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Avibase - a database system for managing and organizing taxonomic concepts.

Lepage D, Vaidya G, Guralnick R - Zookeys (2014)

Bottom Line: Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage.We present the on-line database Avibase as one possible approach to organizing taxonomic concepts.Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bird Studies Canada, P.O. Box 160, 115 Front St., Port Rowan, ON Canada N0E 1M0.

ABSTRACT
Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use.

No MeSH data available.


Related in: MedlinePlus

Fractional weights (w) can be used to validate the taxonomic arrangements within a particular authority. In this example, in any valid listing of the concepts within an authority, the sum of all taxonomic concepts related to the superspecies Vireo solitarius should add up to 1.0 at both the species and the subspecies levels.
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Figure 4: Fractional weights (w) can be used to validate the taxonomic arrangements within a particular authority. In this example, in any valid listing of the concepts within an authority, the sum of all taxonomic concepts related to the superspecies Vireo solitarius should add up to 1.0 at both the species and the subspecies levels.

Mentions: Parent-child relationships and concept trees may be used both to identify relationships in new publications and to validate existing relationships. The algorithm used by Avibase assigns and stores fractional weights for each node of a concept tree, starting with a weight of 1.0 for the top concept in a tree. Child nodes recursively receive an equal fraction of the weight of their parent. Vireo solitarius, cassinii and plumbeus, for instance, would each receive a weight of 0.333 (Fig. 4). The two subspecies of solitarius and cassinii would each receive a weight of 0.167 (half of their parent node), and the five recognized subspecies of plumbeus would each receive (0.067) (one-fifth of their parent node). Finally, the subsumed subspecies jacksoni and the nominal plumbeus that excludes jacksoni would each receive a weight of 0.033. Within any authority with global coverage, such as a global bird checklist, there should always be at least one alternate tree for which the sum of weights yields a total of 1.0 for a suite of related species concepts. In the Vireo example, the two valid options at the species level are listing Vireo solitariuss.l. alone (total weight = 1.0), or the three forms individually (total weight = 0.333 + 0.333 + 0.333 = 1.0). For authorities that are restricted in coverage or incomplete in scope, such as a checklist of North American birds, the same approach can be used but with weights recalculated to exclude portions of the trees that are not covered by the scope of the authority. It is possible for a set of incorrect arrangements to add up to 1.0 by chance; Avibase uses a series of rules (listed in Table 3) to detect such cases.


Avibase - a database system for managing and organizing taxonomic concepts.

Lepage D, Vaidya G, Guralnick R - Zookeys (2014)

Fractional weights (w) can be used to validate the taxonomic arrangements within a particular authority. In this example, in any valid listing of the concepts within an authority, the sum of all taxonomic concepts related to the superspecies Vireo solitarius should add up to 1.0 at both the species and the subspecies levels.
© Copyright Policy - creative-commons-attribution
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4109484&req=5

Figure 4: Fractional weights (w) can be used to validate the taxonomic arrangements within a particular authority. In this example, in any valid listing of the concepts within an authority, the sum of all taxonomic concepts related to the superspecies Vireo solitarius should add up to 1.0 at both the species and the subspecies levels.
Mentions: Parent-child relationships and concept trees may be used both to identify relationships in new publications and to validate existing relationships. The algorithm used by Avibase assigns and stores fractional weights for each node of a concept tree, starting with a weight of 1.0 for the top concept in a tree. Child nodes recursively receive an equal fraction of the weight of their parent. Vireo solitarius, cassinii and plumbeus, for instance, would each receive a weight of 0.333 (Fig. 4). The two subspecies of solitarius and cassinii would each receive a weight of 0.167 (half of their parent node), and the five recognized subspecies of plumbeus would each receive (0.067) (one-fifth of their parent node). Finally, the subsumed subspecies jacksoni and the nominal plumbeus that excludes jacksoni would each receive a weight of 0.033. Within any authority with global coverage, such as a global bird checklist, there should always be at least one alternate tree for which the sum of weights yields a total of 1.0 for a suite of related species concepts. In the Vireo example, the two valid options at the species level are listing Vireo solitariuss.l. alone (total weight = 1.0), or the three forms individually (total weight = 0.333 + 0.333 + 0.333 = 1.0). For authorities that are restricted in coverage or incomplete in scope, such as a checklist of North American birds, the same approach can be used but with weights recalculated to exclude portions of the trees that are not covered by the scope of the authority. It is possible for a set of incorrect arrangements to add up to 1.0 by chance; Avibase uses a series of rules (listed in Table 3) to detect such cases.

Bottom Line: Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage.We present the on-line database Avibase as one possible approach to organizing taxonomic concepts.Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bird Studies Canada, P.O. Box 160, 115 Front St., Port Rowan, ON Canada N0E 1M0.

ABSTRACT
Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use.

No MeSH data available.


Related in: MedlinePlus