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The Convention on Biological Diversity (CBD), known informally as the Biodiversity Convention, is a multilateral treaty. The convention has three main goals: the conservation of biological diversity ; the sustainable use of its components; and the fair and equitable sharing of benefits arising from genetic resources. Its objective is to develop national strategies for the conservation and sustainable use of biological diversity, and it is often seen as the key document regarding sustainable development.
In biology, taxonomy is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum, class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binominal nomenclature for naming organisms.
The Integrated Taxonomic Information System (ITIS) is an American partnership of federal agencies designed to provide consistent and reliable information on the taxonomy of biological species. ITIS was originally formed in 1996 as an interagency group within the US federal government, involving several US federal agencies, and has now become an international body, with Canadian and Mexican government agencies participating. The database draws from a large community of taxonomic experts. Primary content staff are housed at the Smithsonian National Museum of Natural History and IT services are provided by a US Geological Survey facility in Denver. The primary focus of ITIS is North American species, but many biological groups exist worldwide and ITIS collaborates with other agencies to increase its global coverage.
The Global Biodiversity Information Facility (GBIF) is an international organisation that focuses on making scientific data on biodiversity available via the Internet using web services. The data are provided by many institutions from around the world; GBIF's information architecture makes these data accessible and searchable through a single portal. Data available through the GBIF portal are primarily distribution data on plants, animals, fungi, and microbes for the world, and scientific names data.
SNOMED CT or SNOMED Clinical Terms is a systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting. SNOMED CT is considered to be the most comprehensive, multilingual clinical healthcare terminology in the world. The primary purpose of SNOMED CT is to encode the meanings that are used in health information and to support the effective clinical recording of data with the aim of improving patient care. SNOMED CT provides the core general terminology for electronic health records. SNOMED CT comprehensive coverage includes: clinical findings, symptoms, diagnoses, procedures, body structures, organisms and other etiologies, substances, pharmaceuticals, devices and specimens.
Life Science Identifiers are a way to name and locate pieces of information on the web. Essentially, an LSID is a unique identifier for some data, and the LSID protocol specifies a standard way to locate the data. They are a little like DOIs used by many publishers.
Biodiversity Informatics is the application of informatics techniques to biodiversity information, such as taxonomy, biogeography or ecology. Modern computer techniques can yield new ways to view and analyze existing information, as well as predict future situations. Biodiversity informatics is a term that was only coined around 1992 but with rapidly increasing data sets has become useful in numerous studies and applications, such as the construction of taxonomic databases or geographic information systems. Biodiversity Informatics contrasts with "bioinformatics", which is often used synonymously with the computerized handling of data in the specialized area of molecular biology.
Geospatial metadata is a type of metadata applicable to geographic data and information. Such objects may be stored in a geographic information system (GIS) or may simply be documents, data-sets, images or other objects, services, or related items that exist in some other native environment but whose features may be appropriate to describe in a (geographic) metadata catalog.
The World Geographical Scheme for Recording Plant Distributions (WGSRPD) is a biogeographical system developed by the international Biodiversity Information Standards (TDWG) organization, formerly the International Working Group on Taxonomic Databases. The WGSRPD standards, like other standards for data fields in botanical databases, were developed to promote "the wider and more effective dissemination of information about the world's heritage of biological organisms for the benefit of the world at large". The system provides clear definitions and codes for recording plant distributions at four scales or levels, from "botanical continents" down to parts of large countries. Current users of the system include the International Union for Conservation of Nature (IUCN), the Germplasm Resources Information Network (GRIN), and the World Checklist of Selected Plant Families (WCSP).
The Access to Biological Collections Data (ABCD) schema is a highly structured data exchange and access model for taxon occurrence data, i.e. primary biodiversity data.
Darwin Core is an extension of Dublin Core for biodiversity informatics. It is meant to provide a stable standard reference for sharing information on biological diversity. The terms described in this standard are a part of a larger set of vocabularies and technical specifications under development and maintained by Biodiversity Information Standards (TDWG).
A taxonomic database is a database created to hold information related to biological taxa - for example groups of organisms organized by species name or other taxonomic identifier - for efficient data management and information retrieval as required. Today, taxonomic databases are routinely used for the automated construction of biological checklists such as floras and faunas, both for print publication and online; to underpin the operation of web based species information systems; as a part of biological collection management ; as well as providing, in some cases, the taxon management component of broader science or biology information systems. They are also a fundamental contribution to the discipline of biodiversity informatics.
Plazi is a Swiss-based international non-profit association supporting and promoting the development of persistent and openly accessible digital bio-taxonomic literature. Plazi is cofounder of the Biodiversity Literature Repository and is maintaining this digital taxonomic literature repository at Zenodo to provide access to FAIR data converted from taxonomic publications using the TreatmentBank service, enhances submitted taxonomic treatments by creating a version in the XML format Taxpub, and educates about the importance of maintaining open access to scientific discourse and data. It is a contributor to the evolving e-taxonomy in the field of Biodiversity Informatics.
AnimalBase is a project brought to life in 2004 and is maintained by the University of Göttingen, Germany. The goal of the AnimalBase project is to digitize early zoological literature, provide copyright-free open access to zoological works, and provide manually verified lists of names of zoological genera and species as a free resource for the public. AnimalBase contributed to opening up the classical taxonomic literature, which is considered as useful because access to early literature can be difficult for researchers who need the old sources for their taxonomic research.
Darwin Core Archive (DwC-A) is a biodiversity informatics data standard that makes use of the Darwin Core terms to produce a single, self-contained dataset for species occurrence, checklist, sampling event or material sample data. Essentially it is a set of text (CSV) files with a simple descriptor (meta.xml) to inform others how your files are organized. The format is defined in the Darwin Core Text Guidelines. It is the preferred format for publishing data to the GBIF network.
A GeoPackage (GPKG) is an open, non-proprietary, platform-independent and standards-based data format for geographic information system implemented as a SQLite database container. Defined by the Open Geospatial Consortium (OGC) with the backing of the US military and published in 2014, GeoPackage has seen wide widespread support from various government, commercial, and open source organizations.
Plinian Core is a set of vocabulary terms that can be used to describe different aspects of biological species information. Under "biological species Information" all kinds of properties or traits related to taxa—biological and non-biological—are included. Thus, for instance, terms pertaining descriptions, legal aspects, conservation, management, demographics, nomenclature, or related resources are incorporated.
The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database which attempts to cover published genus names for all domains of life from 1758 in zoology up to the present, arranged in a single, internally consistent taxonomic hierarchy, for the benefit of Biodiversity Informatics initiatives plus general users of biodiversity (taxonomic) information. In addition to containing over 490,000 published genus name instances as at March 2020, the database holds over 1.7 million species names, although this component of the data is not maintained in as current or complete state as the genus-level holdings. IRMNG can be queried online for access to the latest version of the dataset and is also made available as periodic snapshots or data dumps for import/upload into other systems as desired.
Tony Rees is a software developer, data manager and biologist resident in Australia since 1986, and reviously a data manager with CSIRO Marine and Atmospheric Research. He is responsible for, among other systems:
References
- ↑ "TDWG History". TDWG. Archived from the original on 2017-08-03. Retrieved 2016-12-07.CS1 maint: discouraged parameter (link)
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