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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

The relationships between Pterodroma arminjoniana, Pterodroma heraldica and Pterodroma atrata, with two alternative arrangements (A and B) of biological concepts found in taxonomic authorities. Concepts with the same lowercase letters in brackets in the two diagrams represent congruent circumscriptions.
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Figure 3: The relationships between Pterodroma arminjoniana, Pterodroma heraldica and Pterodroma atrata, with two alternative arrangements (A and B) of biological concepts found in taxonomic authorities. Concepts with the same lowercase letters in brackets in the two diagrams represent congruent circumscriptions.

Mentions: Alternate concept trees are required in those relatively rare cases (5.7% of all Avibase IDs) where several mutually contradictory arrangements have been proposed. For instance, the superspecies Pterodroma arminjoniana is now considered three distinct species (Pterodroma arminjoniana, Pterodroma heraldica and Pterodroma atrata), but several arrangements of those have been proposed which involve at least two different relationship trees (Fig. 3): one in which atrata is included in heraldicas.l. and one in which it is not. From these two alternative taxonomic trees, four different valid combinations of taxonomic concepts are possible and have been published within the same checklist: 1) the superspecies Pterodroma arminjoniana (abc) alone, 2) Pterodroma arminjoniana (ab, including heraldica) and Pterodroma atrata (c), 3) Pterodroma heraldica (ac, including atrata) and Pterodroma arminjoniana (b) and 4) Pterodroma heraldica (a), Pterodroma arminjoniana (b) and Pterodroma atrata (c) as distinct species. The use of those concepts by various checklists can be visualized in a grid (http://avibase.bsc-eoc.org/species.jsp?avibaseid=A26C9D6B5C859E5E&sec=taxontable). Note that in all four combinations of concepts, the three letters representing the finer levels (a, b and c) are always included, and included only once. This property of the relationship trees can be used to validate the arrangements and map the taxonomic concepts to Avibase IDs (see section “Validating parent-child relationships across checklists using fractional weights”). One should also note that taxon concept combinations 1 and 4 are present in both taxonomic trees A and B. In checklists that use those combinations, it is not possible to determine which alternate tree applies, nor is it necessary because both trees lead to the same solution for mapping taxonomic concepts and Avibase IDs.


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

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

The relationships between Pterodroma arminjoniana, Pterodroma heraldica and Pterodroma atrata, with two alternative arrangements (A and B) of biological concepts found in taxonomic authorities. Concepts with the same lowercase letters in brackets in the two diagrams represent congruent circumscriptions.
© Copyright Policy - creative-commons-attribution
Related In: Results  -  Collection

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

Figure 3: The relationships between Pterodroma arminjoniana, Pterodroma heraldica and Pterodroma atrata, with two alternative arrangements (A and B) of biological concepts found in taxonomic authorities. Concepts with the same lowercase letters in brackets in the two diagrams represent congruent circumscriptions.
Mentions: Alternate concept trees are required in those relatively rare cases (5.7% of all Avibase IDs) where several mutually contradictory arrangements have been proposed. For instance, the superspecies Pterodroma arminjoniana is now considered three distinct species (Pterodroma arminjoniana, Pterodroma heraldica and Pterodroma atrata), but several arrangements of those have been proposed which involve at least two different relationship trees (Fig. 3): one in which atrata is included in heraldicas.l. and one in which it is not. From these two alternative taxonomic trees, four different valid combinations of taxonomic concepts are possible and have been published within the same checklist: 1) the superspecies Pterodroma arminjoniana (abc) alone, 2) Pterodroma arminjoniana (ab, including heraldica) and Pterodroma atrata (c), 3) Pterodroma heraldica (ac, including atrata) and Pterodroma arminjoniana (b) and 4) Pterodroma heraldica (a), Pterodroma arminjoniana (b) and Pterodroma atrata (c) as distinct species. The use of those concepts by various checklists can be visualized in a grid (http://avibase.bsc-eoc.org/species.jsp?avibaseid=A26C9D6B5C859E5E&sec=taxontable). Note that in all four combinations of concepts, the three letters representing the finer levels (a, b and c) are always included, and included only once. This property of the relationship trees can be used to validate the arrangements and map the taxonomic concepts to Avibase IDs (see section “Validating parent-child relationships across checklists using fractional weights”). One should also note that taxon concept combinations 1 and 4 are present in both taxonomic trees A and B. In checklists that use those combinations, it is not possible to determine which alternate tree applies, nor is it necessary because both trees lead to the same solution for mapping taxonomic concepts and Avibase IDs.

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