Plazi

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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 maintaining a digital taxonomic literature repository to enable archiving of taxonomic treatments, enhances submitted taxonomic treatments by creating version in the XML formats TaxonX [1] and Taxpub, [2] 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. [3]

A disciplinary repository is an online archive containing works or data associated with these works of scholars in a particular subject area. Disciplinary repositories can accept work from scholars from any institution. A disciplinary repository shares the roles of collecting, disseminating, and archiving work with other repositories, but is focused on a particular subject area. These collections can include academic and research papers.

XML Markup language developed by the W3C for encoding of data

Extensible Markup Language (XML) is a markup language that defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. The World Wide Web Consortium's XML 1.0 Specification of 1998 and several other related specifications—all of them free open standards—define XML.

Contents

The approach was originally developed in a binational National Science Foundation (NSF) and German Research Foundation (DFG) digital library program to the American Museum of Natural History and the University of Karlsruhe, respectively, to create an XML schema modeling the content of bio-systematic literature. The TaxonX schema is applied to legacy publications using GoldenGATE, [4] a semiautomatic editor. In its current state GoldenGATE is a complex mark up tool allowing community involvement in the process of rendering documents into semantically enhanced documents.

National Science Foundation United States government agency

The National Science Foundation (NSF) is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health. With an annual budget of about US$7.8 billion, the NSF funds approximately 24% of all federally supported basic research conducted by the United States' colleges and universities. In some fields, such as mathematics, computer science, economics, and the social sciences, the NSF is the major source of federal backing.

Deutsche Forschungsgemeinschaft German research foundation

The Deutsche Forschungsgemeinschaft is a German research funding organization.

American Museum of Natural History Natural history museum in New York City

The American Museum of Natural History, located on the Upper West Side of Manhattan, New York City, is the largest natural history museum in the world. Located in Theodore Roosevelt Park across the street from Central Park, the museum complex comprises 28 interconnected buildings housing 45 permanent exhibition halls, in addition to a planetarium and a library. The museum collections contain over 33 million specimens of plants, animals, fossils, minerals, rocks, meteorites, human remains, and human cultural artifacts, of which only a small fraction can be displayed at any given time, and occupies more than 2 million square feet (190,000 m2). The museum has a full-time scientific staff of 225, sponsors over 120 special field expeditions each year, and averages about five million visits annually.

Plazi developed ways to make distribution records in published taxonomic literature accessible through a TAPIR service that is harvested by the Global Biodiversity Information Facility (GBIF). [5] Similarly, the Species Page Model (SPM) transfer schema has been implemented to allow harvesting of treatments (the scientific descriptions of species and higher taxa) by third parties such as the Encyclopedia of Life (EOL). If available, the treatments are enhanced with links to external databases such as GenBank, The Hymenoptera Name Server for scientific names or ZooBank, the registry of zoological names.

Global Biodiversity Information Facility aggregator of scientific data on biodiversity; data portal

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.

<i>Encyclopedia of Life</i> collaborative project intended to create an encyclopedia documenting all living species known to science

The Encyclopedia of Life (EOL) is a free, online collaborative encyclopedia intended to document all of the 1.9 million living species known to science. It is compiled from existing databases and from contributions by experts and non-experts throughout the world. It aims to build one "infinitely expandable" page for each species, including video, sound, images, graphics, as well as text. In addition, the Encyclopedia incorporates content from the Biodiversity Heritage Library, which digitizes millions of pages of printed literature from the world's major natural history libraries. The project was initially backed by a US$50 million funding commitment, led by the MacArthur Foundation and the Sloan Foundation, who provided US$20 million and US$5 million, respectively. The additional US$25 million came from five cornerstone institutions—the Field Museum, Harvard University, the Marine Biological Laboratory, the Missouri Botanical Garden, and the Smithsonian Institution. The project was initially led by Jim Edwards and the development team by David Patterson. Today, participating institutions and individual donors continue to support EOL through financial contributions.

The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence Database Collaboration (INSDC).

Plazi claims it adheres to copyright law and argues that taxonomic treatments do not qualify as literary and artistic work. Plazi claims that such works are therefore in the public domain and can be freely used and disseminated (with scientific practice requiring appropriate citation). [6] [7]

The public domain consists of all the creative work to which no exclusive intellectual property rights apply. Those rights may have expired, been forfeited, expressly waived, or may be inapplicable.

See also

Biodiversity Information Standards (TDWG) is a non-profit scientific and educational association that works to develop open standards for the exchange of biodiversity data, facilitating biodiversity informatics. It is affiliated with the International Union of Biological Sciences. It is best known for the Darwin Core standard for exchanging biodiversity, which has been used by the Global Biodiversity Information Facility to collect millions of biological observations from museums and other organizations from around the world.

Related Research Articles

Integrated Taxonomic Information System Authoritative taxonomic information on plants, animals, fungi, and microbes

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 Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) is a protocol developed for harvesting metadata descriptions of records in an archive so that services can be built using metadata from many archives. An implementation of OAI-PMH must support representing metadata in Dublin Core, but may also support additional representations.

Biomedical text mining refers to the methods and study of how text mining may be applied to texts and literature of the biomedical and molecular biology domains. As a field of research, biomedical text mining incorporates ideas from natural language processing, bioinformatics, medical informatics and computational linguistics. The strategies developed through studies in this field are frequently applied to the biomedical and molecular biology literature available through services such as PubMed.

The following outline is provided as an overview of and topical guide to library science:

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 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.

The National Centre for Text Mining (NaCTeM) is a publicly funded text mining (TM) centre. It was established to provide support, advice, and information on TM technologies and to disseminate information from the larger TM community, while also providing tailored services and tools in response to the requirements of the United Kingdom academic community.

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).

PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees and associated data. The structure of phyloXML is described by XML Schema Definition (XSD) language.

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.

Computational Resources for Drug Discovery (CRDD) is one of the important silico modules of Open Source for Drug Discovery (OSDD). The CRDD web portal provides computer resources related to drug discovery on a single platform. It provides computational resources for researchers in computer-aided drug design, a discussion forum, and resources to maintain Wikipedia related to drug discovery, predict inhibitors, and predict the ADME-Tox property of molecules One of the major objectives of CRDD is to promote open source software in the field of chemoinformatics and pharmacoinformatics.

BioStor is a free-to-access archive of biodiversity-related scientific papers, in the Biodiversity Heritage Library. It was created and is operated by Roderic Page.

Pensoft Publishers are a publisher of scientific literature based in Sofia, Bulgaria. Pensoft was founded in 1994, by two academics: Lyubomir Penev and Sergei Golovatch. It has published nearly 1000 academic and professional books and currently publishes 24 peer-reviewed open access scientific journals including ZooKeys, PhytoKeys, Check List, Comparative Cytogenetics, Journal of Hymenoptera Research, Deutsche Entomologische Zeitschrift, and Zoosystematics and Evolution.

Catherine Norton was an American librarian. She was the first Director of Information Systems at the Marine Biological Laboratory (MBL).

BacDive scientific database for bacteria

BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.

Hydryphantidae family of arachnids

Hydryphantidae is a family of mites in the order Trombidiformes. There are more than 30 genera and 130 described species in Hydryphantidae.

Cocceupodidae

Cocceupodidae is a family of mites in the order Trombidiformes. There are at least 3 genera and about 23 described species in Cocceupodidae.

Neotrombidiidae

Neotrombidiidae is a family of velvet mites and chiggers in the order Trombidiformes. There are at least four genera in Neotrombidiidae.

Interim Register of Marine and Nonmarine Genera Taxonomic database

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 1753 in zoology up to approximately 2014, arranged in a single, internally consistent taxonomic hierarchy, for the benefit Biodiversity Informatics initiatives plus general users of biodiversity (taxonomic) information. In addition to containing over 490,000 published genus name instances as at March 2019, 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.

Hydryphantoidea

Hydryphantoidea is a superfamily of mites in the order Trombidiformes. There are about 6 families and more than 250 described species in Hydryphantoidea.

<i>Nomenclator Zoologicus</i>

Nomenclator Zoologicus is one of the major compendia in the field of zoological nomenclature, compiled by Sheffield Airey Neave and his successors and published in 9 volumes over the period 1939–1994, under the auspices of the Zoological Society of London; a tenth, electronic-only volume was also produced before the project ceased. It contains over 340,000 published name instances with their authorities and details of their original publication, certain nomenclatural notes and cross references, and an indication of the taxonomic group to which each is assigned. An electronic (digitised) version of volumes 1-10 was released online by the uBio project, based at the Marine Biological Laboratory, Woods Hole, in 2004–2005.

References

  1. Catapano, Terry. "TaxonX". Plazi. Retrieved 27 October 2009.
  2. Catapano, Terry. "Taxpub". Plazi. Retrieved 27 October 2009.
  3. Zauner, H (2009). "Evolving e-taxonomy". BMC Evolutionary Biology. 9: 141. doi:10.1186/1471-2148-9-141. PMC   2714837 . PMID   19555493.
  4. Sautter, Guido. "GoldenGATE Editor". Plazi, Technische Hochschule Karlsruhe. Retrieved 27 October 2009.
  5. "Plazidata in GBIF". Plazi. Archived from the original on 3 March 2016. Retrieved 27 October 2009.
  6. Agosti D, Egloff W (2009). "Taxonomic information exchange and copyright: the Plazi approach" (PDF). BMC Research Notes. 2: 53. doi:10.1186/1756-0500-2-53. PMC   2673227 . PMID   19331688.
  7. Costello M J (2009). "Motivating Online Publication of Data". BioScience. 59:5 (5): 418. doi:10.1525/bio.2009.59.5.9.