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Biological names can be thought of as text labels, or words, that represent some definition or concept. A taxon concept defines what the name actually means. It might be used in reference to a set of living organisms ("All the fish I examined are Pomatomus saltatrix") or it might refer to a set of shared characteristics ("Sharks have skeletons of cartilage"). The problem is that the same name may represent different concepts and it may be difficult or impossible to differentiate one from the other.
Two different people may use the same name to refer to different sets of organisms. In fact, the same person, over time, may change their opinion as to what a name defines. This problem is exacerbated by the fact that most of the time the only information that is actually recorded with a data object is the name itself with no way of determining what the person who used the name was thinking at the time it was written down.
uBio draws upon taxon concepts to represent different taxonomic viewpoints and serves these viewpoints via data structures that can be used for indexing, retrieval, and organization. The ClassificationBank taxonomic model is only one of many taxonomic data models. The separation of ClassificationBank from NameBank is, in fact, to enable different taxonomic models to disagree on taxonomic concept definition while still sharing basic nomenclatural facts.
Taxon concepts represent an opinion. The recorded expression of that opinion falls within a continuum of precision. A minimal expression of a taxon concept within uBio combines a NameBank record with a reference to an author or agency asserting an opinion. A minimal assertion regarding a NameBank record might be that the name is considered valid or invalid.
A more defined opinion places a valid taxon with a hierarchy to create a classification of valid taxon names. The Howard and Moore 3rd edition Birds of the World represents a contemporary viewpoint on bird taxa. [See Anser fabalis fabalis]
Synonymies provide additional information regarding what is actually circumscribed by the taxon concept. We define two distinct types of synonymies: implicit and explicit.
Implicit synonymies are lists of names that are asserted to be synonymous with a taxon but provide no additional information regarding how this synonymy is derived. The implication is (perhaps) that the types were examined but there is no direct relationship between any name-bearing data object (vouchered specimen or other) and the synonymy itself. The USDA ITIS database serves an implicit taxon concept. [See Globicephala melas, ITIS]
Implicit taxon concepts can provide additional synonyms that may be used as query terms. This can include heterotypic synonyms that would not be part of a NameBank name concept. One criticism of the use of implicit synonyms is that while it may have value as an index, there is no relationship between the concept itself and any data object that may bear a synonymous name.
Explicit taxon concepts are circumscribed by references to specimens or taxa that themselves are circumscribed by specimens. Specimens may be indirectly referenced (represented by bibliographic citation) or directly referenced (represented by specific vouchered specimen references). The nomenclature circumscribed by the specimens and reconciled against the relevant nomenclatural codes determines the valid name and synonymy of the concept. Extension of the synonymy to data objects outside of the explicit circumscription can only be inferential.
The uBio ClassificationBank can represent and serve both implicit and explicit taxon concepts. The current ClassificationBank, with it's publication orientation, serves only indirectly-referenced explicit taxon concepts. The bibliographic circumscription is derived from NameBank chresonyms. The factual basis of the chresonym defintion enables a single specimen reference to be re-interpreted within different taxon concepts. [See Globicephala melaena melaena, Hershkovitz]
Qu'est-ce qu'un taxon? - Taxon concepts
Biological names can be thought of as text labels, or words, that represent some definition or concept. A taxon concept defines what the name actually means. It might be used in reference to a set of living organisms ("All the fish I examined are Pomatomus saltatrix") or it might refer to a set of shared characteristics ("Sharks have skeletons of cartilage"). The problem is that the same name may represent different concepts and it may be difficult or impossible to differentiate one from the other.
Two different people may use the same name to refer to different sets of organisms. In fact, the same person, over time, may change their opinion as to what a name defines. This problem is exacerbated by the fact that most of the time the only information that is actually recorded with a data object is the name itself with no way of determining what the person who used the name was thinking at the time it was written down.
uBio draws upon taxon concepts to represent different taxonomic viewpoints and serves these viewpoints via data structures that can be used for indexing, retrieval, and organization. The ClassificationBank taxonomic model is only one of many taxonomic data models. The separation of ClassificationBank from NameBank is, in fact, to enable different taxonomic models to disagree on taxonomic concept definition while still sharing basic nomenclatural facts.
Taxon concepts represent an opinion. The recorded expression of that opinion falls within a continuum of precision. A minimal expression of a taxon concept within uBio combines a NameBank record with a reference to an author or agency asserting an opinion. A minimal assertion regarding a NameBank record might be that the name is considered valid or invalid.
A more defined opinion places a valid taxon with a hierarchy to create a classification of valid taxon names. The Howard and Moore 3rd edition Birds of the World represents a contemporary viewpoint on bird taxa. [See Anser fabalis fabalis]
Synonymies provide additional information regarding what is actually circumscribed by the taxon concept. We define two distinct types of synonymies: implicit and explicit.
Implicit synonymies are lists of names that are asserted to be synonymous with a taxon but provide no additional information regarding how this synonymy is derived. The implication is (perhaps) that the types were examined but there is no direct relationship between any name-bearing data object (vouchered specimen or other) and the synonymy itself. The USDA ITIS database serves an implicit taxon concept. [See Globicephala melas, ITIS]
Implicit taxon concepts can provide additional synonyms that may be used as query terms. This can include heterotypic synonyms that would not be part of a NameBank name concept. One criticism of the use of implicit synonyms is that while it may have value as an index, there is no relationship between the concept itself and any data object that may bear a synonymous name.
Explicit taxon concepts are circumscribed by references to specimens or taxa that themselves are circumscribed by specimens. Specimens may be indirectly referenced (represented by bibliographic citation) or directly referenced (represented by specific vouchered specimen references). The nomenclature circumscribed by the specimens and reconciled against the relevant nomenclatural codes determines the valid name and synonymy of the concept. Extension of the synonymy to data objects outside of the explicit circumscription can only be inferential.
The uBio ClassificationBank can represent and serve both implicit and explicit taxon concepts. The current ClassificationBank, with it's publication orientation, serves only indirectly-referenced explicit taxon concepts. The bibliographic circumscription is derived from NameBank chresonyms. The factual basis of the chresonym defintion enables a single specimen reference to be re-interpreted within different taxon concepts. [See Globicephala melaena melaena, Hershkovitz]