Biodiversity informatics
Biodiversity informatics is the application of
Overview
Biodiversity informatics (different but linked to bioinformatics) is the application of information technology methods to the problems of organizing, accessing, visualizing and analyzing primary biodiversity data. Primary biodiversity data is composed of names, observations and records of specimens, and genetic and morphological data associated to a specimen. Biodiversity informatics may also have to cope with managing information from unnamed taxa such as that produced by environmental sampling and sequencing of mixed-field samples. The term biodiversity informatics is also used to cover the computational problems specific to the names of biological entities, such as the development of algorithms to cope with variant representations of identifiers such as species names and authorities, and the multiple classification schemes within which these entities may reside according to the preferences of different workers in the field, as well as the syntax and semantics by which the content in taxonomic databases can be made machine queryable and interoperable for biodiversity informatics purposes...
History of the discipline
Biodiversity Informatics can be considered to have commenced with the construction of the first computerized
History of the term
According to correspondence reproduced by Walter Berendsohn,
Digital taxonomy (systematics)
Global list of all species
One major goal for biodiversity informatics is the creation of a complete master list of currently recognised species of the world. This goal has been achieved to a large extent by the Catalogue of Life project which lists >2 million species in its 2022 Annual Checklist.[8] A similar effort for fossil taxa, the Paleobiology Database[9] documents some 100,000+ names for fossil species, out of an unknown total number.
Genus and species scientific names as unique identifiers
Application of the Linnaean system of binomial nomenclature for species, and uninomials for genera and higher ranks, has led to many advantages but also problems with homonyms (the same name being used for multiple taxa, either inadvertently or legitimately across multiple kingdoms), synonyms (multiple names for the same taxon), as well as variant representations of the same name due to orthographic differences, minor spelling errors, variation in the manner of citation of author names and dates, and more. In addition, names can change through time on account of changing taxonomic opinions (for example, the correct generic placement of a species, or the elevation of a subspecies to species rank or vice versa), and also the circumscription of a taxon can change according to different authors' taxonomic concepts. One proposed solution to this problem is the usage of Life Science Identifiers (LSIDs) for machine-machine communication purposes, although there are both proponents and opponents of this approach.
A consensus classification of organisms
Organisms can be classified in a multitude of ways (see main page
Biodiversity Maps
Biodiversity maps provide a
Biodiversity maps can be produced in a variety of ways: traditionally range maps were hand-drawn based on literature reports but increasingly large-scale data, e.g. from citizen science projects (e.g. iNaturalist) and digitized museum collections (e.g. VertNet) are used. GIS tools such as ArcGIS or R packages such as dismo can specifically aid in species distribution modeling (ecological niche modeling) and even predict impacts of ecological change on biodiversity.[13] GBIF, OBIS, and IUCN are large web-based repositories of species spatial-temporal data that source many existing biodiversity maps.
Biodiversity Maps | Description | Link |
---|---|---|
Map of Life (MOL) | A scalable web platform geared for large biodiversity and environmental data[14] | mol.org |
The Map of Biodiversity Importance | Identifies areas of biodiversity importance critical to preventing extinctions in the contiguous United States | https://www.natureserve.org/map-biodiversity-importance |
Biodiversity Maps (National Biodiversity Data Centre) | An overview of the state of knowledge on the distribution of Ireland's biodiversity | https://maps.biodiversityireland.ie/ |
Saving Nature | Biodiversity Maps that depict patterns to guide conservation efforts. | https://savingnature.com/our-biodiversity-maps/ |
Mobilizing primary biodiversity information
"Primary" biodiversity information can be considered the basic data on the occurrence and diversity of species (or indeed, any recognizable taxa), commonly in association with information regarding their distribution in either space, time, or both. Such information may be in the form of retained specimens and associated information, for example as assembled in the natural history collections of
As a secondary source of biodiversity data, relevant
Standards and protocols
In common with other data-related disciplines, Biodiversity Informatics benefits from the adoption of appropriate
Current activities
At the 2009 e-Biosphere conference in the U.K.,[20] the following themes were adopted, which is indicative of a broad range of current Biodiversity Informatics activities and how they might be categorized:
- Application: Conservation / Agriculture / Fisheries / Industry / Forestry
- Application: Invasive Alien Species
- Application: Systematic and Evolutionary Biology
- Application: Taxonomy and Identification Systems
- New Tools, Services and Standards for Data Management and Access
- New Modeling Tools
- New Tools for Data Integration
- New Approaches to Biodiversity Infrastructure
- New Approaches to Species Identification
- New Approaches to Mapping Biodiversity
- National and Regional Biodiversity Databases and Networks
A post-conference workshop of key persons with current significant Biodiversity Informatics roles also resulted in a Workshop Resolution that stressed, among other aspects, the need to create durable, global registries for the resources that are basic to biodiversity informatics (e.g., repositories, collections); complete the construction of a solid taxonomic infrastructure; and create ontologies for biodiversity data.[21]
Example projects
Global:
- The Ocean Biogeographic Information System(OBIS) (for marine species)
- The ITIS (Integrated Taxonomic Information System), and Catalogue of Lifeprojects
- Global Names
- EOL, The Encyclopedia of Life project
- The Consortium for the Barcode of Life project
- The Map of Life project
- The Reptile Database project
- The AmphibiaWeb project
- The uBio Universal Biological Indexer and Organizer, from the Woods Hole Marine Biological Laboratory
- The Index to Organism Names (ION) from Clarivate Analytics, providing access to scientific names of taxa from numerous journals as indexed in the Zoological Record
- The Interim Register of Marine and Nonmarine Genera (IRMNG)
- ZooBank, the registry for nomenclatural acts and relevant systematic literature in zoology
- The Index Nominum Genericorum, compilation of generic names published for organisms covered by the International Code of Botanical Nomenclature, maintained at the Smithsonian Institutionin the U.S.A.
- The International Plant Names Index
- fungi
- The List of Prokaryotic names with Standing in Nomenclature (International Code of Nomenclature of Bacteria
- The Biodiversity Heritage Library project - digitising biodiversity literature
- Wikispecies, open source (community-editable) compilation of taxonomic information, companion project to Wikipedia
- TaxonConcept.org, a Linked Dataproject that connects disparate species databases
- Instituto de Ciencias Naturales. Universidad Nacional de Colombia. Virtual Collections and Biodiversity Informatics Unit
- ANTABIF. The Antarctic Biodiversity Information Facility gives free and open access to Antarctic Biodiversity data, in the spirit of the Antarctic Treaty.
- Genesys, database of plant genetic resources maintained in national, regional and international gene banks
- VertNet, Access to vertebrate primary occurrence data from data sets worldwide.
Regional / national projects:
- Fauna Europaea
- Atlas of Living Australia
- Pan-European Species directories Infrastructure (PESI)
- Symbiota
- iDigBio, Integrated Digitized Biocollections (USA)
- i4Life project
- Sistema de Información sobre Biodiversidad de Colombia
- India Biodiversity Portal (IBP)
- Bhutan Biodiversity Portal (BBP)
- Weed Identification and Knowledge in the Western Indian Ocean (WIKWIO)
- LifeWatch is proposed by ESFRI as a pan-European research (e-)infrastructure to support Biodiversity research and policy-making.
- Vermont Atlas of Life
A listing of over 600 current biodiversity informatics related activities can be found at the TDWG "Biodiversity Information Projects of the World" database.[22]
See also
- Web-based taxonomy
- List of biodiversity databases
References
- ^ Soberón, J., & Peterson, A. T. (2004). Biodiversity informatics: Managing and applying primary biodiversity data. Philosophical Transactions of the Royal Society B: Biological Sciences, 359(1444), 689–698.
- hdl:1808/16508.
- doi:10.1641/0006-3568(2001)051[0363:PSIUEN]2.0.CO;2. Archived from the original(PDF) on 2016-08-07. Retrieved 2009-10-09.
- ^ "Bioinformatics for Biodiversity?". Science. 289: 2229–2440. 2000.
- ^ "Biodiversity Informatics". BMC Bioinformatics. 10 Suppl 14. 2009. Archived from the original on 2010-01-27. Retrieved 2009-11-15.
- ^ ""Biodiversity Informatics", The Term". Retrieved 2009-08-06.
- S2CID 31852825.
- ^ "Catalogue of Life - 2016 Annual Checklist : The 2016 Annual Checklist". www.catalogueoflife.org. Retrieved 2021-09-08.
- ^ "the Paleobiology Database". Retrieved 2009-08-06.
- ^ "Towards a management hierarchy (classification) for the Catalogue of Life. Draft Discussion Document by Dr. Dennis P. Gordon, May 2009". Archived from the original on 2009-08-08. Retrieved 2009-08-06.
- PMID 25923521.
- ^ "Biodiversity Maps: Transforming Data into Visual Tools into Meaningful Action for Biodiversity Conservation -". 2016-11-30. Retrieved 2022-05-05.
- S2CID 82987545, retrieved 2022-05-05
- PMID 22019413.
- ^ "TaxonX". SourceForge. Retrieved 2021-09-08.
- ^ "Taxonomic Concept Transfer Schema (TCS)". Biodiversity Information Standards (TDWG).
- ^ "Structured Descriptive Data". Biodiversity Information Standards (TDWG).
- ^ "Access to Biological Collection Data (ABCD)". Biodiversity Information Standards (TDWG).
- ^ "GitHub - tdwg/tapir: TDWG Access Protocol for Information Retrieval (TAPIR)". GitHub. 16 June 2020. Retrieved 2021-09-08.
- ^ "Home". e-biosphere09.org.
- ^ "Archived copy" (PDF). www.e-biosphere09.org. Archived from the original (PDF) on 26 February 2012. Retrieved 12 January 2022.
{{cite web}}
: CS1 maint: archived copy as title (link) - ^ "TDWG: Biodiversity Information Projects of the World". www.tdwg.org. Archived from the original on 14 July 2009. Retrieved 12 January 2022.
Further reading
- OECD Megascience Forum Working Group on Biological Informatics (1999). Final Report of the OECD Megascience Forum Working Group on Biological Informatics, January 1999. pp. 1–74. Archived from the original on 2009-03-05. Retrieved 2018-03-21.
- Canhos, V.P.; Souza, S.; Giovanni, R. & Canhos, D.A.L. (2004). "Global biodiversity informatics: setting the scene for a "new world" of ecological modeling". Biodiversity Informatics. 1: 1–13. .
- Soberón, J. & Peterson, A.T. (2004). "Biodiversity informatics: managing and applying primary biodiversity data". Phil. Trans. R. Soc. Lond. B359 (1444): 689–698. PMID 15253354.
- Chapman, A.D. (2005). Uses of Primary Species-Occurrence Data (PDF). Copenhagen: Global Biodiversity Information Facility. pp. 1–106. Archived from the original (PDF) on 2010-02-16. Retrieved 2009-08-12.
- Johnson, N.F. (2007). "Biodiversity informatics". Annual Review of Entomology. 52: 421–438. PMID 16956323.
- Sarkar, I.N. (2007). "Biodiversity informatics: organizing and linking information across the spectrum of life". Briefings in Bioinformatics. 8 (5): 347–357. PMID 17704120.
- Guralnick, R.P.; Hill, A (2009). "Biodiversity Informatics: Automated Approaches for Documenting Global Biodiversity Patterns and Processes". Bioinformatics. 25 (4): 421–428. PMID 19129210.
External links
- Biodiversity Informatics (journal)