Difference between revisions of "Taxonomy ontology"

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The taxonomy ontology will be based on the Catalog of Fishes.
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This page contains accumulated design notes for taxonomy ontologies.  They focus on the [[Teleost Taxonomy Ontology]] and the [[Taxonomic Rank Vocabulary]], but the most recent information for each will appear on their respective home pages.
 +
 
 +
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==
 
==Resources==
  
−
Here are some useful resources for creating the taxonomy ontology:
+
Here are some useful resources related to the taxonomy ontology (TTO)
 +
 
 +
* [[TTO Changes|Change list (relative to November 2007 CoF update) for TTO.]] This list is current for recent changes - older changes will be added.
 +
* [[Incubator | Suggested ideas for taxonomy browser and other tools]]
 +
* [[Data_Jamboree_2/Notes#Taxon Concepts | 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 [http://www.berkeleybop.org/ontologies/obo-all/ncbi_taxonomy/ncbi_taxonomy.obo NCBI Taxonomy in OBO format] - ''this file is huge!''
 
* Chris Mungall's [http://www.berkeleybop.org/ontologies/obo-all/ncbi_taxonomy/ncbi_taxonomy.obo NCBI Taxonomy in OBO format] - ''this file is huge!''
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==Taxonomy ontology structure==
 
==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:
 
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:
Line 85: Line 113:
  
 
<p>
 
<p>
−
There is now a rough draft Taxonomy ontology directly from (somewhat dated) dump files from the Catalog of Fishes.  It is will be available soon. <br>
+
There is now a rough draft Taxonomy ontology directly from (somewhat dated) dump files from the Catalog of Fishes.
 +
[[Media:TTO.obo.txt|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.<br>
  
 
<br>
 
<br>
Line 482: Line 514:
 
is_a: TTO:taxonomic_rank ! taxonomic_rank
 
is_a: TTO:taxonomic_rank ! taxonomic_rank
 
</pre>
 
</pre>
 +
 +
=Alternative Designs=
 +
Note: This section describes some design alternatives for taxonomic ontologies that refer to or include terms for ranks. 
 +
 +
A taxonomic rank ontology allows particular taxa to be treated as historical individuals instead of as universal types.
 +
 +
[[Image:TaxonomicRankDiagram.png|750px|thumb|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 [http://www.ifomis.org/bfo 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.
 +
 +
===Inference with an ontology of taxonomic ranks + instance graph of taxa===
 +
 +
===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.
 +
 +
 +
See also the [[Taxonomic Rank Vocabulary]] which was released in January 2010.
 +
 +
== Developing an Ontology for Taxonomic Ranks ==
 +
 +
When the Teleost Taxonomy Ontology (TTO) was submitted to OBO, the suggestion was made that the terms for taxonomic ranks (e.g., Family, Genus, Species) should be broken out.  At present, taxonomic ranks are included in the TTO and cross referenced to similar terms in the NCBI taxonomy ontology.  Although the process of constructing an ontology of rank terms is straightforward, there are some semantic issues that need to be resolved.
 +
 +
The current implementation can be diagrammed as follows:
 +
 +
 +
 +
        Cyprinidae  -------------------->  Family
 +
            ^            has_rank
 +
            |
 +
        is_a |
 +
            |
 +
          Devario    -------------------->  Genus
 +
            ^            has_rank
 +
            |
 +
        is_a |
 +
            |
 +
  Devario aequipinnatus ---------------->  Species
 +
                          has_rank
 +
 +
 +
In the first draft of the ranks ontology, submitted to Chris Mungal and Michael Ashburner, the rank terms are simply subclasses of taxonomic_rank.  There is no relation defined between the rank terms.  The has_rank relation, as defined in the NCBO ontology is a meta_data relation (c.f. OWL annotation properties), which means it is intended to be ignored by any reasoner.
 +
 +
As there is clearly an ordering among the rank terms, it would be worthwhile to define an ordering relation between terms so that the term 'family' is indicated as 'larger' or 'more inclusive' than the term 'genus.'
 +
 +
The proposed situation is
 +
 +
          TTO                                TaxonRank Ontology
 +
 +
        Cyprinidae  -------------------->  Family
 +
            ^            has_rank          ^
 +
            |                                |
 +
        is_a |                                |  "rank_order"
 +
            |                                |
 +
          Davario    -------------------->  Genus
 +
            ^            has_rank          ^
 +
            |                                |
 +
        is_a |                                |  "rank_order"
 +
            |                                |
 +
  Davario aequipinnatus ---------------->  Species
 +
                          has_rank
 +
 +
 +
There has been some question as to the nature of this ordering relation.  There appear to be two points of view:
 +
<ol>
 +
<li>A special relation exists between taxonomic ranks.  It would be transitive and antisymmetric.
 +
<li>The relation is simply part_of.  Part_of is transitive and antisymmetric.
 +
</ol>
 +
<br>
 +
 +
Chris Mungall's response to this question was:
 +
 +
  3. What about imposing an ordering among ranks and, if so, is part_of the appropriate relation?
 +
 +
so with any ontology you should ask "what are the instances". In this case, the instances are best considered
 +
to be terms/classes/categories rather than something tangible in nature. This takes us close to weird metaclass
 +
modeling territory.
 +
 +
but not to worry. I would say reserve part_of for "real" part_of relations, between objects and processes. I
 +
would just go with a custom relation for ranks. I don't have strong opinions on what you name it - above/below?
 +
more_ancestral_than?
 +
 +
Declare the relation transitive
 +
 +
There is another property of the 'rank ordering' that should be noted.  The current TTO currently uses a rather limited number of taxonomic ranks.  However, if this ontology is intended to be shared across OBO projects, it will need to incorporate additional taxonomic level terms.  For example, the NCBI taxnomy defines over 30 rank terms.  As other groups develop taxonomies they will want to add ranks that are used in their systems.  Furthermore, the system of ranks is open-ended, so any particular group might need to add additional ranks in the future.  However, any one taxonomy will only use a subset of these terms, which means that in most cases, the is_a relation between two taxa will frequently correspond to more than one link up the rank taxonomy.  Another case where this situation comes up, even for a single taxonomy, is an incertae sedis taxa.  Thus a definition for the ordering relation needs to work without depending on having every step in the rank chain correspond to a taxonomic term in each tip to root path in the tree.
 +
 +
 +
Resolving this issue may depend on the resolution of a second, closely related issue that may have to be reopened for discussion.
 +
 +
== Modeling Taxa ==
 +
 +
Following the example of the OBO translation of the NCBI taxonomy, the TTO models taxa as a hierarchy of classes, defined by an is_a relation based on set theory.  This means that classes, hence taxa terms are represented as sets.  The taxon as set model extends all the way down to and including the species level.
 +
 +
However, an increasingly influential view among philosophers of biology is that species should be not be seen as either classes (or natural kinds), but as evolutionary units, and hence as individuals (e.g., Hull 1974, Ghiselin 1978).  In this view, species are not sets of individual organisms, rather there is a part_of relation between organisms and their species.  The particular part_of relation is commonly portrayed as species (and other clades) being composed of lineages and lineages consisting of related individual organisms.
 +
 +
This view can be extended to consider clades as individuals, since they, like species are comprised of lineages.  Individuals comprised of lineages might be modeled as instances of the class 'portion of clade', which might include species (the class of all individual species) as a particular subclass because individual species are evolutionary units, unlike larger clades.
 +
 +
Modeled this way, the TTO and taxon rank ontology might look as follows:
 +
 +
                          TTO                                TaxonRank Ontology
 +
 +
 +
                        is_a
 +
  "portion of clade" <--------------  Cyprinidae  -------------------->  Family
 +
                                          ^            has_rank          ^
 +
                                          |                                |
 +
                                  part_of |                                |  "rank_order"
 +
                        is_a            |                                |
 +
  "portion of clade" <-----------      Davario    -------------------->  Genus
 +
                                          ^            has_rank          ^
 +
                                          |                                |
 +
                                  part_of |                                |  "rank_order"
 +
                      is_a              |                                |
 +
  "portion of clade" <------- Davario aequipinnatus ---------------->  Species
 +
                                                    has_rank
 +
 +
 +
Or even:
 +
 +
 +
      TTO                                      TaxonRank Ontology
 +
 +
 +
                        is_a                        is_a
 +
  Cyprinidae  -------------------->  Family ------------------> "portion of clade"
 +
        ^                                ^
 +
        |                                |
 +
        | part_of                        |  "rank_order"
 +
        |                is_a            |
 +
    Davario    -------------------->  Genus ------------------> "portion of clade"
 +
        ^                                ^        is_a
 +
        |                                |
 +
        | part_of                        |  "rank_order"
 +
        |                  is_a          |
 +
  Davario aequipinnatus ------------>  Species -----------------> "portion of clade"
 +
 +
 +
This approach also provides a natural bridge to the use of Phylogenetic definitions, which more or less restrict taxonomic labels to monophyletic clades.  A more detailed description of this approach can be found [[Taxonomic Rank Ontology|here]].
 +
 +
The major difficulties with such a model are potential conflicts with the OBO ontologies focus on classes, rather than individuals.
 +
 +
=Other Notes=
 +
;1. Taxonomic ranks - keep in TTO or make into separate ontology?
 +
- This issue has been resolved see [[Taxonomic Rank Vocabulary]].
 +
 +
;2. Representing unknown/unnamed species in ontology
 +
:a. Examples:
 +
:i. Chela sp.
 +
:ii. Esomus sp.
 +
:      iii. Danio aff. dangila
 +
:b. Solution? Instead of assigning a rank, create new entities for these, with appropriate genus as the parent and reference publication information, possibly in the name, e.g.  ‘Chela sp. (Fang 2003)’
 +
 +
- We decided to follow solution given in 2b.  We will call these species whatever the author calls them, i.e. if Fang 2003 calls a species ‘Danio aff. dangila’, we will request the name ‘Danio aff. dangila (Fang 2003)’ from Peter.
 +
 +
- We will make requests for new species names through the TTO Tracker (vs. email to Peter.
 +
 +
- If there are multiple entries for an unknown species in the materials list (e.g., ‘Chela sp.’ is listed multiple times with different voucher numbers), we will create only one entity for the unknown species.  If in the future these multiple vouchers are identified as different species, then we will update our annotations to reflect the new species designation.
 +
 +
- All these names will be assigned ‘high’ ids, pending their incorporation into CoF or demotion to synonyms as appropriate in the future.
 +
 +
 +
;3. Representing incertae sedis in ontology
 +
 +
- We will represent incertae sedis as currently done (point species directly to appropriate level in ontology)
 +
 +
- We discussed creating duplicate taxonomic category for incertae sedis (for example, ‘Cyprinidae incertae sedis’) but this implies that all species within this category are a family and we want to avoid that
 +
 +
- We also discussed creating new taxonomic ranks for incertae sedis (e.g. Family incertae sedis, Order incertae sedis) to which we would annotate incertae sedis taxa (vs. assigning e.g. Order or Family rank); creates categories that are not ontologically sound, so no.
 +
 +
- Issue with representing uncertainly monophyletic genera – we think we can deal with this by giving users the options to view trees with alternative taxonomy for these species
 +
 +
- Tree views will solve many incertae sedis issues.
 +
 +
- I’m not sure how this will interact with groups where intermediate levels are added – lots of families might be incertae sedis at the level of tribe for example – (Peter).
 +
 +
 +
;4. Incomplete tracking of synonyms from CoF to TTO
 +
 +
-      Synonym extraction has been implemented in the [[TTOUpdate tool]].  There is still room for improvement in the extraction algorithm.
 +
 +
 +
;5. Error reports to Peter – continue to send by email?  Thoughts to setting up a tracker?
 +
 +
- There is a tracker for requests and error reports within the [https://sourceforge.net/tracker/?atid=1046550&group_id=76834&func=browse OBO sourceforge site].
 +
 +
[[Category:Ontology]]
 +
[[Category:Taxonomy]]

Latest revision as of 17:01, 31 August 2010

This page contains accumulated design notes for taxonomy ontologies. They focus on the Teleost Taxonomy Ontology and the Taxonomic Rank Vocabulary, but the most recent information for each will appear on their respective home pages.

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)

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

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

Alternative Designs

Note: This section describes some design alternatives for taxonomic ontologies that refer to or include terms for ranks.

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.

Inference with an ontology of taxonomic ranks + instance graph of taxa

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.


See also the Taxonomic Rank Vocabulary which was released in January 2010.

Developing an Ontology for Taxonomic Ranks

When the Teleost Taxonomy Ontology (TTO) was submitted to OBO, the suggestion was made that the terms for taxonomic ranks (e.g., Family, Genus, Species) should be broken out. At present, taxonomic ranks are included in the TTO and cross referenced to similar terms in the NCBI taxonomy ontology. Although the process of constructing an ontology of rank terms is straightforward, there are some semantic issues that need to be resolved.

The current implementation can be diagrammed as follows: 


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


In the first draft of the ranks ontology, submitted to Chris Mungal and Michael Ashburner, the rank terms are simply subclasses of taxonomic_rank. There is no relation defined between the rank terms. The has_rank relation, as defined in the NCBO ontology is a meta_data relation (c.f. OWL annotation properties), which means it is intended to be ignored by any reasoner.

As there is clearly an ordering among the rank terms, it would be worthwhile to define an ordering relation between terms so that the term 'family' is indicated as 'larger' or 'more inclusive' than the term 'genus.'

The proposed situation is 

         TTO                                TaxonRank Ontology

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


There has been some question as to the nature of this ordering relation. There appear to be two points of view:

  1. A special relation exists between taxonomic ranks. It would be transitive and antisymmetric.
  2. The relation is simply part_of. Part_of is transitive and antisymmetric.


Chris Mungall's response to this question was: 

 3. What about imposing an ordering among ranks and, if so, is part_of the appropriate relation?

so with any ontology you should ask "what are the instances". In this case, the instances are best considered
to be terms/classes/categories rather than something tangible in nature. This takes us close to weird metaclass
modeling territory.

but not to worry. I would say reserve part_of for "real" part_of relations, between objects and processes. I
would just go with a custom relation for ranks. I don't have strong opinions on what you name it - above/below?
more_ancestral_than?

Declare the relation transitive

There is another property of the 'rank ordering' that should be noted. The current TTO currently uses a rather limited number of taxonomic ranks. However, if this ontology is intended to be shared across OBO projects, it will need to incorporate additional taxonomic level terms. For example, the NCBI taxnomy defines over 30 rank terms. As other groups develop taxonomies they will want to add ranks that are used in their systems. Furthermore, the system of ranks is open-ended, so any particular group might need to add additional ranks in the future. However, any one taxonomy will only use a subset of these terms, which means that in most cases, the is_a relation between two taxa will frequently correspond to more than one link up the rank taxonomy. Another case where this situation comes up, even for a single taxonomy, is an incertae sedis taxa. Thus a definition for the ordering relation needs to work without depending on having every step in the rank chain correspond to a taxonomic term in each tip to root path in the tree.


Resolving this issue may depend on the resolution of a second, closely related issue that may have to be reopened for discussion.

Modeling Taxa

Following the example of the OBO translation of the NCBI taxonomy, the TTO models taxa as a hierarchy of classes, defined by an is_a relation based on set theory. This means that classes, hence taxa terms are represented as sets. The taxon as set model extends all the way down to and including the species level.

However, an increasingly influential view among philosophers of biology is that species should be not be seen as either classes (or natural kinds), but as evolutionary units, and hence as individuals (e.g., Hull 1974, Ghiselin 1978). In this view, species are not sets of individual organisms, rather there is a part_of relation between organisms and their species. The particular part_of relation is commonly portrayed as species (and other clades) being composed of lineages and lineages consisting of related individual organisms.

This view can be extended to consider clades as individuals, since they, like species are comprised of lineages. Individuals comprised of lineages might be modeled as instances of the class 'portion of clade', which might include species (the class of all individual species) as a particular subclass because individual species are evolutionary units, unlike larger clades.

Modeled this way, the TTO and taxon rank ontology might look as follows: 

                         TTO                                TaxonRank Ontology



                       is_a
 "portion of clade" <--------------  Cyprinidae   -------------------->  Family
                                         ^             has_rank           ^
                                         |                                |
                                 part_of |                                |  "rank_order"
                        is_a             |                                |
 "portion of clade" <-----------      Davario    -------------------->  Genus
                                         ^             has_rank           ^
                                         |                                |
                                 part_of |                                |  "rank_order"
                      is_a               |                                |
 "portion of clade" <------- Davario aequipinnatus ---------------->  Species
                                                   has_rank


Or even: 


      TTO                                       TaxonRank Ontology



                       is_a                        is_a
  Cyprinidae   -------------------->  Family ------------------> "portion of clade"
       ^                                 ^
       |                                 |
       | part_of                         |  "rank_order"
       |                is_a             |
    Davario    -------------------->   Genus ------------------> "portion of clade"
       ^                                 ^         is_a
       |                                 |
       | part_of                         |  "rank_order"
       |                   is_a          |
 Davario aequipinnatus ------------>  Species -----------------> "portion of clade"


This approach also provides a natural bridge to the use of Phylogenetic definitions, which more or less restrict taxonomic labels to monophyletic clades. A more detailed description of this approach can be found here.

The major difficulties with such a model are potential conflicts with the OBO ontologies focus on classes, rather than individuals.

Other Notes

1. Taxonomic ranks - keep in TTO or make into separate ontology?

- This issue has been resolved see Taxonomic Rank Vocabulary.

2. Representing unknown/unnamed species in ontology
a. Examples:
i. Chela sp.
ii. Esomus sp.
iii. Danio aff. dangila
b. Solution? Instead of assigning a rank, create new entities for these, with appropriate genus as the parent and reference publication information, possibly in the name, e.g. ‘Chela sp. (Fang 2003)’

- We decided to follow solution given in 2b. We will call these species whatever the author calls them, i.e. if Fang 2003 calls a species ‘Danio aff. dangila’, we will request the name ‘Danio aff. dangila (Fang 2003)’ from Peter.

- We will make requests for new species names through the TTO Tracker (vs. email to Peter.

- If there are multiple entries for an unknown species in the materials list (e.g., ‘Chela sp.’ is listed multiple times with different voucher numbers), we will create only one entity for the unknown species. If in the future these multiple vouchers are identified as different species, then we will update our annotations to reflect the new species designation.

- All these names will be assigned ‘high’ ids, pending their incorporation into CoF or demotion to synonyms as appropriate in the future.


3. Representing incertae sedis in ontology

- We will represent incertae sedis as currently done (point species directly to appropriate level in ontology)

- We discussed creating duplicate taxonomic category for incertae sedis (for example, ‘Cyprinidae incertae sedis’) but this implies that all species within this category are a family and we want to avoid that

- We also discussed creating new taxonomic ranks for incertae sedis (e.g. Family incertae sedis, Order incertae sedis) to which we would annotate incertae sedis taxa (vs. assigning e.g. Order or Family rank); creates categories that are not ontologically sound, so no.

- Issue with representing uncertainly monophyletic genera – we think we can deal with this by giving users the options to view trees with alternative taxonomy for these species

- Tree views will solve many incertae sedis issues.

- I’m not sure how this will interact with groups where intermediate levels are added – lots of families might be incertae sedis at the level of tribe for example – (Peter).


4. Incomplete tracking of synonyms from CoF to TTO

- Synonym extraction has been implemented in the TTOUpdate tool. There is still room for improvement in the extraction algorithm.


5. Error reports to Peter – continue to send by email? Thoughts to setting up a tracker?

- There is a tracker for requests and error reports within the OBO sourceforge site.

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