Limits...
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 the taxonomic entities related to the Vireo solitarius superspecies. Numbers under each name refer to Avibase IDs. The concept for the nominal plumbeussec. Oberholser, 1974 is therefore distinct from the concept for the nominal subspecies plumbeus when jacksoni is subsumed. It is worth noting however that the recognition or not of jacksoni does not affect the higher related concepts, such as the plumbeus species, any of its other subspecies, or the rest of the Vireo solitarius complex because they are either orthogonal to those alternative arrangements or they completely include both. In the database model (Fig. 1), these trees are maintained with the parent-child relationship table in which each Avibase ID only needs to identify its immediate parent, while other relationships can be calculated programmatically.
© Copyright Policy - creative-commons-attribution
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4109484&req=5

Figure 2: The relationships between the taxonomic entities related to the Vireo solitarius superspecies. Numbers under each name refer to Avibase IDs. The concept for the nominal plumbeussec. Oberholser, 1974 is therefore distinct from the concept for the nominal subspecies plumbeus when jacksoni is subsumed. It is worth noting however that the recognition or not of jacksoni does not affect the higher related concepts, such as the plumbeus species, any of its other subspecies, or the rest of the Vireo solitarius complex because they are either orthogonal to those alternative arrangements or they completely include both. In the database model (Fig. 1), these trees are maintained with the parent-child relationship table in which each Avibase ID only needs to identify its immediate parent, while other relationships can be calculated programmatically.

Mentions: As an example of a concept tree, we consider the Solitary Vireo complex. The 6th edition of the AOU North American Checklist (American Ornithologists’ Union 1983) recognized a single species in this complex, Vireo solitarius. In the Forty-first Supplement (Banks et al. 1997), two groups of subspecies within this species were raised to full species: Vireo plumbeus (including subspecies plumbeus, pinicolus, repetens, montanus and notius) and Vireo cassinii (including subspecies cassinii and lucasanus). There are therefore two separate taxonomic concepts in Avibase, with separate Avibase IDs but the same name Vireo solitarius: one represents Vireo solitariussensu lato, which includes plumbeus and cassinii, and the other represents Vireo solitariussensu stricto, which does not overlap with plumbeus and cassinii. In Avibase, all three forms of the Solitary Vireo (Vireo plumbeus, Vireo cassinii and Vireo solitariuss.s.) are children of Vireo solitariuss.l. (Fig. 2). Each of these three forms can in turn have their own subspecies. This type of relatively simple model with a single tree represents a majority of relationships among related taxonomic concepts.


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

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

The relationships between the taxonomic entities related to the Vireo solitarius superspecies. Numbers under each name refer to Avibase IDs. The concept for the nominal plumbeussec. Oberholser, 1974 is therefore distinct from the concept for the nominal subspecies plumbeus when jacksoni is subsumed. It is worth noting however that the recognition or not of jacksoni does not affect the higher related concepts, such as the plumbeus species, any of its other subspecies, or the rest of the Vireo solitarius complex because they are either orthogonal to those alternative arrangements or they completely include both. In the database model (Fig. 1), these trees are maintained with the parent-child relationship table in which each Avibase ID only needs to identify its immediate parent, while other relationships can be calculated programmatically.
© Copyright Policy - creative-commons-attribution
Related In: Results  -  Collection

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

Figure 2: The relationships between the taxonomic entities related to the Vireo solitarius superspecies. Numbers under each name refer to Avibase IDs. The concept for the nominal plumbeussec. Oberholser, 1974 is therefore distinct from the concept for the nominal subspecies plumbeus when jacksoni is subsumed. It is worth noting however that the recognition or not of jacksoni does not affect the higher related concepts, such as the plumbeus species, any of its other subspecies, or the rest of the Vireo solitarius complex because they are either orthogonal to those alternative arrangements or they completely include both. In the database model (Fig. 1), these trees are maintained with the parent-child relationship table in which each Avibase ID only needs to identify its immediate parent, while other relationships can be calculated programmatically.
Mentions: As an example of a concept tree, we consider the Solitary Vireo complex. The 6th edition of the AOU North American Checklist (American Ornithologists’ Union 1983) recognized a single species in this complex, Vireo solitarius. In the Forty-first Supplement (Banks et al. 1997), two groups of subspecies within this species were raised to full species: Vireo plumbeus (including subspecies plumbeus, pinicolus, repetens, montanus and notius) and Vireo cassinii (including subspecies cassinii and lucasanus). There are therefore two separate taxonomic concepts in Avibase, with separate Avibase IDs but the same name Vireo solitarius: one represents Vireo solitariussensu lato, which includes plumbeus and cassinii, and the other represents Vireo solitariussensu stricto, which does not overlap with plumbeus and cassinii. In Avibase, all three forms of the Solitary Vireo (Vireo plumbeus, Vireo cassinii and Vireo solitariuss.s.) are children of Vireo solitariuss.l. (Fig. 2). Each of these three forms can in turn have their own subspecies. This type of relatively simple model with a single tree represents a majority of relationships among related taxonomic concepts.

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