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''(This article was taken from Wikipedia)''
[[File:Phanerozoic Biodiversity.png|thumb|500px|right|Graphical representations of prehistoric biodiversity data like this are slowly becoming easier with the advancement of biodiversity informatics standards and tools.]]
'''Biodiversity informatics''' is the application of informatics techniques to biodiversity [[information]] for improved management, presentation, discovery, exploration, and analysis. It typically builds on a foundation of taxonomic, biogeographic, and synecologic information stored in digital form, which, with the application of modern computer techniques, can yield new ways to view and analyze existing information, as well as predictive models for information that does not yet exist.<ref name="BerendsohnBio">{{cite journal |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234432/ |journal=ZooKeys |title=Biodiversity information platforms: From standards to interoperability |author=Berendsohn, W. G.; Güntsch, A.; Hoffmann, N.; Kohlbecker, A.; Luther, K.; Müller, A. |issue=150 |pages=71–87 |year=2011 |month=November |doi=10.3897/zookeys.150.2166 |pmc=3234432 |accessdate=18 June 2014}}</ref>


'''Biodiversity Informatics''' is the application of informatics techniques to biodiversity [[information]] for improved management, presentation, discovery, exploration and analysis. It typically builds on a foundation of taxonomic, biogeographic, or ecological information stored in digital form, which, with the application of modern computer techniques, can yield new ways to view and analyse existing information, as well as predictive models for information that does not yet exist. Biodiversity informatics is a relatively young discipline (the term was coined in or around 1992) but has hundreds of practitioners worldwide, including the numerous individuals involved with the design and construction of taxonomic databases. The term "Biodiversity Informatics" is generally used in the broad sense to apply to computerized handling of any biodiversity information; the somewhat broader term "[[bioinformatics]]" is often used synonymously with the computerized handling of data in the specialized area of molecular biology.
Biodiversity informatics has also been described by others as "the creation, integration, analysis, and understanding of information regarding biological diversity"<ref name="BIJournal">{{cite web |url=https://journals.ku.edu/index.php/jbi |title=Biodiversity Informatics |publisher=University of Kansas Libraries |accessdate=18 June 2014}}</ref> and a field of science "that brings information science and technologies to bear on the data and information generated by the study of organisms, their genes, and their interactions."<ref name="eBiosphere">{{cite web |url=http://www.e-biosphere09.org/ |title=e-Biosphere '09: International Conference on Biodiversity Informatics |publisher=Smithsonian Institution |date=2009 |accessdate=18 June 2014}}</ref>


== Overview ==
==History==
According to correspondence reproduced by Walter Berendsohn<ref name="BITheTerm">{{cite web |url=http://www.bgbm.org/BioDivInf/TheTerm.htm |archiveurl=https://web.archive.org/web/20130511091435/http://www.bgbm.org/BioDivInf/TheTerm.htm |title="Biodiversity Informatics", The Term |author=Güntsch, Anton; Berendsohn, Walter |publisher=Botanic Garden and Botanical Museum Berlin-Dahlem |date=18 August 2010 |archivedate=11 May 2013 |accessdate=18 June 2014}}</ref>, the term "biodiversity informatics" was coined by John Whiting in 1992 to cover the activities of an entity known as the Canadian Biodiversity Informatics Consortium (CBIC), a group involved with fusing basic biodiversity information with environmental economics and geospatial information. Subsequently it appears to have lost at least some connection with the geospatial world, becoming more closely associated with the computerized management of biodiversity information.<ref name="BisbyRevo">{{cite journal |url=http://www.sciencemag.org/content/289/5488/2309.abstract |journal=Science |title=The Quiet Revolution: Biodiversity Informatics and the Internet |author=Bisby, Frank A. |volume=289 |issue=5488 |pages=2309–2312 |year=2000 |month=September |doi=10.1126/science.289.5488.2309 |pmid=11009408 |accessdate=18 June 2014}}</ref> However, modern efforts to document global biodiversity patterns and processes using georeferencing and other [[geoinformatics]] tools have re-emphasized some of the original spirit of the CBIC.<ref name="GuralnickBio">{{cite journal |url=http://bioinformatics.oxfordjournals.org/content/25/4/421.full |journal=Bioinformatics |title=Biodiversity Informatics: Automated Approaches for Documenting Global Biodiversity Patterns and Processes |author=Guralnick, R. P. |volume=25 |issue=4 |pages=421–428 |year=2009 |month=January |pmid=19129210 |doi=10.1093/bioinformatics/btn659}}</ref>


Biodiversity informatics has been defined as "the creation, integration, analysis, and understanding of information regarding biological diversity"<ref name="BIJournal">{{cite web|url = https://journals.ku.edu/index.php/jbi| accessdate = 2009-08-06 | title = Website of the Journal 'Biodiversity Informatics'}}</ref>, and "[the] field that brings information science and technologies to bear on the data and information generated by the study of organisms, their genes, and their interactions"<ref name="eBiosphere">{{cite web|url = http://www.e-biosphere09.org/| accessdate = 2009-08-06 | title = Website of the 2009 "e-Biosphere" Conference on Biodiversity Informatics, London, June 2009}}</ref>. Broadly speaking, it seeks to draw upon and integrate information held in various taxonomic databases and other digital sources to answer biodiversity questions at scales ranging from global to local. Such questions might range from "How many described species exist in the world?" (answer: still not known for certain, as all the relevant data are not currently compiled in any coherent manner) to "Predict the effects of a global temperature rise of X degrees C. on the geographic range of species Y", a question which involves not only biodiversity in the basic sense but related domains of ecology, geographic distributions of environmental parameters, global climate models, and more. In addition to handling formally named taxa, 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.
Biodiversity informatics itself likely grew from the construction of the first computerized taxonomic databases in the early 1970s, progressing through the subsequent development of distributed search tools towards the late 1990s, including Species Analyst, the North American Biodiversity Information Network (NABIN), and CONABIO.<ref name="KrishtalkaCan">{{cite journal |url=http://bioscience.oxfordjournals.org/content/50/7/611.full |journal=BioScience |title=Can Natural History Museums Capture the Future? |author=Krishtalka, L.; Humphrey, P. S. |volume=50 |issue=7 |pages=611–617 |year=2000 |doi=10.1641/0006-3568(2000)050[0611:CNHMCT]2.0.CO;2 |accessdate=18 June 2014}}</ref> Other contributions came in the form of a variety of niche modeling tools and algorithms to process digitized biodiversity data from the mid-1980s onwards.<ref name="PetersonPredict">{{cite journal |url=http://www.cria.org.br/eventos/mfmpe/19_20jun2002_docs/BioScience%202001.pdf |journal=BioScience |title=Predicting Species Invasions Using Ecological Niche Modeling: New Approaches from Bioinformatics Attack a Pressing Problem |author=Peterson, A. T.; Vieglais, D. |volume=51 |issue=5 |pages=363–371 |year=2001 |month=May |doi=10.1641/0006-3568(2001)051[0363:PSIUEN]2.0.CO;2 |accessdate=18 June 2014}}</ref>


== History of the discipline of Biodiversity Informatics ==
The U.S. journal ''Science'' devoted a special issue to "Bioinformatics for Biodiversity" in September 2000<ref name="ScienceBI">{{cite journal |url=http://www.sciencemag.org/content/289/5488.toc |journal=Science |title=Bioinformatics for Biodiversity |volume=289 |issue=5488 |pages=2229–2440 |year=2000 |month=September |accessdate=18 June 2014}}</ref>, the Global Biodiversity Information Facility (GBIF) was officially formed in 2001<ref name="GBIFAbout">{{cite web |url=http://www.gbif.org/whatisgbif |title=What is GBIF? |publisher=GBIF |accessdate=18 June 2014}}</ref>, the journal ''Biodiversity Informatics'' commenced publication in 2004, and several international conferences brought together biodiversity researchers during the twenty-first century.<ref name="eBiosphere" /><ref name="EBIC">{{cite web |url=http://conference.lifewatch.unisalento.it/index.php/EBIC/index/index |title=Biodiversity Informatics Horizons 2013 |publisher=LifeWatch |year=2013 |accessdate=18 June 2014}}</ref>


Biodiversity Informatics can be considered to have commenced with the construction of the first computerized taxonomic databases in the early 1970s, and progressed through subsequent developing of distributed search tools towards the late 1990s including the Species Analyst from Kansas University, the North American Biodiversity Information Network NABIN, CONABIO in Mexico, and others<ref name="Krishtalka2000">{{cite journal|author=Krishtalka L & Humphrey PS|year= 2000|title=Can Natural History Museums Capture the Future?|journal=BioScience|volume=50|pages=611–617|url=http://www.bioone.org/doi/pdf/10.1641/0006-3568%282000%29050%5B0611%3ACNHMCT%5D2.0.CO%3B2|doi=10.1641/0006-3568(2000)050[0611:CNHMCT]2.0.CO;2}}</ref>, the establishment of the Global Biodiversity Information Facility in 2001, and the parallel development of a variety of niche modelling and other tools to operate on digitized biodiversity data from the mid 1980s onwards (e.g. see <ref name="Peterson2001">{{cite journal|author=Peterson AT & Vieglais D|year= 2001|title=Predicting Species Invasions Using Ecological Niche Modeling: New Approaches from Bioinformatics Attack a Pressing Problem|journal=BioScience|volume=51|pages=363–371|url=http://www.cria.org.br/eventos/mfmpe/19_20jun2002_docs/BioScience%202001.pdf|doi=10.1641/0006-3568(2001)051[0363:PSIUEN]2.0.CO;2}}</ref>). In September 2000, the U.S. journal ''Science'' devoted a special issue to "Bioinformatics for Biodiversity"<ref name="Science_Sep_2000">{{cite journal|year= 2000|title=Bioinformatics for Biodiversity?|journal=Science|volume=289|pages=2229–2440|url=http://www.sciencemag.org/content/vol289/issue5488/index.dtl}}</ref>, the journal "Biodiversity Informatics" commenced publication in 2004, and several international conferences through the 2000s have brought together Biodiversity Informatics practitioners, most recently the London [http://www.e-biosphere09.org/ e-Biosphere] conference in June 2009. A recent supplement to the journal BMC Bioinformatics (Volume 10 Suppl 14<ref name="BMC_Bioinformatics2009">{{cite journal|year= 2009|title=Biodiversity Informatics|journal=BMC Bioinformatics|volume=10 Suppl 14|url=http://www.biomedcentral.com/1471-2105/10?issue=S14}}</ref>) published in November 2009 also deals with Biodiversity Informatics.
==Application==
Biodiversity informatics can help tackle problems and tasks such as the following<ref name="eBiosphere" /><ref name="eBio09Reso">{{cite web |url=http://www.e-biosphere09.org/assets/files/workshop/Resolution.pdf |format=PDF |title=e-Biosphere 09 Planning Workshop - Resolution |publisher=Smithsonian Institution |date=05 June 2009 |accessdate=18 June 2014}}</ref><ref name="GordonHier">{{cite web |url=http://www.catalogueoflife.org/col/info/hierarchy |title=Towards a management hierarchy (classification) for the Catalogue of Life |author=Gordon, Dennis P. |publisher=Catalogue of Life |date=May 2009 |accessdate=18 June 2014}}</ref>:


== History of the term "Biodiversity Informatics" ==
* the tracking of invasive species
* the creation of new biodiversity mapping, infrastructure, and species identification models
* the development of new modeling and data integration tools
* the creation of global registries for the resources that are basic to biodiversity informatics
* the construction of a solid global taxonomic infrastructure
* the creation of ontologies for biodiversity data
* the creation of a single-consensus classification system
* the development of algorithms to cope with variant representations of identifiers such as species names and authorities
* the transition of content in taxonomic databases to a machine-readable and -queryable format


According to correspondence reproduced by Walter Berendsohn<ref name="BITheTerm">{{cite web|url = http://www.bgbm.org/BioDivInf/TheTerm.htm| accessdate = 2009-08-06 | title = "Biodiversity Informatics", The Term}}</ref>, the term "Biodiversity Informatics" was coined by John Whiting in 1992 to cover the activities of an entity known as the Canadian Biodiversity Informatics Consortium, a group involved with fusing basic [[biodiversity]] information with environmental economics and geospatial information in the form of GPS and GIS. Subsequently it appears to have lost any obligate connection with the GPS/GIS world and be associated with the computerized management of any aspects of biodiversity information (e.g. see <ref name="Bisby2000">{{cite journal|author=Bisby FA. et al.|year= 2000|title=The Quiet Revolution: Biodiversity Informatics and the Internet|journal=Science|volume=289|pages=2309–2312|url=http://www.sciencemag.org/cgi/content/abstract/289/5488/2309|doi=10.1126/science.289.5488.2309|pmid=11009408|issue=5488}}</ref>).
==Informatics==
Providing online, coherent, standardized digital access to the vast collection of disparate primary biodiversity data is a task at the heart of regional and global biodiversity data networks. Secondary sources of biodiversity data, including relevant scientific literature, can be potentially parsed by specialized information retrieval algorithms to extract the relevant primary biodiversity information that is reported therein, sometimes in summary form, but more frequently as primary observations in narrative or tabular form.<ref name="BerendsohnBio" /> The Biodiversity Heritage Library is an example of this, aiming to digitize substantial portions of the out-of-copyright taxonomic literature, which is then subjected to OCR (optical character recognition) so as to be amenable to further processing.<ref name="BHLAbout">{{cite web |url=http://biodivlib.wikispaces.com/About |title=Biodiversity Heritage Library - About |publisher=Tangient LLC |date=18 June 2014 |accessdate=18 June 2014}}</ref>


== Current Biodiversity Informatics issues ==
Like other data-related disciplines, biodiversity informatics benefits from the adoption of appropriate standards and protocols in order to support machine-machine transmission and interoperability of information within its particular domain. Examples of relevant standards include<ref name="BerendsohnBio" />:
=== Global list of all species ===


One major issue for biodiversity informatics at a global scale is the present absence of a machine queryable (or even non-digital) master list of currently recognised species of the world, although this is an aim of the Catalogue of Life project which has been quoted as aiming to achieve this goal (for extant species only) by 2012; in its 2009 Annual Checklist edition a total of 1.16 million valid species names and 0.76 million synonyms were included, out of an estimated target 1.8 million extant described species<ref name="EOLPressRelease2007">{{cite web|url = http://www.eol.org/content/page/press_2007_5_9| accessdate = 2009-08-06 | title = A Leap for All Life: World’s Leading Scientists Announce Creation of “Encyclopedia of Life” (EOL Press Release, May 2007)}}</ref>. A similar effort for fossil taxa, the Paleobiology Database<ref name="PaleoDB">{{cite web|url = http://paleodb.org/| accessdate = 2009-08-06 | title = the Paleobiology Database}}</ref> documents some 100,000+ names for fossil species, out of an unknown total number.
* [http://rs.tdwg.org/dwc/terms/guides/xml/ Darwin Core XML], an [[Extensible Markup Language|XML]] schema for specimen- and observation-based biodiversity data
* [http://www.tdwg.org/standards/117/ Taxonomic Concept Transfer Schema], a schema for taxonomic information providers to exchange information with other such providers
* [http://www.tdwg.org/standards/116/ Structured Descriptive Data], a standard for the capture, transport, caching and archiving of descriptive data
* [http://www.tdwg.org/standards/115/ Access to Biological Collection Data], a standard for access to and exchange of data about specimens and observations
* [http://www.tdwg.org/standards/449/ TDWG Access Protocol for Information Retrieval] (TAPIR), a request and response protocol for accessing structured biodiversity data


=== Problems with genus and species scientific names as unique and persistent identifiers ===
==Further reading==
* {{cite web |url=http://www.oecd.org/science/sci-tech/2105199.pdf |format=PDF |title=Final Report of the OECD Megascience Forum Working Group on Biological Informatics, January 1999 |author=OECD Megascience Forum Working Group on Biological Informatics |publisher=OECD |pages=1–74 |date=January 1999}}
* {{cite journal |url=https://journals.ku.edu/index.php/jbi/article/viewFile/3/1 |format=PDF |journal=Biodiversity Informatics |title=Global Biodiversity Informatics: Setting the Scene for a "New World" of Ecological Modeling |author=Canhos, V. P.; Souza, S.; Giovanni, R.; Canhos, D. A. L. |year=2004 |volume=1 |pages=1–13}}
* {{cite journal |url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693343/pdf/15253354.pdf |format=PDF |journal=Philosophical Transactions of the Royal Society of London |title=Biodiversity Informatics: Managing and Applying Primary Biodiversity Data |author=Soberón, J.; Peterson, A. T. |year=2004 |month=March |volume=B359 |pages=689–698 |doi=10.1098/rstb.2003.1439}}
* {{cite book |url=http://www.gbif.org/resources/2834 |title=Uses of Primary Species-Occurrence Data |author=Chapman, A. D. |publisher=Global Biodiversity Information Facility |location=Copenhagen |year=2005 |pages=1–106}}
* {{cite journal |url=http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ento.52.110405.091259 |journal=Annual Review of Entomology |title=Biodiversity Informatics |author=Johnson, N. F. |volume=52 |pages=421–438 |year=2007 |doi=10.1146/annurev.ento.52.110405.091259 |pmid=16956323}}
* {{cite journal |url=http://bib.oxfordjournals.org/content/8/5/347.full |journal=Briefings in Bioinformatics |title=Biodiversity Informatics: Organizing and Linking Information Across the Spectrum of Life |author=Sarkar, I. N. |volume=8 |issue=5 |pages=347–357 |year=2007 |month=August |pmid=17704120 |doi=10.1093/bib/bbm037}}


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.
==External links==
 
* [http://www.biodiversitylibrary.org/ Biodiversity Heritage Library]
=== Achieving a consensus classification of organisms ===
* [http://journals.ku.edu/index.php/jbi Biodiversity Informatics] open-access journal
 
* [http://www.biomedcentral.com/bmcbioinformatics/supplements/10/S14 Biodiversity Informatics at BMC Bioinformatics]
Organisms can be classified in a multitude of ways, which can create design problems for Biodiversity Informatics systems aimed at incorporating either a single or multiple classification to suit the needs of users, or to guide them towards a single "preferred" system. Whether a single consensus classification system can ever be achieved is probably an open question, however in an attempt to provide at least a degree of consensus, the Catalogue of Life project has recently released a document<ref name="CoL2009Gordon">{{cite web|url = http://www.catalogueoflife.org/info_hierarchy.php| accessdate = 2009-08-06 | title = Towards a management hierarchy (classification) for the Catalogue of Life. Draft Discussion Document by Dr. Dennis P. Gordon, May 2009}}</ref> that attempts to list some of the issues in this area, and may lead to a more coherent classification that can be promoted via that project's future products at least.
* [http://www.tdwg.org/biodiv-projects Biodiversity Information Projects of the World]
 
* [http://www.tdwg.org/ Biodiversity Information Standards]
== Mobilizing primary biodiversity information ==
* [http://www.catalogueoflife.org/ Catalogue of Life]
 
* [http://eol.org/ Encyclopedia of Life]
"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 museums and herbaria, or as observational records, for example either from formal faunal or floristic surveys undertaken by professional biologists and students, or as amateur and other planned or unplanned observations including those increasingly coming under the scope of citizen science. Providing online, coherent digital access to this vast collection of disparate primary data is a core Biodiversity Informatics function that is at the heart of regional and global biodiversity data networks, examples of the latter including OBIS and GBIF.
* [http://www.pensoftonline.net/zookeys ZooKeys] open-access journal
 
As a secondary source of biodiversity data, relevant scientific literature can be parsed either by humans or (potentially) by specialized information retrieval algorithms to extract the relevant primary biodiversity information that is reported therein, sometimes in aggregated / summary form but frequently as primary observations in narrative or tabular form. Elements of such activity (such as extracting key taxonomic identifiers, keywording / index terms, etc.) have been practiced for many years at a higher level by selected academic databases and search engines. However, for the maximum Biodiversity Informatics value, the actual primary occurrence data should ideally be retrieved and then made available in a standardized form or forms; for example both the Plazi and [http://www.inotaxa.org/ INOTAXA] projects are transforming taxonomic literature into XML formats that can then be read by client applications, the former using [http://sourceforge.net/projects/taxonx/ TaxonX-XML] and the latter using the taXMLit format. The Biodiversity Heritage Library is also making significant progress in its aim to digitize substantial portions of the out-of-copyright taxonomic literature, which is then subjected to OCR (optical character recognition) so as to be amenable to further processing using Biodiversity Informatics tools.
 
== Biodiversity Informatics standards and protocols ==
 
In common with other data-related disciplines, Biodiversity Informatics benefits from the adoption of appropriate standards and protocols in order to support machine-machine transmission and interoperability of information within its particular domain. Examples of relevant standards include the Darwin Core XML schema for specimen- and observation-based biodiversity data developed from 1998 onwards, plus extensions of the same, [http://www.tdwg.org/standards/117/ Taxonomic Concept Transfer Schema], plus standards for [http://www.tdwg.org/standards/116/ Structured Descriptive Data] and [http://www.tdwg.org/standards/115/ Access to Biological Collection Data] (ABCD); while data retrieval and transfer protocols include [http://digir.sourceforge.net/ DiGIR] (now mostly superseded) and [http://www.tdwg.org/standards/449/ TAPIR] (TDWG Access Protocol for Information Retrieval). Many of these standards and protocols are currently maintained, and their development overseen, by the Taxonomic Databases Working Group (TDWG).
 
== Current Biodiversity Informatics activities ==


At the recent (2009), large scale [http://www.e-biosphere09.org/ e-Biosphere] conference in the U.K., contributions (e.g. as posters) were grouped into the following themes, which is indicative of a broad range of current Biodiversity Informatics activities and how they might be categorized:
==Notes==


* Application: Conservation / Agriculture / Fisheries / Industry / Forestry
This article reuses some content from [http://en.wikipedia.org/wiki/Biodiversity_informatics the Wikipedia article].
* 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 [http://www.e-biosphere09.org/assets/files/workshop/Resolution.pdf 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.
 
== Biodiversity Informatics projects of the world ==
Among current significant global scale biodiversity informatics projects can be included the following:
 
* The Global Biodiversity Information Facility(GBIF), and the Ocean Biogeographic Information System  (OBIS) (for marine species)
* The Species 2000, ITIS (Integrated Taxonomic Information System), and Catalogue of Life projects
* EOL, The Encyclopedia of Life project
* The Consortium for the Barcode of Life project
* The [http://www.ubio.org/ uBio] Universal Biological Indexer and Organizer, from the Woods Hole Marine Biological Laboratory
* The [http://www.organismnames.com/ Index to Organism Names] (ION) from Thomson Reuters, providing access to scientific names of taxa from numerous journals as indexed in the Zoological Record
* ZooBank, the registry for nomenclatural acts and relevant systematic literature in zoology
* The [http://botany.si.edu/ing/ Index Nominum Genericorum], compilation of generic names published for organisms covered by the International Code of Botanical Nomenclature, maintained at the Smithsonian Institution in the U.S.A.
* The International Plant Names Index
* MycoBank, documenting new names and combinations for fungi
* The [http://www.bacterio.cict.fr/ List of Prokaryotic names with Standing in Nomenclature] (LPSN) - Official register of valid names for bacteria and archaea, as governed by the 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
* [http://www.taxonconcept.org TaxonConcept.org], a Linked_Data project that connects disparate species databases
* [http://www.icn.unal.edu.co Instituto de Ciencias Naturales]. Universidad Nacional de Colombia. [http://www.biovirtual.unal.edu.co Virtual Collections and Biodiversity Informatics Unit]
 
 
Notable regional and national scale syntheses include the following:
 
* Fauna Europaea
* [http://www.ala.org.au/ Atlas of Living Australia]
* [http://www.eu-nomen.eu A Pan-European Species-directories Infrastructure (PESI)]
 
* LifeWatch is proposed by ESFRI as a pan-European research (e-)infrastructure to support Biodiversity research and policy-making.
 
A listing of over 600 current biodiversity informatics related activities can be found at the [http://www.tdwg.org/biodiv-projects/ TDWG "Biodiversity Information Projects of the World" database].
 
== See also ==
* [[Biodiversity]]


==References==
==References==
<references/>
<references/>


==Further reading==
<!---Place all category tags here-->
* {{cite book |author=OECD Megascience Forum Working Group on Biological Informatics |title=Final Report of the OECD Megascience Forum Working Group on Biological Informatics, January 1999 |year=1999 |pages=1–74 |url=http://www.gbif.org/GBIF_org/facility/BIrepfin}}
* {{cite journal |author=Canhos, V.P., Souza, S., Giovanni, R. & Canhos, D.A.L. |year=2004 |title=Global biodiversity informatics: setting the scene for a "new world" of ecological modeling |journal=Biodiversity Informatics |volume=1 |pages=1–13 |url=https://journals.ku.edu/index.php/jbi/article/viewFile/3/1}}
* {{cite journal |author=Soberón, J. & Peterson, A.T. |year=2004 |title=Biodiversity informatics: managing and applying primary biodiversity data |journal=Phil. Trans. R. Soc. Lond. |volume=B359 |pages=689–698 |url=http://journals.royalsociety.org/content/p8hcuwema8uk692g/}}
* {{cite book |author=Chapman, A.D. |title=Uses of Primary Species-Occurrence Data |publisher=Global Biodiversity Information Facility |location=Copenhagen |year=2005 |pages=1–106 |url=http://www2.gbif.org/UsesPrimaryData.pdf}}
* {{cite journal |author=Johnson, N.F. |year=2007 |title=Biodiversity informatics |journal=Annual Review of Entomology  |volume=52 |pages=421–438 |url=http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ento.52.110405.091259 |doi=10.1146/annurev.ento.52.110405.091259 |pmid=16956323}}
* {{cite journal |author=Sarkar, I.N. |year=2007 |title=Biodiversity informatics: organizing and linking information across the spectrum of life |journal=Briefings in Bioinformatics |volume=8 |pages=347–357 |url=http://bib.oxfordjournals.org/cgi/content/abstract/8/5/347 |pmid=17704120 |doi=10.1093/bib/bbm037 |issue=5}}
* {{cite journal |author=Guralnick, R.P. |year=2009 |title=Biodiversity Informatics: Automated Approaches for Documenting Global Biodiversity Patterns and Processes |journal=Bioinformatics |volume=25 |pages=421–428. |url=http://bioinformatics.oxfordjournals.org/cgi/content/full/25/4/421 |pmid=19129210 |doi=10.1093/bioinformatics/btn659 |last2=Hill |first2=A |issue=4}}
 
==External links==
* [http://journals.ku.edu/index.php/jbi Biodiversity Informatics] (journal)
* [http://systbio.org/?q=node/150 Phyloinformatics] (journal; closed business in 2006)
* [http://www.pensoftonline.net/zookeys ZooKeys] (journal)
* [http://www.e-biosphere09.org/ Website of the 2009 e-Biosphere International Conference on Biodiversity Informatics]
* [http://www.henley.reading.ac.uk/IRC/Postgraduatetaught/irc-pgt-bioi.asp Biodiversity Informatics at the University of Reading]
* [http://cbcreatures.webs.com/](Interesting information about the snakes)
 
[[Category:Informatics]]
[[Category:Informatics]]

Latest revision as of 16:39, 22 August 2014

Graphical representations of prehistoric biodiversity data like this are slowly becoming easier with the advancement of biodiversity informatics standards and tools.

Biodiversity informatics is the application of informatics techniques to biodiversity information for improved management, presentation, discovery, exploration, and analysis. It typically builds on a foundation of taxonomic, biogeographic, and synecologic information stored in digital form, which, with the application of modern computer techniques, can yield new ways to view and analyze existing information, as well as predictive models for information that does not yet exist.[1]

Biodiversity informatics has also been described by others as "the creation, integration, analysis, and understanding of information regarding biological diversity"[2] and a field of science "that brings information science and technologies to bear on the data and information generated by the study of organisms, their genes, and their interactions."[3]

History

According to correspondence reproduced by Walter Berendsohn[4], the term "biodiversity informatics" was coined by John Whiting in 1992 to cover the activities of an entity known as the Canadian Biodiversity Informatics Consortium (CBIC), a group involved with fusing basic biodiversity information with environmental economics and geospatial information. Subsequently it appears to have lost at least some connection with the geospatial world, becoming more closely associated with the computerized management of biodiversity information.[5] However, modern efforts to document global biodiversity patterns and processes using georeferencing and other geoinformatics tools have re-emphasized some of the original spirit of the CBIC.[6]

Biodiversity informatics itself likely grew from the construction of the first computerized taxonomic databases in the early 1970s, progressing through the subsequent development of distributed search tools towards the late 1990s, including Species Analyst, the North American Biodiversity Information Network (NABIN), and CONABIO.[7] Other contributions came in the form of a variety of niche modeling tools and algorithms to process digitized biodiversity data from the mid-1980s onwards.[8]

The U.S. journal Science devoted a special issue to "Bioinformatics for Biodiversity" in September 2000[9], the Global Biodiversity Information Facility (GBIF) was officially formed in 2001[10], the journal Biodiversity Informatics commenced publication in 2004, and several international conferences brought together biodiversity researchers during the twenty-first century.[3][11]

Application

Biodiversity informatics can help tackle problems and tasks such as the following[3][12][13]:

  • the tracking of invasive species
  • the creation of new biodiversity mapping, infrastructure, and species identification models
  • the development of new modeling and data integration tools
  • the creation of global registries for the resources that are basic to biodiversity informatics
  • the construction of a solid global taxonomic infrastructure
  • the creation of ontologies for biodiversity data
  • the creation of a single-consensus classification system
  • the development of algorithms to cope with variant representations of identifiers such as species names and authorities
  • the transition of content in taxonomic databases to a machine-readable and -queryable format

Informatics

Providing online, coherent, standardized digital access to the vast collection of disparate primary biodiversity data is a task at the heart of regional and global biodiversity data networks. Secondary sources of biodiversity data, including relevant scientific literature, can be potentially parsed by specialized information retrieval algorithms to extract the relevant primary biodiversity information that is reported therein, sometimes in summary form, but more frequently as primary observations in narrative or tabular form.[1] The Biodiversity Heritage Library is an example of this, aiming to digitize substantial portions of the out-of-copyright taxonomic literature, which is then subjected to OCR (optical character recognition) so as to be amenable to further processing.[14]

Like other data-related disciplines, biodiversity informatics benefits from the adoption of appropriate standards and protocols in order to support machine-machine transmission and interoperability of information within its particular domain. Examples of relevant standards include[1]:

Further reading


External links

Notes

This article reuses some content from the Wikipedia article.

References

  1. ↑ 1.0 1.1 1.2 Berendsohn, W. G.; Güntsch, A.; Hoffmann, N.; Kohlbecker, A.; Luther, K.; Müller, A. (November 2011). "Biodiversity information platforms: From standards to interoperability". ZooKeys (150): 71–87. doi:10.3897/zookeys.150.2166. PMC 3234432. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234432/. Retrieved 18 June 2014. 
  2. ↑ "Biodiversity Informatics". University of Kansas Libraries. https://journals.ku.edu/index.php/jbi. Retrieved 18 June 2014. 
  3. ↑ 3.0 3.1 3.2 "e-Biosphere '09: International Conference on Biodiversity Informatics". Smithsonian Institution. 2009. http://www.e-biosphere09.org/. Retrieved 18 June 2014. 
  4. ↑ Güntsch, Anton; Berendsohn, Walter (18 August 2010). ""Biodiversity Informatics", The Term". Botanic Garden and Botanical Museum Berlin-Dahlem. Archived from the original on 11 May 2013. https://web.archive.org/web/20130511091435/http://www.bgbm.org/BioDivInf/TheTerm.htm. Retrieved 18 June 2014. 
  5. ↑ Bisby, Frank A. (September 2000). "The Quiet Revolution: Biodiversity Informatics and the Internet". Science 289 (5488): 2309–2312. doi:10.1126/science.289.5488.2309. PMID 11009408. http://www.sciencemag.org/content/289/5488/2309.abstract. Retrieved 18 June 2014. 
  6. ↑ Guralnick, R. P. (January 2009). "Biodiversity Informatics: Automated Approaches for Documenting Global Biodiversity Patterns and Processes". Bioinformatics 25 (4): 421–428. doi:10.1093/bioinformatics/btn659. PMID 19129210. http://bioinformatics.oxfordjournals.org/content/25/4/421.full. 
  7. ↑ Krishtalka, L.; Humphrey, P. S. (2000). "Can Natural History Museums Capture the Future?". BioScience 50 (7): 611–617. doi:10.1641/0006-3568(2000)050[0611:CNHMCT]2.0.CO;2. http://bioscience.oxfordjournals.org/content/50/7/611.full. Retrieved 18 June 2014. 
  8. ↑ Peterson, A. T.; Vieglais, D. (May 2001). "Predicting Species Invasions Using Ecological Niche Modeling: New Approaches from Bioinformatics Attack a Pressing Problem". BioScience 51 (5): 363–371. doi:10.1641/0006-3568(2001)051[0363:PSIUEN]2.0.CO;2. http://www.cria.org.br/eventos/mfmpe/19_20jun2002_docs/BioScience%202001.pdf. Retrieved 18 June 2014. 
  9. ↑ "Bioinformatics for Biodiversity". Science 289 (5488): 2229–2440. September 2000. http://www.sciencemag.org/content/289/5488.toc. Retrieved 18 June 2014. 
  10. ↑ "What is GBIF?". GBIF. http://www.gbif.org/whatisgbif. Retrieved 18 June 2014. 
  11. ↑ "Biodiversity Informatics Horizons 2013". LifeWatch. 2013. http://conference.lifewatch.unisalento.it/index.php/EBIC/index/index. Retrieved 18 June 2014. 
  12. ↑ "e-Biosphere 09 Planning Workshop - Resolution" (PDF). Smithsonian Institution. 5 June 2009. http://www.e-biosphere09.org/assets/files/workshop/Resolution.pdf. Retrieved 18 June 2014. 
  13. ↑ Gordon, Dennis P. (May 2009). "Towards a management hierarchy (classification) for the Catalogue of Life". Catalogue of Life. http://www.catalogueoflife.org/col/info/hierarchy. Retrieved 18 June 2014. 
  14. ↑ "Biodiversity Heritage Library - About". Tangient LLC. 18 June 2014. http://biodivlib.wikispaces.com/About. Retrieved 18 June 2014. 
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