taxonomic rank (see figure above).

Taxonomic Rank Ontology + Instance Graph of Taxonomy

Species are increasingly seen to be better modelled as individuals.

Advantages

• Taxa are modeled as individuals.
• Taxonomic rank terms are ordered through their part_of relationships.
• Multiple part_of parents introduce fewer problems in inference than multiple is_a parents. This is important as more cases of reticulate phylogeny, caused by, for example, cross species hybridization or horizontal gene transfer, are discovered.

Individuals/Instances

Implementing this approach will require Tool support for Instances.

Taxonomic Ranks as Metaclasses

An approach that allows taxa to be viewed as both classes and individuals is to view rank terms, such as 'genus' as metaclasses. A metaclass is a class of classes. This would mean that a particular genus, e.g., Danio is both a subclass of Cyprinidae and an instance of genus. Metaclasses are used when assigning particular properties to a class itself, rather than its members. The property 'extinct' might be such a class-level property, as opposed to 'dead' a property that inheres in individuals. Extinct is a property we want to inhere in certain taxa only when all their individual constituents are dead. However, there are classes, such as anatomical parts, or behavior patterns that would not be subject to the possiblity of extinction.

This approach is attractive because it allows taxa to be both classes, in line with traditional taxonomies and reasoning with description logic classifiers, and individuals, with the greater fidelity to current biological thinking.

Disadvantages

The main disadvantage with this approach is its complexity, both for human understanding and for reasoning.