Biodiversity informatics

Biodiversity Informatics is the application of informatics techniques for biodiversity information for 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 analyze existing information. yet exist (see niche modeling). Biodiversity Informatics is a Relatively young discipline (the term coined Was in gold around 1992) HAS goal Hundreds of Practitioners worldwide, Including the Numerous Individuals Involved with the design and building of taxonomic databases . The term “Biodiversity Informatics” is generally used in the broad sense of the term; The term ” bioinformatics ” is often used synonymously with the computerized handling of data in the specialized area of molecular biology .

Overview

Biodiversity informatics is a method for the application of information technology 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 with a specimen. Biodiversity informatics may also be copied with the help of such information and the production of environmental sampling and sequencing of mixed-field samples. The term biodiversity is also used to cover the problems The following are the names of different names, such as the development of algorithms with different representations of identifiers, the identification of different species, and the multiple classification schemes. and more …

History of the discipline of Biodiversity Informatics

Biodiversity Informatics can be regarded to-have commenced with the building of the first computerized taxonomic databases in the early 1970s, and Progressed through subsequent Developing of distributed search tools Reviews towards the late 1990s Including the Species Analyst from Kansas University, the North American Biodiversity Information Network NABIN , CONABIO in Mexico, and others, [1] the establishment of the Global Biodiversity Information Facility in 2001, and the parallel development of a variety of niche modeling and other tools to operate on the digitization of data from the mid-1980s onwards (eg [2] ). In September 2000, the US journal Science”Bioinformatics for Biodiversity”, [3] The journal “Biodiversity Informatics”, published in 2004, and several international conferences through the 2000s brought together Biodiversity Informatics practitioners, including the London e-Biosphereconference in June 2009. A supplement to the BMC Bioinformatics Journal (Volume 10 Suppl 14 [4] ) published in November 2009 also deals with Biodiversity Informatics.

History of the term “Biodiversity Informatics”

Selon connection Reproduced by Walter Berendsohn, [5] 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 be associated with the GPS / GIS world and be associated with the computerized management of any aspect of biodiversity information (eg see [6] )

Current Biodiversity Informatics issues

Global list of all species

One major issue for biodiversity informatics at a global scale is the current lack of a full master list of Currently Recognized species of the world , ALTHOUGH this is an aim of the Catalog of Life project qui HAS ca. 1.65 million species of an estimated 1.9 million species in its 2016 Annual Checklist . A similar effort for fossil taxa, the Paleobiology Database [7] documents some 100,000+ names for fossil species, out of an unknown total number.

Problems with genus and species scientific names as unique and persistent identifiers

Application of the Linnaean system of binomial nomenclature for species , and uninomials for genera and Higher ranks, Has led to many advantages goal aussi problems with homonyms (le même name used for multiple taxa being white, gold Either inadvertently legitimately across multiple kingdoms), synonyms(multiple nouns for the same taxon), as well as variations of the name of orthographic differences, minor spelling errors, variation in the manner of quoting author names and dates, and more. In addition, the expression of a taxonomic change in the taxonomy of a taxpayer or a taxpayer or a taxpayer or a taxpayer or a taxpayer may be changed to different authors’ taxonomic concepts. Proposed solution to this problem is the use of the term LSIDs for machine-machine communication purposes, although there are both proponents and opponents of this approach.

Achieving a consensus classification of organisms

Organisms can be classified in a multitude of ways (see main page Biological classification ), which can create design problems for Biodiversity Informatics systems aims at incorporating or a single or multiple classification to 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 the Catalog of Life Has commissioned activity in this area [8] qui has-been succeeded by a published system Proposed in 2015 by Ruggiero and co-workers. [9]

Mobilizing primary biodiversity information

The term “primary” is used for information on the occurrence and diversity of species (or indeed, any recognizable taxa), commonly in association with information about their distribution in either space, time, or both. Such information May be in the form of Retained specimens and associated information, for example have assembled in the natural history collections of museums and herbaria , gold 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 coming under the scope of citizen science. Providing online, coherent digital access to this vast collection of disparate primary data is a core of Biodiversity Informatics which is at the heart of regional and global biodiversity data networks, examples of the latter including OBIS and GBIF .

As a secondary source of biodiversity data, the scientific literature may be divided by 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 bothPlazi and INOTAXA projects are transforming taxonomic literature into XML formats that can be read by client applications, the form using TaxonX-XML and the latter using the taXMLit format. The Biodiversity Heritage Library is also making significant progress in its scope of publication. It is also subject to OCR ( Optical Character Recognition ).

Biodiversity Informatics standards and protocols

Biodiversity Informatics Benefits, Inc. (2004), Biodiversity Informatics Benefits of the Approval of Appropriate Standards and Protocols in Support of Machine-to-Computer Transmission and Interoperability of Information. Examples of relevant standards include the Darwin Core XML schema for speci fi c and observa- tion-based biodiversity data from 1998 onwards, plus extensions of the same, Taxonomic Concept Transfer Schema , plus standards for Structured Descriptive Data and Access to Biological Collection Data (ABCD) ; while data retrieval and transfer protocols include DiGIR(now mostly superseded) and TAPIR (TDW 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 2009 e-Biosphere conference in the UK, [10] 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 a significant role in Biodiversity Informatics roles in a workshop that is stressed, among other aspects, the need to create sustainable, global registries for the resources that are basic to biodiversity informatics (eg, repositories, collections ); complete the construction of a solid taxonomic infrastructure; and create ontologies for biodiversity data.

Biodiversity Informatics projects of the world

Global projects:

  • The Global Biodiversity Information Facility (GBIF), and the Ocean Biogeographic Information System (OBIS) (for marine species)
  • The Species 2000 , Integrated Taxonomic Information System ( ITIS ), and Catalog of Life Projects
  • Global Names
  • EOL , The Encyclopedia of Life project
  • The Consortium for the Barcode of Life project
  • The Map of Life project
  • The uBio Universal Biological Indexer and Organizer, from the Woods Hole Marine Biological Laboratory
  • The Index to Organisms Names (ION) from Thomson Reuters, providing access to scientific names of taxa from numerous journals in the Zoological Record
  • ZooBank , the registry for nomenclatural acts and falling systematic literature in zoology
  • The Index Nominum Genericorum , a compilation of generic names published by the International Code of Botanical Nomenclature , maintained at the Smithsonian Institution in the USA
  • The International Plant Names Index
  • MycoBank , documenting new names and combinations for fungi
  • The 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
  • Wikispecies , open source (community-editable) compilation of taxonomic information, companion project to Wikipedia
  • TaxonConcept.org , a Linked Data project that connects disparate databases
  • Instituto de Ciencias Naturales . Universidad Nacional de Colombia. Virtual Collections and Biodiversity Informatics Unit
  • ANTABIF . The Antarctic Biodiversity Information Facility provides Antarctic Biodiversity data, in the spirit of the Antarctic Treaty.
  • Genesys (website) , 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 and national projects:

  • Fauna Europaea
  • Atlas of Living Australia
  • A Pan-European Species-Directories Infrastructure (PESI)
  • Symbiota
  • i4Life project
  • Sistema de Información sober Biodiversidad de Colombia
  • India Biodiversity Portal (IBP)
  • Bhutan Biodiversity Portal (BBP)
  • Weed Identification and Knowledge in the Western Indian Ocean (WIKWIO)
This section needs expansion . You can help by adding to it . (May 2010)
  • 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 related activities can be found at the TDWG’s “Biodiversity Information Projects of the World” database .

See also

  • Biodiversity
  • Global biodiversity
  • Taxonomic database
  • Web-based taxonomy
  • List of multiple databases

References

  1. Jump up^ Krishtalka L & Humphrey PS (2000). “Can Natural History Museums Capture the Future?” . BioScience . 50 : 611-617. doi : 10.1641 / 0006-3568 (2000) 050 [0611: CNHMCT] 2.0.CO; 2 .
  2. Jump up^ Peterson AT & English D (2001). “Predicting Species Invasions Using Ecological Niche Modeling: New Approaches from Bioinformatics Attack to Pressing Problem” (PDF) . BioScience . 51 : 363-371. doi : 10.1641 / 0006-3568 (2001) 051 [0363: PSIUEN] 2.0.CO; 2 .
  3. Jump up^ “Bioinformatics for Biodiversity?” . Science . 289 : 2229-2440. 2000.
  4. Jump up^ “Biodiversity Informatics” . BMC Bioinformatics . 10 Suppl 14. 2009.
  5. Jump up^ ” ” Biodiversity Informatics “, The Term” . Retrieved 2009-08-06 .
  6. Jump up^ Bisby FA; et al. (2000). “The Quiet Revolution: Biodiversity Informatics and the Internet” . Science . 289 (5488): 2309-2312. doi : 10.1126 / science.289.5488.2309 . PMID  11009408 .
  7. Jump up^ “the Paleobiology Database” . Retrieved 2009-08-06 .
  8. Jump up^ “Towards a Management Hierarchy (Classification) for the Catalog of Life.” Discussion Paper by Dr. Dennis P. Gordon, May 2009 ” . Archived from the original on 2009-08-08 . Retrieved 2009-08-06 .
  9. Jump up^ Ruggiero, MA; Gordon, DP; Orrell, TM; Bailly, N .; Bourgoin, T .; Brusca, RC; et al. (2015). “A higher level classification of all living organisms” . PLoS ONE . 10 (4): e0119248. doi : 10.1371 / journal.pone.0119248 . PMC  4418965  . PMID  25923521 .
  10. Jump up^ http://www.e-biosphere09.org/