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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

Simplified schema of Avibase primary tables, The Avibase ID table is the central element of Avibase, to which all other concepts are related, and which aims to represent all distinct taxonomic concepts ever published for birds. Published taxonomic concepts (species and subspecies, as well as subspecies groups in some cases), along with their scientific and common names as recognized in the publication, are each mapped to a single Avibase ID. A table of parent-child relationships is used to describe relationships between different Avibase IDs. Because all taxonomic concepts are congruent with Avibase IDs, relationships among taxonomic concepts themselves are not needed. Biological properties (geographic range, life-history, etc.) are linked directly to Avibase ID, as are synonyms, a table that partly overlaps with the names used by taxonomic concepts, but that can also extend to vernacular names in multiple languages. Name concepts, which relate to names attached to original type specimens, are a property of taxonomic concepts, and can themselves be linked to ITIS Taxonomic Serial Number (TSN) identifiers.
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Figure 1: Simplified schema of Avibase primary tables, The Avibase ID table is the central element of Avibase, to which all other concepts are related, and which aims to represent all distinct taxonomic concepts ever published for birds. Published taxonomic concepts (species and subspecies, as well as subspecies groups in some cases), along with their scientific and common names as recognized in the publication, are each mapped to a single Avibase ID. A table of parent-child relationships is used to describe relationships between different Avibase IDs. Because all taxonomic concepts are congruent with Avibase IDs, relationships among taxonomic concepts themselves are not needed. Biological properties (geographic range, life-history, etc.) are linked directly to Avibase ID, as are synonyms, a table that partly overlaps with the names used by taxonomic concepts, but that can also extend to vernacular names in multiple languages. Name concepts, which relate to names attached to original type specimens, are a property of taxonomic concepts, and can themselves be linked to ITIS Taxonomic Serial Number (TSN) identifiers.

Mentions: At the heart of Avibase is the notion of transparent and consistent representation of distinct taxonomic concepts. While there are vast numbers of taxonomic concepts in the "shallow" sense of unique name/source combinations (concept labels), there are far fewer "deeper", taxonomically unique (non-congruent) concept clusters that represent unique circumscriptions. Avibase assigns a unique database identifier to each of these distinct concept clusters (called an Avibase ID), composed of a random hexadecimal key (e.g. 2624054ED644AABB). The table of Avibase IDs, the central component around which the entire database is constructed (Fig. 1), attempts to capture all distinct taxonomic concepts ever published in those major authoritative sources. If one includes all taxonomic concepts that have been originally published as species and subspecies, as well as superspecies, subspecies groups, hybrid forms and phenotypic forms (sometimes originally described as valid species), there are 50,696 unique taxonomic concepts that have so far received an Avibase ID. Of these, 38,755 are from the 151 bird checklists in Avibase; the remaining 11,941 concepts are from other publications or represent unique taxon assemblages and were added separately (Table 2).


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

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

Simplified schema of Avibase primary tables, The Avibase ID table is the central element of Avibase, to which all other concepts are related, and which aims to represent all distinct taxonomic concepts ever published for birds. Published taxonomic concepts (species and subspecies, as well as subspecies groups in some cases), along with their scientific and common names as recognized in the publication, are each mapped to a single Avibase ID. A table of parent-child relationships is used to describe relationships between different Avibase IDs. Because all taxonomic concepts are congruent with Avibase IDs, relationships among taxonomic concepts themselves are not needed. Biological properties (geographic range, life-history, etc.) are linked directly to Avibase ID, as are synonyms, a table that partly overlaps with the names used by taxonomic concepts, but that can also extend to vernacular names in multiple languages. Name concepts, which relate to names attached to original type specimens, are a property of taxonomic concepts, and can themselves be linked to ITIS Taxonomic Serial Number (TSN) identifiers.
© Copyright Policy - creative-commons-attribution
Related In: Results  -  Collection

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

Figure 1: Simplified schema of Avibase primary tables, The Avibase ID table is the central element of Avibase, to which all other concepts are related, and which aims to represent all distinct taxonomic concepts ever published for birds. Published taxonomic concepts (species and subspecies, as well as subspecies groups in some cases), along with their scientific and common names as recognized in the publication, are each mapped to a single Avibase ID. A table of parent-child relationships is used to describe relationships between different Avibase IDs. Because all taxonomic concepts are congruent with Avibase IDs, relationships among taxonomic concepts themselves are not needed. Biological properties (geographic range, life-history, etc.) are linked directly to Avibase ID, as are synonyms, a table that partly overlaps with the names used by taxonomic concepts, but that can also extend to vernacular names in multiple languages. Name concepts, which relate to names attached to original type specimens, are a property of taxonomic concepts, and can themselves be linked to ITIS Taxonomic Serial Number (TSN) identifiers.
Mentions: At the heart of Avibase is the notion of transparent and consistent representation of distinct taxonomic concepts. While there are vast numbers of taxonomic concepts in the "shallow" sense of unique name/source combinations (concept labels), there are far fewer "deeper", taxonomically unique (non-congruent) concept clusters that represent unique circumscriptions. Avibase assigns a unique database identifier to each of these distinct concept clusters (called an Avibase ID), composed of a random hexadecimal key (e.g. 2624054ED644AABB). The table of Avibase IDs, the central component around which the entire database is constructed (Fig. 1), attempts to capture all distinct taxonomic concepts ever published in those major authoritative sources. If one includes all taxonomic concepts that have been originally published as species and subspecies, as well as superspecies, subspecies groups, hybrid forms and phenotypic forms (sometimes originally described as valid species), there are 50,696 unique taxonomic concepts that have so far received an Avibase ID. Of these, 38,755 are from the 151 bird checklists in Avibase; the remaining 11,941 concepts are from other publications or represent unique taxon assemblages and were added separately (Table 2).

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