Avibase

Avibase is an online taxonomic database that organizes bird taxonomic and distribution data globally. At its core, the database relies on the notion of taxonomic concepts.[1][2] rather than taxonomic names[3] (see also[4][5][6] for the rationale of using taxonomic concepts). Avibase incorporates and organizes taxonomic data from the main avian taxonomic publishers (The Clements Checklist of Birds of the World,[7] Handbook of the Birds of the World, BirdLife International,[8] IOC Checklist[9] and the Howard and Moore Complete Checklist of the Birds of the World[10]) and other regional sources (e.g. all editions of the American Ornithological Society Checklist of North American Birds since 1886). Taxonomic concepts in over 230 different taxonomic sources have been mapped and cross-referenced to Avibase concepts.

Avibase
Type of site
Taxonomic database
Available in105 languages
Created byDenis Lepage
URLavibase.bsc-eoc.org
Launched2003
Current statusActive

The website also offers checklists for more than 20,000 geographic regions of the world, species pages with taxonomic information and synonyms, and tools for observers to maintain their own sightings and obtain reports (e.g. map showing countries or eBird hotspots with the number of target species that are missing from one of their life list).

History and purpose

Avibase has been created and is maintained by Denis Lepage, currently senior director, data science and technology at Birds Canada. The data contained in Avibase has been gathered starting around 1991.[11] The Avibase website was launched in June 2003 and has been hosted by Birds Canada (formerly Bird Studies Canada) since its inception.

Features

Taxonomic concepts. The database is organized primarily around a table of unique taxonomic concepts. Each concept represents a unique biological circumscription and has been assigned a unique alphanumeric ID called Avibase ID. Avibase IDs allow the tracking of congruent taxonomic concepts among publication sources. There are approximately 58,000 unique taxonomic concepts described in Avibase. These include concepts traditionally recognized as species and subspecies, but also other taxonomic groupings (subspecies groups), various alternative taxonomic treatments recognized historically, and other concepts representing hybrids, color morphs and invalid or dubious forms.

Nomenclature data. Each scientific name is also described to include citation data and the name associated with the original description. Approximately 48,000 acts have been recorded in Avibase, and various types of synonyms are also available.

Regional species checklists are available for more than 20,000 regions of the world. This includes all countries, territories and dependencies, and most regions defined in the GADM subnational layers such as provinces, states, prefectures, counties, departments, municipalities and districts (GADM levels 1 and 2), as well as over 2,500 islands. Regional checklists are available in several taxonomic formats, and can also incorporate common names in a variety of languages. Data for regional checklists has come from a wide number of sources, such as the eBird EBD dataset and forums such as the Facebook Global Rare Bird Alert.

Common names and synonyms are available in 271 different languages and regional variants, and there are 21 languages that have a coverage greater than 85% of species with a known common name.

MyAvibase, launched in 2013, provides free tools for users who want to maintain their life lists and generate reports that are focused on finding target species that the observer has not yet seen (where to go, what to see, when to go, how long to visit), or general regional statistics (e.g. total number of species by country).

Use of database information

Avibase is used as a source data in many web and peer-reviewed publications. For instance, it is often used as the primary source on Wikipedia. It has also been cited, and its data have been used, in more than 600 publications,[12] particularly in the fields of ecology,[13] conservation,[14] parasitology,[15] human health,[16] taxonomy[17][18] and bioinformatics.[19]

Avibase IDs are used as a way to resolve ambiguities in scientific names of birds, and have been adopted by the AOS Checklist of North American Birds,[20] and they are available in the Wikidata taxon project.[21] Avibase is also used as a reference for taxonomic information by research groups such as the Influenza Research Database.

Notes
  1. "The concept of 'potential taxa' in databases." Berendsohn WG (1995) Taxon 44: 207–212.
  2. "Standard data model representation for taxonomic information." Kennedy J, Hyam R, Kukla R, Paterson T (2006). OMICS: A Journal of Integrative Biology 10: 220–230.
  3. "Avibase – a Database System for Managing and Organizing Taxonomic Concepts.", Lepage, Denis, Gaurav Vaidya, and Robert Guralnick, ZooKeys, 420 (June 25, 2014): 117–35.
  4. "Taxonomy for Humans or Computers? Cognitive Pragmatics for Big Data." Sterner, Beckett, and Nico M. Franz. 2017. Biological Theory 12 (2): 99–111.
  5. To Increase Trust, Change the Social Design behind Aggregated Biodiversity Data. Franz, Nico M., and Beckett W. Sterner. 2018. Database 2018 (January).
  6. "Controlling the Taxonomic Variable: Taxonomic Concept Resolution for a Southeastern United States Herbarium Portal." Franz, Nico, Edward Gilbert, Bertram Ludäscher, and Alan Weakley. 2016. Research Ideas and Outcomes 2 (September): e10610.
  7. The eBird/Clements Checklist of Birds of the World: v2019 Clements, J. F., T. S. Schulenberg, M. J. Iliff, S. M. Billerman, T. A. Fredericks, B. L. Sullivan, and C. L. Wood. 2019.
  8. Handbook of the Birds of the World and BirdLife International digital checklist of the birds of the world. Version 4. HBW and BirdLife International (Dec. 2019)
  9. IOC World Bird List (v10.1) Gill F, D Donsker & P Rasmussen (Eds). 2020.
  10. The Howard and Moore Complete Checklist of the Birds of the World, version 4.1 (Downloadable checklist) Christidis et al. 2018.
  11. "Avibase - The World Bird Database". avibase.bsc-eoc.org.
  12. "Avibase - The World Bird Database". avibase.bsc-eoc.org.
  13. "Global Evolutionary Isolation Measures Can Capture Key Local Conservation Species in Nearctic and Neotropical Bird Communities." Redding, David W., Arne O. Mooers, Çağan H. Şekercioğlu, and Ben Collen. 2015. Philosophical Transactions of the Royal Society B: Biological Sciences 370 (1662): 20140013.
  14. "Conservation in Austral and Neotropical America: Building Scientific Capacity Equal to the Challenges." Rodríguez, Jon Paul, Javier A. Simonetti, Andrea Premoli, and Miguel Ângelo Marini. 2005. Conservation Biology 19 (3): 969–72.
  15. "Unexpected Bird–Feather Mite Associations Revealed by DNA Metabarcoding Uncovers a Dynamic Ecoevolutionary Scenario." Doña, Jorge, David Serrano, Sergey Mironov, Alicia Montesinos‐Navarro, and Roger Jovani. 2019. Molecular Ecology 28 (2): 379–90.
  16. "Global Drivers of Human Pathogen Richness and Prevalence." Dunn, Robert R., T. Jonathan Davies, Nyeema C. Harris, and Michael C. Gavin. 2010. Proceedings of the Royal Society B: Biological Sciences 277 (1694): 2587–95.
  17. "Coordinating Dissent as an Alternative to Consensus Classification: Insights from Systematics for Bio-Ontologies." Sterner, Beckett, Joeri Witteveen, and Nico Franz. 2020. History and Philosophy of the Life Sciences 42 (1): 8.
  18. "Taxonomy Needs Pluralism, but a Controlled and Manageable One.". Minelli, Alessandro. 2020. Megataxa 1 (1): 9–18.
  19. "A Standardized Reference Data Set for Vertebrate Taxon Name Resolution." Zermoglio, Paula F., Robert P. Guralnick, and John R. Wieczorek. 2016. PLoS ONE 11 (1): e0146894.
  20. "Check-list of North American Birds (online)." Chesser, R. T., K. J. Burns, C. Cicero, J. L. Dunn, A. W. Kratter, I. J. Lovette, P. C. Rasmussen, J. V. Remsen, Jr., D. F. Stotz, and K. Winker. 2019. American Ornithological Society.
  21. "Wikidata taxon project".

References
  • Dickinson, Edward C. (2016), "Reinforcing the Foundations of Ornithological Nomenclature: Filling the Gaps in Sherborn's and Richmond's Historical Legacy of Bibliographic Exploration.", ZooKeys (550): 107–134, doi:10.3897/zookeys.550.9546, PMID 26877660
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