Glossary of Terms

From iDigBio
Jump to: navigation, search


This table provides acronymns, abbreviations, research and collections tools, terms, and organizations and projects useful to the iDigBio community for research, data management, education and other primary biodiversity data uses. Tags can be used to sort the different categories found in this table. Updated June 2016. Click here for a landscape-printable version.

Short Name Long Name Tag URL Definition
A2iA
A2iA
OCR, software http://www.a2ia.com/ Handwriting recognition software
ABBYY
ABBYY FineReader Engine
OCR, software
http://www.abbyy.com/ Commercial OCR software that can be used to convert typed and typeface label data from specimens into digital text.
Adobe Acrobat
Adobe Acrobat
software
https://acrobat.adobe.com Pro software can batch data extraction from TIFF & JPG formats. Current version is Adobe Acrobat DC.
Amazon EC2
Amazon Elastic Compute Cloud cloud computing http://aws.amazon.com/ec2/ Amazon Elastic Compute Cloud (Amazon EC2) is a web service that provides resizable compute capacity in the cloud. It is designed to make web-scale computing easier for developers. Amazon EC2's simple web service interface allows you to obtain and configure capacity with minimal friction. It provides you with complete control of your computing resources and lets you run on Amazon's proven computing environment. Amazon EC2 reduces the time required to obtain and boot new server instances to minutes, allowing you to quickly scale capacity, both up and down, as your computing requirements change. Amazon EC2 changes the economics of computing by allowing you to pay only for capacity that you actually use. Amazon EC2 provides developers the tools to build failure resilient applications and isolate themselves from common failure scenarios.
ABLS
American Bryological & Lichenological Society organization http://www.abls.org/ Professional association of brytologists and lichenologists. The society was founded in 1898, is devoted to the scientific study of all aspects of the biology of bryophytes and lichen-forming fungi, and is one of the nation's oldest botanical organizations. Membership is open to all persons (professionals and amateurs) with interest in these organisms.
ACIS Advanced Computing and Information Systems Laboratory organization http://acis.ufl.edu/ Associated with the Department of Electrical and Computer Engineering at the University of Florida (UF). Since 2001, the ACIS Lab has pioneered research and development in machine and application virtualization in distributed computing and web-based science gateways, high-performance wide-area overlay virtual networks, social and peer-to-peer virtual private networks, and self-configuring virtual appliances. The ACIS Lab hosts one of the main funded sites of the NSF FutureGrid project. The ACIS Lab has excellent connectivity to national and international networks through either 1-Gigabit or 10-Gigabit fiber connections.
ADBC Advancing Digitization of Biodiversity Collections project https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503559
https://www.idigbio.org/content/nsf-adbc-program-information
This program encourages new collaborations to develop thematic networks and an innovative national resource coordinating organization, the purpose of which is to create a national resource of digital data documenting existing biological collections and advancing scientific knowledge by improving access to digitized information (including images) residing in vouchered scientific collections across the United States.
ADW Animal Diversity Web data aggregator, education, taxonomy http://animaldiversity.org/ Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology at the University of Michigan. Data include descriptions, still images, video, and audio.
AIM-UP! Advancing Integration of Museums into Undergraduate Programs education http://www.aim-up.org/ Natural history collections form a crucial physical basis for understanding the diversity and history of life. Often these collections are associated with universities, yet their depth and significance is accessible almost exclusively to practicing researchers. AIM-UP! is an NSF-funded Research Coordination Network (RCN) exploring the use of natural history collections in undergraduate education. Five themes are proposed for the five years of the project: Integrative Inventories: Complex Biotic Associations Across Space and Time; Geographic Variation; Evolutionary Dynamics of Genomes; Biotic Response to Climate Change; Co-evolving Communities of Pathogens and Hosts as Related to Emerging Disease.
ALA Atlas of Living Australia data aggregator http://www.ala.org.au/ The Atlas of Living Australia is a joint initiative to build a national database of Australia's flora and fauna. The project brings together a huge array of information on Australia's biodiversity, accessible through a single website. Partners in this collaborative project include CSIRO, museums, herbaria, other biological collections, the Australian Government, and the community.
AmphibiaWeb
AmphibiaWeb
data aggregator http://amphibiaweb.org/
An online system that provides access to information on amphibian declines, conservation, natural history, and taxonomy. Includes georeferenced distribution maps utilizing Berkeley Mapper.
APC
Australian Plant Census
nomenclature http://www.chah.gov.au/apc/about-APC.html
Database of the accepted scientific names for the Australian vascular flora, both native and introduced, and lists synonyms and misapplications for these names.
API
Application Programming Interface
protocol, software http://en.wikipedia.org/wiki/Application_programming_interface
http://api.idigbio.org/
An Application Programming Interface provides a means for software components to interact with each other and generally hides the underlying complexity of the component or system providing the API. The iDigBio API is documented at iDigBio API.
APNI
Australian Plant Names Index
nomenclature http://www.cpbr.gov.au/apni/
Plant names and their usage in the scientific literature, whether as a current name or synonym.
Arbor Arbor Revolutionary Workflows software http://www.arborworkflows.com/ Arbor is workflow software for comparative methods. You can use Arbor to carry out a wide range of comparative analyses.
ArcGIS
ArcGIS
data visualization, software http://www.esri.com/products/index.html State-of-the-art, industry standard geographical information system software built by ESRI.
Arctos Arctos data management http://arctos.database.museum/home.cfm Arctos is an ongoing effort to integrate access to specimen data, collection-management tools, and external resources on the internet. Nearly all that is known about a specimen can be included in Arctos, and, except for some data encumbered for proprietary reasons, data are open to the public. Arctos is a multidisciplinary collection management information system for natural history. It integrates access to diverse types of collections (paleontology, entomology, botany, ornithology, mammalogy, herpetology) and data types, including specimen records, observations, tissues, parasites, stomach contents, fieldnotes and other documents, and media such as images and audio recordings. It also integrates data with projects and publications that either contribute to the collections or that use data from the collections.
ARK Archival Resource Key identifier http://www.cdlib.org/services/uc3/arkspec.pdf The ARK (Archival Resource Key) naming scheme is designed to facilitate the high-quality and persistent identification of information objects.
ARPHA Authoring, Reviewing, Publishing, Hosting and Archiving data repository, publishing http://arphahub.com/ ARPHA is the first end-to-end, narrative- and data-integrated publishing solution that supports the full life cycle of a manuscript, from authoring to reviewing, publishing and dissemination. Developed by Pensoft, ARPHA provides accomplished and streamlined production workflows that can be customized according to the journal's needs.​ Supports online direct import of specimen records from iDigBio, GBIF and other data portal infrastructure into taxonomic manuscripts.
AudioNote AudioNote Notepad and Voice Recorder software http://luminantsoftware.com/iphone/audionote.html AudioNote combines the functionality of note-taking and voice recording apps to create a powerful tool that will save you time while improving the quality of your notes.
Audubon Core Audubon Media Extension standard http://terms.tdwg.org/wiki/Audubon_Core The Audubon Core is a set of vocabularies designed to represent metadata for biodiversity multimedia resources and collections. These vocabularies aim to represent information that will help to determine whether a particular resource or collection will be fit for some particular biodiversity science application before acquiring the media. Among others, the vocabularies address such concerns as the management of the media and collections, descriptions of their content, their taxonomic, geographic, and temporal coverage, and the appropriate ways to retrieve, attribute and reproduce them.
AutoMontage AutoMontage software http://www.syncroscopy.com/syncroscopy/products.asp A software package produced by Syncroscopy and designed to produce clearly focused digital images with extreme depth-of-field.
Axiell Axiell: Archives, Libraries, Museums data management, software http://alm.axiell.com/ Axiell is the leading provider of collections management software solutions for Archives, Libraries and Museums. We offer a suite of full-featured collections management systems in Adlib, Calm, EMu and Mimsy XG. Although each has been adopted by Archives, Libraries and Museums of all sizes, each one has strengths, qualities and features which suit certain types of collection and institution.
bccvl Biodiversity and Climate Change Virtual Laboratory data analysis, visualization http://www.bccvl.org.au/ The Biodiversity and Climate Change Virtual Laboratory (BCCVL) is a “one stop modelling shop” that simplifies the process of biodiversity-climate change modelling. Its mission is to connect the research community to Australia’s national computation infrastructure by integrating a suite of tools in a coherent online environment where researchers can access data and perform data analysis and modelling.
BCoN Biodiversity Collections Network community https://bcon.aibs.org/ The Biodiversity Collections Network (BCoN) is a five-year national initiative funded by the U.S. National Science Foundation (NSF DBI 1441785) to support the development of a new, sustainable community of practice that will ensure that all U.S. biodiversity collections are digitally available for research, education, informed decision-making, and other scholarly and creative activities.
BoL Barcode of Life data aggregator http://www.barcodeoflife.org
In 2003, Paul Hebert, researcher at the University of Guelph in Ontario, Canada, proposed “DNA barcoding” as a way to identify species. Barcoding uses a very short genetic sequence from a standard part of the genome the way a supermarket scanner distinguishes products using the black stripes of the Universal Product Code (UPC). Two items may look very similar to the untrained eye, but in both cases the barcodes are distinct.
BerkeleyMapper BerkeleyMapper visualization https://github.com/BNHM/berkeleymapper
BerkeleyMapper 2.0 is a mapping interface for Collections (or other) Databases built on top of Google Maps. Users can configure their mapping interface through a simple XML configuration script while mapping data from tab-delimited text files.
BHL
Biodiversity Heritage Library
literature http://www.biodiversitylibrary.org//
The Biodiversity Heritage Library (BHL) is a consortium of natural history and botanical libraries that cooperate to digitize and make accessible the legacy literature of biodiversity held in their collections and to make that literature available for open access and responsible use as a part of a global biodiversity commons. BHL also serves as the foundational literature component of the Encyclopedia of Life (EOL). BHL content may be freely viewed through the online reader or downloaded in part or as a complete work in PDF, OCR text, or JPG2000 file formats.
BHL - China
Biodiversity Heritage Library China
literature http://www.bhl-china.org/
Digitization of biodiversity literature in China.
BHL - Europe
Biodiversity Heritage Library Europe
literature http://www.bhl-europe.eu/
Digitization of biodiversity literature in Europe. 3 year project, involving 28 major natural history museums, botanical gardens and other cooperating institutions.
Bio2RDF
Bio2RDF::Bioportal
data repository, ontology http://bio2rdf.org/ BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies.
BioCASe
Biological Collection Access Service
data aggregator http://www.biocase.org
Transnational network of biological collections of all kinds. BioCASE enables widespread unified access to distributed and heterogeneous European collection and observational databases using open-source, system-independent software and open data standards and protocols.
biocode
Moorea Biocode Project project http://biocode.berkeley.edu/ The Moorea Biocode Project aims to create the first comprehensive inventory of all non-microbial life in a complex tropical ecosystem.
BioGeoMancer BioGeoMancer Consortium community, georeferencing http://www.gbif.org/resource/80536 A worldwide collaboration of natural history and geospatial data experts. The primary goal of the project is to maximize the quality and quantity of biodiversity data that can be mapped in support of scientific research, planning, conservation, and management. The project promotes discussion, manages geospatial data and data standards, and develops software tools in support of this mission.
BioGUID BioGUID identifier http://bioguid.org/ BioGUID.org is a service for indexing and cross-linking identifiers for data objects within the realm of Biodiversity informatics.
BioNames BioNames
data aggregator http://bionames.org/
A database linking taxonomic names to their original descriptions, to taxa, and to phylogenies. See http://dx.doi.org/10.7717/peerj.190 for background
BioOffice
BioOffice
data management http://www.biooffice.at/
Tool widely acknowledged by a growing user community including leading Austrian museums and universities, as well as public authorities and non-profit organisations. The BioOffice application is used for the registration and documentation of biological collections as well as for archiving and evaluation of project-related data such as cartography of flora and fauna.
BioSharing BioSharing.org Information Resources data repository http://www.biosharing.org/ BioSharing works at the global level to build stable linkages between journals and funders implementing data sharing policies, and well-constituted standardization efforts in the biosciences domain, to expedite the communication and the production of an integrated standards-based framework for the capture and sharing of high-throughput genomics and functional genomic bioscience data. BioSharing works with other organisations to: 1.develop catalogues to centralize bioscience data policies and reporting standards. ◦enrich these progressively by linking to other related portals and resources to serve those seeking information on systems serving or implementing the standards 2.moderate a communication forum for funders and stakeholders. ◦promote mutual support and cross-project activities to ensure the difference among the policies and standards do not impede seamless interoperability of the data.
BIOTA
Biota: The Biodiversity Database Manager data management http://viceroy.eeb.uconn.edu/biota
Manages specimen-based, spatially and taxonomically referenced data for ecologists, conservation biologists, evolutionary biologists, systematists, museums and herbaria.
BioVeL
Biodiversity Virtual e-Laboratory data management, web services https://www.biovel.eu/ BioVeL supports scientists to carry out research on biodiversity by offering computerized tools ("workflows") to process large amounts of data from your own and cross-disciplinary sources, as well as tools for designing and running workflows.
BiSciCol
Biological Science Collections identifiers http://biscicol.org BiSciCol (Biological Science Collections) Tracker is an NSF-funded collaborative project with the goal of building an infrastructure designed to tag and track scientific collections and all of their derivatives. BiSciCol is designed on the simple premise that changes to data objects are trackable with GUIDs, and that semantic relationships are assignable and discoverable among physical and data objects.
BISON
Biodiversity Information Serving Our Nation data aggregator http://bison.usgs.ornl.gov/
An integrated and permanent resource for biological occurrence data from the United States. Product of the U.S. Geological Survey's Biological Informatics Program. BISON allows users to explore and analyze U.S. species occurrence data from participating data providers.
BITC Biodiversity Informatice Training Curriculum education http://biodiversity-informatics-training.org/ The primary goal of this site is to consolidate information and resources relating to biodiversity informatics – ultimately developing into a global, online training ‘curriculum’ for biodiversity informatics.
BOLDSystems Barcode of Life Data Systems data repository http://www.boldsystems.org/
The Barcode of Life Data Systems (BOLD) is a web platform that provides an integrated environment for the assembly and use of DNA barcode data. It delivers an online database for the collection and management of specimen, distributional, and molecular data as well as analytical tools to support their validation.
BONAP
The Biota of North America Program, North American Vascular Flora organization, data repository http://www.bonap.org/
Taxonomic Data Center and North American Plant Atlas.
BSA
Botanical Society of America organization http://www.botany.org/
Promoting research and teaching in all fields of plant biology to facilitate cooperation among plant scientists worldwide and to disseminate knowledge of plants.
BugGuide BugGuide.Net taxonomy http://bugguide.net/ Identification, Images, & Information For Insects, Spiders & Their Kin For the United States & Canada
CABIN
Central African Biodiversity Information Network
community http://gbif.africamuseum.be/CABINPortal/index
Funded for a period of 5 years by the Belgian Cooperation and Development Agency, is the implementation of a network of databases on biodiversity information, in collaboration with several research institutions based in Central Africa (mainly Congo DRC, Rwanda and Burundi). The project is a multidisciplinary initiative involving the different departments and units of RMCA.
CalPhotos
CalPhotos
data aggregator http://calphotos.berkeley.edu/ CalPhotos is a collection of 413,043 photos of plants, animals, fossils, people, and landscapes from around the world. A variety of organizations and individuals have contributed photographs to CalPhotos.
Canadensys
Canadensys data aggregator http://www.canadensys.net/
Mission to unlock the specimen information held by Canadian university-based biological collections and share this via a network of distributed databases, compatible with other biodiversity information networks like the Canadian Biodiversity Information Facility (CBIF) and the Global Biodiversity Information Facility (GBIF).
CartoDB CartoDB API, cloud computing, visualization https://cartodb.com/ CartoDB is a Software as a Service (SaaS) cloud computing platform that provides GIS and web mapping tools for display in a web browser. CartoDB users can use the company's free platform or deploy their own instance of the open source software.
Catalogue of Life
Catalogue of Life data aggregator http://www.catalogueoflife.org/ Indexing world's known species.
CBIF
Canadian Biodiversity Information Facility
data aggregator http://www.cbif.gc.ca/
Member of the Global Biodiversity Information Facility (GBIF).
CCH
Consortium of California Herbaria
community, data aggregator http://ucjeps.berkeley.edu/consortium/
Gateway to information from California vascular plant specimens that are housed in herbaria throughout the state. The database now (October 2011) includes information from more than 1.3 million specimens, all searchable through a single interface.
CF21 Cyberinfrastructure Framework for 21st Century Science and Engineering project http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504730 CIF21 will provide a comprehensive, integrated, sustainable, and secure cyberinfrastructure (CI) to accelerate research and education and new functional capabilities in computational and data-intensive science and engineering, thereby transforming our ability to effectively address and solve the many complex problems facing science and society.
COOL
Cercopoidea Organised On Line
taxonomy http://hemiptera-databases.org/cool/index.php?&lang=en&lang=en COOL is a taxonomic database dedicated to the insects Cercopoidea, which belong to the Hemiptera order.
CETAF
Consortium of European Taxonomic Facilities
community http://www.cetaf.org/
Networked consortium of scientific institutions in Europe formed to promote training, research and understanding of systematic biology and palaeobiology.
CNABH
Consortium of North American Bryophyte Herbaria
data aggregator http://bryophyteportal.org/
iDigBio summary
The Consortium of North American Bryophyte Herbaria (CNABH) was created to serve as a gateway to distributed data resources of interest to the taxonomic and environmental research community in North America. Through a common web interface, we offer tools to locate, access and work with a variety of data, starting with searching databased herbarium records. A suite of data access technologies and a distributed network of universities, museums, and agencies that provide taxonomic and environmental information.
CNALH
Consortium of North American Lichen Herbaria
data aggregator http://lichenportal.org/
iDigBio summary
The Consortium of North American Lichen Herbaria (CNALH) was created to serve as a gateway to distributed data resources of interest to the taxonomic and environmental research community in North America. Through a common web interface, we offer tools to locate, access and work with a variety of data, such as keying to species. A suite of data access technologies and a distributed network of universities, botanical gardens, museums, and agencies that provide taxonomic and environmental information. Initially created to integrate databases between Arizona State University and the Santa Barbara Botantical Garden, the consortium is growing to extend its network to other partners within North America.
CollectiveAccess CollectiveAccess data management, software http://www.collectiveaccess.org/ CollectiveAccess is free open-source software for managing and publishing museum and archival collections, and allows you to create catalogues that closely conform to your needs without custom programming.
Collections Education Connecting Students to Citizen Science and Curated Collections education http://www.collectionseducation.org/ Curriculum that integrates traditional taxonomic practices, ongoing citizen science initiatives, and digital-age herbarium curatorial skills.
CollectionsWeb
CollectionsWeb Research Coordination Network community No website found
http://www.nsf.gov/awardsearch/showAward?AWD_ID=0639214
CollectionsWeb was formerly an outreach of The Research Coordination Network (RCN) for Building a National Community of Natural History Collections, which started as a way to build communication among people at natural history collections, researchers using those collections, other programs dealing with issues important to collections, and other stakeholders. The goal of this project is to build community among natural history collections and for CollectionsWeb to serve as an online hub for collections-based activities. It provides links to sites with specimen data, but does not deliver data, itself. DBI-0639214
Colorbrewer 2.0
Colorbrewer 2.0: color advice for cartography visualization http://colorbrewer2.org/ Diagnostic tool for evaluating the robustness of individual color schemes in mapping.
CombineZ CombineZ software http://www.hadleyweb.pwp.blueyonder.co.uk/ Freeware stacking software designed to produce a single, clearly focused image with high depth-of-field. Supports batch processing.
CONABIO Comisión Nacional Para el Conocimiento y Uso de la Biodiversidad data aggregator http://www.conabio.gob.mx/ The National Commission for Knowledge and Use of Biodiversity (CONABIO) is a permanent interdepartmental commission, created in 1992. The mission of CONABIO is to promote, coordinate, support and carry out activities aimed at increasing awareness of biodiversity and its conservation and sustainable use for the benefit of society.
COS Center for Open Science data management, reproducible research https://cos.io/ COS is a non-profit technology company providing free and open services to increase inclusivity and transparency of research. COS supports shifting incentives and practices to align more closely with scientific values.
CIPA
Computer aided Identification of Phlebotomine sandflies of the Americas
taxonomy http://www.scielo.br/pdf/mioc/v88n2/vol88(f2)_047-056.pdf
http://cipa.snv.jussieu.fr/
CIPA includes information on 418 neotropical sandfly (Phlebotominae) species. These blood-sucking insects are important as vectors transmitting human and animal diseases, e.g. leishmaniasis, bartonellosis, arboviruses. In addition to the data contributed to the Catalogue of Life, CIPA also provides an interactive key and data on the ecology and epidemiology of the group.
CRIA Centro de Referência em Informação Ambiental organization http://www.cria.org.br/ The Reference Center on Environmental Information of Brazil, is an educational, nonprofit organization, which aims to disseminate scientific and technological knowledge and promote education, to promote the conservation and sustainable use of natural resources and the formation of citizenship. See their project speciesLink.
CrossRef Crossref.org citation, identifiers http://www.crossref.org/ Crossref is a not-for-profit membership organization for scholarly publishing working to make content easy to find, link, cite and assess. The Open Funder Registry provides a taxonomy of standardized funder names.
CSIRO Commonwealth Scientific and Industrial Research Organisation organization http://www.csiro.au/ CSIRO is the custodian of the Natioanl Research Collections of Australia, collections of animal and plant specimens and their data that contribute to national and international biological knowledge.
CyVerse
CyVerse
cloud computing, data repository, research tools http://www.cyverse.org/ Formerly iPlant. A community of researchers, educators, and students working to enrich all biological sciences through the development of cyberinfrastructure - the physical computing resources, collaborative environment, virtual machine resources, and interoperable analysis software and data services that are essential components of modern biology.
DAMS Digital Asset Management Systems data management, hardware, software See https://www.idigbio.org/content/webinar-panel-dams-and-archival-issues-large-and-small-collections-options-considerations
https://vimeo.com/idigbio/review/146166848/bca77fe5f2
Digital asset management systems (DAMS) include computer software and hardware systems that aid in the process of digital asset management, the management tasks and decisions surrounding the ingestion, annotation, cataloguing, storage, retrieval and distribution of digital assets.
DataCarpentry
Software Carpentry
DataCarpentry
Software Carpentry
education, organization, software http://www.datacarpentry.org/
http://software-carpentry.org/
Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Software Carpentry has been teaching researchers in science, engineering, medicine, and related disciplines the computing skills they need to get more done in less time and with less pain. The volunteer instructors have run hundreds of events for thousands of scientists in the past two and a half years. All lesson materials are freely reusable under the Creative Commons - Attribution license. The Software Carpentry Foundation and its sibling organization Data Carpentry are members of NumFOCUS, a 501(c)3 non-profit incorporated in the United States.
DataCite
DataCite
organization, standards https://www.datacite.org/ DataCite's purpose is to develop and support methods to locate, identify and cite data and other research objects. DataCIte develops and supports the standards behind persistent identifiers for data, and our members assign them. Provides the DataCite Metatdata Store which is a service for data publishers to mint DOIs and register associated metadata.
DataONE
Data Observation Network for Earth data repository https://www.dataone.org/ Data Observation Network for Earth (DataONE) desires to be the foundation of new innovative environmental science through a distributed framework and sustainable cyberinfrastructure that meets the needs of science and society for open, persistent, robust, and secure access to well-described and easily discovered Earth observational data. Supported by the U.S. National Science Foundation, DataONE will ensure the preservation and access to multi-scale, multi-discipline, and multi-national science data. DataONE will transcend domain boundaries and make biological data available from the genome to the ecosystem; make environmental data available from atmospheric, ecological, hydrological, and oceanographic sources; provide secure and long-term preservation and access; and engage scientists, land-managers, policy makers, students, educators, and the public through logical access and intuitive visualizations. DataONE distributed network.
DataONE Dash
DataONE Dash
data repository https://dash.cdlib.org/ DataONE Dash is a self-service tool for researchers to describe, upload, and share their research data which can exposes data within the DataONE network.
DataTurbine
Open Source Data Turbine Initiative software http://www.dataturbine.org/ DataTurbine is a robust real-time streaming data engine that lets you quickly stream live data from experiments, labs, web cams and even Java enabled cell phones. It acts as a "black box" to which applications and devices send and receive data. Think of it as express delivery for your data, be it numbers, video, sound or text.
DBTNT
Database to Name and Taxa
nomenclature; taxonomy http://hemiptera-databases.org/dbtnt/ PostGreSQL relational database and conceptual schema. A knowledge base that allows a dynamic web edition and exploration of referenced taxonomic data and their associated biological information.
DiGIR Distributed Generic Information Retrieval protocol http://digir.sourceforge.net/ Superceded by IPT. DiGIR is a client/server protocol for retrieving information from distributed resources. It uses HTTP as the transport mechanism and XML for encoding messages sent between client and server. It is an opensource project, originally conceived to be the replacement for the Z39.50 protocol used in the Species Analyst project, but is intended to work with any type of information, not just Natural History collections.
Digital Florida
Digital Florida data management http://www.flmnh.ufl.edu/collections/databases/ Public interface for biodiversity (collections, etc.), including web mapping application, for Florida. Initial proof of concept for FLMNH Biodiversity Institute, but no existing funding.
Digitarium
Digitarium digitization http://digitarium.fi/en High performance digitization of insects and herbarium specimens.
DINA DIgital Information system for NAtural history data community, data management http://www.dina-project.net/wiki/Welcome_to_the_DINA_project! The DINA consortium is an unincorporated international partnership among organizations and individuals for collaborative development of an open-source web-based information management system for natural history data.
Discover Life
Discover Life data aggregator http://www.discoverlife.org Provides free on-line tools to identify species, share ways to teach and study nature's wonders, report findings, build maps, process images, and contribute to and learn from a growing, interactive encyclopedia of life that now has more than one million species pages.
DIVA-GIS
DIVA-GIS software, visualization http://www.diva-gis.org/
Mapping and geographic data analysis; open source GIS.
djatoka djatoka software http://www.dlib.org/dlib/september08/chute/09chute.html
https://github.com/jronallo/djatoka
Open source JPEG2000 image server.
DOI Digital Object Identifier
Digital Object Identifier System
International DOI Foundation
identifier https://www.doi.org/ International DOI Foundation (IDF), a not-for-profit membership organization that is the governance and management body for the federation of Registration Agencies providing Digital Object Identifier (DOI) services and registration, and is the registration authority for the ISO standard (ISO 26324) for the DOI system. The DOI system provides a technical and social infrastructure for the registration and use of persistent interoperable identifiers, called DOIs, for use on digital networks.
DroidDB DroidDB software http://droiddb.syware.com/ DroidDB® database & forms builder makes it easy to create Android apps. With DroidDB, it’s easy to build Android applications with forms to collect information and relational databases to make it most useful.
Drupal Drupal content management, software https://www.drupal.org/ Drupal is content management software. Drupal 8.0 is the most recent release.
Dryad Dryad Data Repository data repository http://datadryad.org/ Dryad is an international repository of data underlying peer-reviewed articles in the basic and applied biosciences. Dryad enables scientists to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies. Dryad is governed by a consortium of journals that collaboratively promote data archiving and ensure the sustainability of the repository. As of Nov 18, 2011, Dryad contained 1090 data packages and 2583 data files, associated with articles in 94 journals.
DSLR Digital Single Lens Reflex Camera hardware http://en.wikipedia.org/wiki/Digital_single-lens_reflex_camera A digital camera, usually with interchangeable lenses, that captures digital images in one or more of a variety of formats.
DwC
DwC Terms
Darwin Core
Darwin Core Terms
standard http://rs.tdwg.org/dwc/
http://rs.tdwg.org/dwc/terms/
The Darwin Core is a body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information. Included are documents describing how these terms are managed, how the set of terms can be extended for new purposes, and how the terms can be used.
EarthCube
EarthCube community, project http://earthcube.org/ EarthCube will enable geoscientists to address the challenges of understanding and predicting a complex and evolving solid Earth, hydrosphere, atmosphere, and space environment systems. By fostering community-governed efforts to develop a common cyberinfrastructure for the purpose of collecting, accessing, analyzing, sharing and visualizing all forms of data and related resources, EarthCube is intended to democratize, and increase access to and use of, advanced technological and computational capabilities for geosciences research.
eBiodiversity
Estonian eBiodiversity data aggregator http://elurikkus.ut.ee/index.php?lang=eng
The aim of eBiodiversity portal is to provide a comprehensive resource on Estonian biodiversity by bringing together scientific and citizen science datasets. The portal provides public access to a wide variety of taxon occurrence types including specimens in scientific collections, observations, sounds, images, videos, references in literature and DNA-based observations.
eBird
eBird citizen science, data aggregator http://ebird.org/ A real-time, online checklist program, eBird has revolutionized the way that the birding community reports and accesses information about birds.
EcoInforma EcoInforma data management, data repository https://www.data.gov/ecosystems/ecoinforma/ This initiative is aimed at sustainably expanding the availability and interoperability of Federal and non-Federal biodiversity, ecosystems, and ecosystem services information for use by researchers, the public, and government decision-makers. Serves BISON, EnviroAtlas and other data.gov resource hubs.
ECOS Environmental Conservation Online System data aggregator http://ecos.fws.gov/tess_public/ US Fish and Wildlife Service (USFWS) information service for rare, threatened, endangered, and extinct species.
Effechecka Effechecka - Taxonomic Checklist Generator data use http://www.effechecka.org/
https://github.com/jhpoelen/effechecka/wiki/About#introduction
The purpose of Effechecka is to create, save, export and follow checklists given specific geospatial, taxonomic and trait constraints using data sources including, but not limited to, GBIF, iDigBio and EOL TraitBank. Example checklists include animals, insects, plants and fungi of McLaren Park in San Francisco, small birds and mammals of the San Francisco Bay Area and big sharks of the Gulf of Mexico.
EMu
KE EMu
Electronic Museum data management, software http://www.kesoftware.com This is a commercial software product provided by AXIELL (formerly KE Software) used by many biological collections. EMu, is a collections management system for all museums, from the small to the very large. Engineered to manage all types of collections, EMu is suited to: Cultural collections, Anthropology, Archaeology, Science and Technology; Paintings, Drawings, Prints, Sculpture and 3-dimensional objects, Decorative Art, Performing Art, Photography, Textiles and Digital Objects; Natural History collections, including Zoology, Earth Sciences, Palaeobiology, Botany, Horticulture and Physical Anthropology; and Special collections, Digital Assets, Historical Societies and Archives.
EnviroAtlas EnviroAtlas data management, visualization https://www.epa.gov/enviroatlas EnviroAtlas provides interactive tools and resources for exploring the benefits people receive from nature or "ecosystem goods and services". Ecosystem goods and services are critically important to human health and well-being, but they are often overlooked due to lack of information. Using EnviroAtlas, many types of users can access, view, and analyze diverse information to better understand the potential impacts of various decisions.
EOL Encyclopedia of Life data aggregator http://eol.org/
Open source web application to organize information by the names of living creatures. EOL's vision is to offer global access to knowledge about life on Earth. Its mission is to increase awareness and understanding of living nature through an Encyclopedia of Life that gathers, generates, and shares knowledge in an open, freely accessible and trusted digital resource.
EpiCollect EpiCollect software http://www.epicollect.net/ EpiCollect.net provides a web and mobile app for the generation of forms (questionnaires) and freely hosted project websites for data collection. Data are collected (including GPS and media) using multiple phones and all data can be viewed centrally (using Google Maps / tables / charts).
ePandda Enhancing Paleontological and Neontological Data Discovery API API https://steppe.org/research/epandda/ Project to develop software tools to connect The Paleobiology Database (PBDB, paleontological, literature-based), iDigPaleo (paleontological, specimen-based), and iDigBio (neontological, specimen-based).
ESFRI European Strategy Forum on Research Infrastructures project http://www.esfri.eu/ ESFRI, the European Strategy Forum on Research Infrastructures, is a strategic instrument to develop the scientific integration of Europe and to strengthen its international outreach. The competitive and open access to high quality Research Infrastructures supports and benchmarks the quality of the activities of European scientists, and attracts the best researchers from around the world.
EPICC Documenting Fossil Marine Invertebrate Communities of the Eastern Pacific - Faunal Responses to Environmental Change over the last 66 million years​ data aggregator, TCN iDigBio summary This project fills a major gap in the documentation of past environmental change, making available digitized data from the especially rich fossil record of the eastern Pacific marine invertebrate communities of the Cenozoic, the 66 million years that have passed since the extinction of the dinosaurs.
EU BON Building the European Biodiversity Observation Network community, project http://www.eubon.eu The main objective of EU BON is to build a substantial part of the Group on Earth Observation’s Biodiversity Observation Network (GEO BON). EU BON’s deliverables include a comprehensive "European Biodiversity Portal" for all stakeholder communities, and strategies for a global implementation of GEO BON and supporting IPBES. Due to EU BON’s contribution overall European capacities and infrastructures for environmental information management will be strengthened. EU BON’s 30 partners from 18 countries are members of networks of biodiversity data-holders, monitoring organisations, and leading scientific institutions. EU BON will build on existing components, in particular GBIF, LifeWatch infrastructures, and national biodiversity data centres.
EUROPEANA
Europeana: think culture
data aggregator http://www.europeana.eu/
Europeana enables people to explore the digital resources of Europe's museums, libraries, archives and audio-visual collections. It promotes discovery and networking opportunities in a multilingual space where users can engage, share in and be inspired by the rich diversity of Europe's cultural and scientific heritage.
Exploring Genomics Data Exploring Genomics Data education http://serc.carleton.edu/exploring_genomics/index.html The Genomics Explorers provide an iterative way for students to choose strategies for asking and addressing biologically interesting questions using a range of genomics tools. See Science article: http://www.sciencemag.org/content/339/6118/408.full?sid=23e3c018-0e58-4eec-8cdc-e73b10bc8f1e
EXIF Exchangeable Image File Format standard http://www.exif.org/ A standard for storing image metadata and interchange information in image files, especially those using JPEG compression. Most digital cameras now use the EXIF format. The format is part of the DCF standard created by JEITA to encourage interoperability between imaging devices.
EZID EZID identifier http://ezid.cdlib.org/ Long-term identifiers made easy. EZID (easy-eye-dee) makes it easy to create & manage unique, long-term identifiers.
Falling rain
Falling Rain Global Gazetteer Version 2.3 gazetteer http://www.fallingrain.com/world/index.html
Global Gazetteer of cities and towns, with browse functionality.
Fauna Europaea
Fauna Europaea: All European Animal SPecies Online data aggregator http://www.fauna-eu.org/
The scientific names of all European land and freshwater animals brought together in one authoritative database.
FIC
Fossil Insect Collaborative: A Deep-Time Approach to Studying Diversification and Response to Environmental Change data aggregator, TCN http://fossilinsects.colorado.edu/
iDigBio summary
The scientific names of all European land and freshwater animals brought together in one authoritative database.
figShare
figShare
data repository https://figshare.com//
figshare is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner. figshare allows users to upload any file format to be previewed in the browser so that any research output, from posters and presentations to datasets and code, can be disseminated in a way that the current scholarly publishing model does not allow.
FilteredPush FilteredPush data management, software, http://etaxonomy.org/mw/FilteredPush http://sourceforge.net/projects/filteredpush/ FilteredPush is an NSF-funded project of the Museum of Comparative Zoology, UC Davis, the Harvard University Herbaria and the UMASS-Boston Biodiversity Informatics Lab to build a platform for distributed annotation of distributed data. It provides feedback to the data provider and any other parties interested in the annotations, based on configurable filters to select notification based on attributes of the annotation or the data. FilteredPush is designed to connect remote sites where annotations can be generated with the authoritative databases of the collections holding the vouchers to which those annotations apply. The name reflects function; Push, as annotations can be pushed from remote corners of the network back to authoritative data sets, Filtered, as the curators of these data sets can filter and reject annotations of their data.
Fishbase FishNet2 Collaborative Georeferencing data aggregator, nomenclature, taxonomy http://www.fishbase.org/ FishNet 2 is a collaborative effort by natural history museums and other biodiversity institutions to establish a global network of Ichthyology collections. There is an open invitation for any institution with a fish collection to join. The current portal is an outgrowth of the original FishNet project with improvements in network stability, georeferencing capabilities, and technical support. Users are provided access to searchable, mappable, and downloadable data that are cached on a regular basis from participating institutions who have published their data via the DiGIR or TAPIR protocols with a Darwin Core schema.
FishNet2 FishNet2 Collaborative Georeferencing data aggregator http://www.fishnet2.net/ FishNet 2 is a collaborative effort by natural history museums and other biodiversity institutions to establish a global network of Ichthyology collections. There is an open invitation for any institution with a fish collection to join. The current portal is an outgrowth of the original FishNet project with improvements in network stability, georeferencing capabilities, and technical support. Users are provided access to searchable, mappable, and downloadable data that are cached on a regular basis from participating institutions who have published their data via the DiGIR or TAPIR protocols with a Darwin Core schema.
FLOW
Fulgoromorpha List On the Web
nomeclature, taxonomy No website found. FLOW: a taxonomic and knowledge base dedicated to planthoppers (Insecta, Hemiptera, Fulgoromorpha).
FOSSIL
The FOSSIL Project (Fostering Opportunities for Synergistic STEM with Informal Learners) citizen science, education http://www.myfossil.org/ FOSSIL is cultivating a networked community (known as a community of practice) in which amateur and professional paleontologists collaborate in learning, the practice of science, and outreach.
From the Page
From the Page
citizen science, transcription http://beta.fromthepage.com/ FromThePage is open source software that allows volunteers to transcribe handwritten documents online.
Fuzzy Gazetteer
Fuzzy Gazetteer
gazetteer http://isodp.hof-university.de/fuzzyg/query/ The Fuzzy Gazetteer enables you to find geographic features even when you do not know their exact names. A list of similar names is returned, web-linked to the JRC Digital Map Archive of the European Commission.
GBIF Global Biodiversity Information Facility
data aggregator, data repository http://www.gbif.org/
The Global Biodiversity Information Facility (GBIF) was established by governments in 2001 to encourage free and open access to biodiversity data, via the Internet. Through a global network of 57 countries and 47 organizations, GBIF promotes and facilitates the mobilization, access, discovery, and use of information about the occurrence of organisms over time and across the planet.
GCI
Grey Card Index
The Gray Herbarium Index of New World Plant Names
nomenclature http://kiki.huh.harvard.edu/databases/
The Gray Card Index (in part) from the Harvard Gray Herbarium is now incorporated into the International Plant Names Index.
GDAL Geospatial Data Abstraction Library API http://www.gdal.org/
Geospatial library for PostgreSQL. Required to implement map server and other spatial applications/libraries in PostgreSQL. Translation library for raster (GDAL) and vector (OGR) geospatial data formats.
GenBank NCBI-GenBank data aggregator http://www.ncbi.nlm.nih.gov/genbank/ GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
geneious geneious software http://www.geneious.com Geneious is a DNA, RNA and protein sequence alignment, assembly and analysis software platform, integrating bioinformatic and molecular biology tools into a simple interface.
Gene Ontology Gene Ontology Consortium vocabulary http://www.geneontology.org/ The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.
Geopaparazzi Geopaparazzi. Because not all paparazzis are evil! software http://geopaparazzi.github.io/geopaparazzi/index.html Geopaparazzi is a tool developed to do very fast qualitative engineering/geologic surveys.
Geotag Photos Pro Geotag Photos Pro software http://www.geotagphotos.net/ Add GPS capabilities to your mobile device for the fraction of the cost of a dedicated GPS logger. consists of a mobile app (for iOS or Android) that records your position while you’re taking great photos and a desktop app that geotags your images using recorded data. All your recorded routes can then be exported as a GPX file via Dropbox, email, or the web.
Thesaurus of Geographic Names Getty Thesaurus of Geographic Names Online gazetteer http://www.getty.edu/research/tools/vocabularies/tgn/ Useful for alternative/synonyms for old place names.
GitHub GitHub data repository, software https://github.com/ A web-based Git repository hosting service. It offers all of the distributed revision control and source code management (SCM) functionality of Git as well as adding its own features.
GIMP GNU Image Manipulation Program software https://www.gimp.org/ GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems. Free, open source software.
GLANSIS Great Lakes Aquatic Nonindigenous Species Information System data aggregator http://www.glerl.noaa.gov/res/Programs/glansis/glansis.html NOAA's GLANSIS database consists of three lists: a core list of species nonindigenous to the Great Lakes basin (not native to any part of the basin), a list of range expansion species (native only to a portion of the basin), and a watchlist (not currently found in the Great Lakes but assessed in the peer-reviewed scientific literature as of 2010 as likely to invade via current pathways).
GloBI Global Biotic Interactions API, data aggregator, data analysis http://www.globalbioticinteractions.org/
https://github.com/jhpoelen/eol-globi-data/wiki#accessing-species-interaction-data
Global Biotic Interactions (GloBI) provides an infrastructure and data service that aggregates or combines existing biotic interaction datasets to provide easy access to biotic interaction data.
GLOBIS Global Butterfly Information System data aggregator http://www.lepidat.org/platform/lex/globis/home/index.do The Global Butterfly Information System provides information on butterflies based on several research projects. It supports data, pictures, and label information on nearly all type specimen of European museum collections. Summary factsheets are also available on a growing number of species.
GNIS Geographic Names Information System gazetteer http://geonames.usgs.gov/
http://geonames.nga.mil/namesviewer/
http://nhd.usgs.gov/gnis.html
The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical (not including roads and highways). The database holds the Federally recognized name of each feature and defines the location of the feature by state, county, USGS topographic map, and geographic coordinates. Other feature attributes include names or spellings other than the official name, feature designations, feature class, historical and descriptive information. The database assigns a unique feature identifier, a random number, that is a key for accessing, integrating, or reconciling GNIS data with other datasets. The GNIS is our Nation's official repository of domestic geographic feature names information.
GEOLocate GEOLocate gazetteer, software, visualization http://www.museum.tulane.edu/geolocate/ Software designed to georeference natural history collections data by interpreting locality data and converting them into specific geographic coordinate pairs, including an estimate of precision based on the point-radius method. GeoLocate may be downloaded as a standalone desktop application, used via a web-based interface, or run as a web service against an existing online database.
Georeferencing
Georeferencing Mapping Resource Hub gazetteer, georeferencing, visualization http://georeferencing.org/
Collection of resources pertaining to the process of georeferencing. See also http://www.herpnet.org/Gazetteer/GeorefResources.htm
Georeferencing Calculator
Georeferencing Calculator
georeferencing http://manisnet.org/gci2.html
https://github.com/VertNet/georefcalculator/
The Georeferencing Calculator is a javascript application created as a tool to aid in the georeferencing of descriptive localities such as those found in museum-based natural history collections.
GEOS Geometry Engine, Open Source API http://trac.osgeo.org/geos/
Complete functionality of Java Topology Suite (JTS) in C++.
Geotools
GeoTools The Open Source Java GIS Toolkit visualization http://www.geotools.org/ GeoTools is an open source Java library that provides tools for geospatial data.
GLI Great Lakes Invasives TCN data aggregator, TCN http://herbarium.wisc.edu/GreatLakes.htm
http://greatlakesinvasives.org/
iDigBio summary
Documenting the Occurrence through Space and Time of Aquatic Non-indigenous Fish, Mollusks, Algae, and Plants Threatening North America's Great Lakes. This project will create a network of herbaria and zoology museums from among the Great Lakes states of MN, WI, IL, IN, MI, OH, and NY to better document the occurrence of exotic species in space and time by imaging and providing online access to the information on the specimens of the critical organisms.
GigaPan
CaptureStudio
GigaPan
CaptureStudio
hardware, software http://gigapan.com Gigapans are gigapixel panoramas, digital images with billions of pixels. Generated using robotic camera harnesses that allow one of numerous DSLR cameras to take multiple images that can be stitched together to form gigapixel, high-resolution image files.
Global Plants
Global Plants on JSTOR
data aggregator https://plants.jstor.org/
Global Plants(formerly JSTOR Plant Science) is an online environment that provides access to foundational content vital to plant science - plant type specimens, taxonomic structures, scientific literature, and related materials. This new environment includes over a million type specimens, paintings, drawings, correspondence, and supporting materials. By 2013, they expect to have over 2.2 million type specimens available, making JSTOR Plant Science the largest collection of its kind in the world. These materials are now truly global in scope representing over 200 partners in 50 countries on 5 continents.
GLoBIS Global Butterfly Information System data aggregator, taxonomy http://www.globis.insects-online.de/ The Global Butterfly Information System provides information on butterflies based on several research projects. It supports data, pictures, and label information on nearly all type specimen of European museum collections. Summary factsheets are also available on a growing number of species.
GLOBIS-B GLOBal Infrastructures for Supporting Biodiversity research project http://www.globis-b.eu/ The GLOBIS-B project “GLOBal Infrastructures for Supporting Biodiversity research” is a Horizon 2020 project within the coordination & support action funding scheme of the H2020-INFRASUPP-2014-2 call of the European Commission. The main aim of the project is to bring together scientists with global research infrastructure operators and legal interoperability experts to address the research needs and infrastructure services required to calculate Essential Biodiversity Variables (EBVs).
GNA Global Names Architecture nomenclature http://www.globalnames.org/
Infrastructure that manages (the strings that serve as) names can discover, index, organize and interconnect on-line information about organisms and serve the needs of biologists.
Google Analytics Google Analytics website analytics http://www.google.com/analytics/ Google Analytics is the enterprise-class web analytics solution that gives you rich insights into your website traffic and marketing effectiveness. Powerful, flexible, and easy-to-use features now let you see and analyze your traffic data in an entirely new way.
Google Earth Google Earth Engine gazetteer, software, visualization https://www.google.com/earth/ Google Earth is a geobrowser that accesses satellite and aerial imagery, ocean bathymetry, and other geographic data over the internet to represent the Earth as a three-dimensional globe.
Google Maps Google Maps gazetteer, visualization https://maps.google.com/ Google Maps is a desktop web mapping service developed by Google. It offers satellite imagery, street maps, 360° panoramic views of streets (Street View), real-time traffic conditions (Google Traffic), and route planning for traveling by foot, car, bicycle (in beta), or public transportation.
GPlates GPlates software, visualization http://www.gplates.org/ GPlates is desktop software for the interactive visualisation of plate-tectonics. GPlates offers a novel combination of interactive plate-tectonic reconstructions, geographic information system (GIS) functionality and raster data visualisation.
GPS Visualizer GPS Visualizer visualization http://www.gpsvisualizer.com/ GPS Visualizer is an online utility that creates maps and profiles from geographic data. It is free and easy to use, yet powerful and extremely customizable. Input can be in the form of GPS data (tracks and waypoints), driving routes, street addresses, or simple coordinates. Use it to see where you've been, plan where you're going, or quickly visualize geographic data (scientific observations, events, business locations, customers, real estate, geotagged photos, etc.).
Grass GIS Grass GIS software, visualization http://grass.osgeo.org/
GIS software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization.
GRBio The Global Registry of Biodiversity Repositories data repository http://grbio.org/ GRBio is a consolidated, comprehensive clearinghouse of information about biological collections in natural history museums, herbaria, and other biorepositories.
GUID
UUID
Globally Unique Identifier
Universally Unique Identifier
identifier https://www.idigbio.org/sites/default/files/iDigBioGuidGuide-2013-06-26_0.pdf
https://www.guidgenerator.com/
GUID (or UUID) is a 128-bit integer number and are commonly displayed as 32 hexadecimal digits with groups separated by hyphens, used to identify resources such as specimens and specimen records.
Hadoop Hadoop software http://hadoop.apache.org/ The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using a simple programming model. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-avaiability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-availabile service on top of a cluster of computers, each of which may be prone to failures.
herbaria@home herbaria@home: recording historical biodiversity transcription http://herbariaunited.org/atHome/
Herbaria@home is a ground-breaking new approach to digitising and documenting the archives of the UK's herbaria. This site provides a web-based method for documenting herbarium sheets. We welcome participation in the project. Volunteers (citizen science) participate to enter label data from Herbarium sheets.
HERBIS Erudite Recorded Botanical Information Synthesizer project No website found This project offers proof of concept and an initial implementation of 'one-button' specimen imaging and data capture by which clicking the shutter on a digital camera would initiate a sequence that culminates with the population of label data and a specimen image into a structured collection database. The ultimate goal is to reduce the total cost of digital collection data capture by significantly reducing human labor required and total project duration. Significant gains can be achieved by developing appropriate protocols and methodologies, then packaging them as web services. Much of this can be accomplished by applying existing technology to data acquisition bottlenecks.
HerpNET Herpetological Network data aggregator http://www.herpnet.org/ HerpNET is a collaborative effort by natural history museums to establish a global network of herpetological collections data, funded by the National Science Foundation (NSF No. 0132303) and a GBIF DIGIT grant. Sixty-four institutions participated in the HerpNET community (43 in the original NSF grant). The VertNet data portal replaced the HerpNET portal in January 2015.
HOLOS HOLOS Berkeley Ecoinformatics Engine data aggregator, data analysis, visualization https://holos.berkeley.edu/ Holos aims to digitize and aggregate many diverse biological and environmental collections into the Berkeley Ecoinformatics Engine ('Ecoengine'), a web service that can be searched and visualized via graphical tools: Explore, Compare, and other Applications. The data in the Ecoengine is global in scope, and since much of the data is sourced from the University of California museums, reserves and partners, the data coverage for California is very good.
HUBzero HUBzero software http://hubzero.org/ HUBzero is a platform created by Purdue University with the collaboration of several other institution and is used to create dynamic web sites for scientific research and educational activities. HUBzero allows users to easily publish research software and related educational materials on the web. It is specifically designed for scientific applications. InvertNet.org is built on this platform.
Hymenoptera Online
Hymenoptera Online data aggregator http://hol.osu.edu/
Hymenoptera database. These data have been gathered with the collaboration of a number of colleagues. Other taxa still need work. Visit the collection page for the C.A. Triplehorn Insect Collection at the Ohio State University for information on its primary and secondary type holdings as well as databased taxa in the collection. Data now available through SCAN and iDigBio.
ICBN International Code on Botanical Nomenclature nomenclature http://ibot.sav.sk/icbn/main.htm The International Code on Botanical Nomenclature (ICBN) acts as adviser and arbiter for the biological community by generating and disseminating information on the correct use of the scientific names of plants. The ICBN is responsible for producing the International Code of Botanical Nomenclature, a set of rules for the naming of plants and the resolution of nomenclatural problems.
ICR Intelligent Character Recognition software http://en.wikipedia.org/wiki/Intelligent_character_recognition An advanced optical character recognition (OCR) or rather more specific handwriting recognition system that allows fonts and different styles of handwriting to be learned by a computer during processing to improve accuracy and recognition levels.
ICZN International Commission on Zoological Nomenclature nomenclature http://iczn.org/ The International Commission on Zoological Nomenclature (ICZN) acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature, a set of rules for the naming of animals and the resolution of nomenclatural problems.
IdentificationKey web service
IdentificationKey web service online service http://www.identificationkey.fr/
Laboratoire Informatique & Systematique gathers biologists and computer specialists grouped together around a common ambition: the development of Interactive Identification Keys (IIK).
iDigBio Integrated Digitized Biocollections data aggregator, project https://www.idigbio.org/ The project funded by the NSF to develop an integrated national infrastructure for digitization of existing biodiversity collections in the U.S. iDigBio is also known as the National Resource for Advancing Digitization of Biological Collections (ADBC).
IDQ iDigQuality software https://github.com/iDigBio/idq iDigBio's data quality standard library.
ISBER
International Society for Biological and Environmental Repositories
organization https://isber.site-ym.com/ ISBER is a global organization which creates opportunities for sharing ideas and innovations in biobanking and harmonizes approaches to evolving challenges for biological and environmental repositories.
IGSN
International Geo Sample Number
identifier http://www.geosamples.org/igsnabout The IGSN is an alphanumeric code that uniquely identifies samples from our natural environment and related sampling features. You can get an IGSN for your sample by registering it in the System for Earth Sample Registration SESAR.
IH
Index Herbariorium
data repository http://sweetgum.nybg.org/science/ih/ The Index Herbariorum (IH) entry for an herbarium includes its physical location, URL, contents (e.g., number and type of specimens), founding date, as well as names, contact information and areas of expertise of associated staff.
IK
Index Kewensis
nomenclature http://www.uk.ipni.org/ik_blurb.html
Indexing names of seed plants at the level of genus and species published since 1753, now totalling over one million records.
ILDIS
International Legume Database & Information Service nomenclature http://www.ildis.org/
International project which maintains a database of plants in the family Fabaceae (Leguminosae) and provides services to scientists and other people interested in these plants, including this web-site for access to the database.
ImageMagick ImageMagick software http://www.imagemagick.org/script/index.php ImageMagick is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. ImageMagick can be used to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bezier curves.
iNaturalist iNaturalist citizen science, data aggregator http://www.inaturalist.org iNaturalist is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world. Observational data is shared with GBIF.
INBio INBio Costa Rica data aggregator http://www.inaturalist.org The National Biodiversity Institute (INBio) of Costa Rica is a private research and biodiversity management center, established in 1989 to support all efforts made to gather knowledge on the country’s biological diversity and promote its sustainable use.
Index Fungorum
Index Fungorum nomenclature http://www.indexfungorum.org/
Global fungal nomenclator coordinated and supported by the Index Fungorum Partnership (CABI, CBS, Landcare Research-NZ), contains names of fungi (including yeasts, lichens, chromistan fungal analogues, protozoan fungal analogues and fossil forms) at all ranks.
InverteBase
InvertEBase: Reaching Back to See the Future: Species-rich Invertebrate Faunas Document Causes and Consequences of Biodiversity Shifts data aggregator, TCN http://www.invertebase.org/
iDigBio summary
The TCN "InvertEBase" is a 4-year collaborative effort to digitize specimen records from ten arthropod and mollusk collections housed at six major US museums in six states, three of them ranking among the top 10 collections in the world.
InvertNet
InvertNet data aggregator, TCN https://invertnet.org/
iDigBio summary
InvertNet, one of the three Thematic Collection Networks (TCNs) funded in the first round of the U.S. National Science Foundation’s Advancing Digitization of Biological Collections (ADBC) program, is tasked with providing digital access to ~60 million specimens housed in 22 arthropod (primarily insect) collections at institutions distributed throughout the upper midwestern USA.
iPlant iPlant Collaborative cloud computing, data management http://www.iplantcollaborative.org/ See CyVerse.
IPNI International Plant Names Index nomenclature http://ipni.org/ The International Plant Names Index (IPNI) is a database of the names and associated basic bibliographical details of seed plants, ferns, and lycophytes. Its goal is to eliminate the need for repeated reference to primary sources for basic bibliographic information about plant names. The data are freely available and are gradually being standardized and checked. IPNI is the product of a collaboration between The Royal Botanic Gardens, Kew, The Harvard University Herbaria, and the Australian National Herbarium.
IPT GBIF Integrated Publishing Toolkit software http://www.gbif.org/ipt
https://github.com/gbif/ipt
The IPT is an open source software server written in Java that allows users to publish and share biodiversity datasets through the Global Biodiversity Information Facility network (GBIF). Designed for interoperability, it enables the publishing of content in databases or text files using open standards; namely the Darwin Core and the Ecological Metadata Language.
IPT 2
GBIF Integrated Publishing Toolkit software http://code.google.com/p/gbif-providertoolkit/
See IPT. Open source web application that makes it easy to share three types of biodiversity-related information: primary taxon occurrence data, taxon checklists, and general metadata about data sources.
IrfanView IrfanView software http://www.irfanview.com/ IrfanView is a very fast, small, compact and innovative FREEWARE (for non-commercial use) graphic viewer for Windows operating systems.
iSamples The Internet of Samples in the Earth Sciences community, data management, project http://earthcube.org/group/isamples The iSamples RCN seeks to advance the use of innovative cyberinfrastructure to connect physical samples and sample collections across the Earth Sciences with digital data infrastructures to revolutionize their utility for science. The ultimate goal of this RCN is to dramatically improve the discovery, access, sharing, analysis, and curation of physical samples and the data generated by their study for the benefit of science and society.
ITIS Integrated Taxonomic Information System nomenclature http://www.itis.gov/ Authoritative, searchable taxonomic information on plants, animals, fungi, and microbes of North America and the world, including synonymous and accepted names.
IUCN
Red List
International Union for Conservation of Nature
The IUCN Red List of Threatened Species
data aggregator, organization http://www.iucn.org/
http://www.iucnredlist.org/
IUCN, International Union for Conservation of Nature, helps the world find pragmatic solutions to our most pressing environment and development challenges. The Red List provides assessments of the conservation status of species, subspecies, varieties, and even selected subpopulations on a global scale for the past 50 years in order to highlight taxa threatened with extinction, and thereby promote their conservation.
IWGSC Interagency Working Group on Scientific Collections organization http://www.whitehouse.gov/sites/default/files/sci-collections-report-2009-rev2.pdf An interagency group studying and characterizing federally held scientific collections and determining their long-term stewardship needs.
JAI
Java Advanced Imaging (JAI) API imaging, software http://www.oracle.com/technetwork/articles/javaee/jai-142803.html The Java Advanced Imaging API provides a set of object-oriented interfaces that support a simple, high-level programming model which lets you manipulate images easily.
Jetstream
Jetstream
cloud computing, data repository http://jetstream-cloud.org/ Jetstream, led by the Indiana University Pervasive Technology Institute (PTI), will add cloud-based computation to the national cyberinfrastructure. Researchers will be able to create virtual machines on the remote resource that look and feel like their lab workstation or home machine, but are able to harness thousands of times the computing power
JPEG 2000
JPEG 2000 standard https://jpeg.org/jpeg2000/ JPEG 2000 (JP2) is an image compression standard and coding system.
JSON JavaScript Object Notation language http://www.json.org/ JSON is a lightweight data-interchange format. It is easy for humans to read and write. It is easy for machines to parse and generate. It is based on a subset of the JavaScript Programming Language, Standard ECMA-262 3rd Edition - December 1999. JSON is a text format that is completely language independent but uses conventions that are familiar to programmers of the C-family of languages, including C, C++, C#, Java, JavaScript, Perl, Python, and many others. These properties make JSON an ideal data-interchange language.
JSTOR
JSTOR
literature http://www.jstor.org/
JSTOR is a growing digital library of academic journals, books, and primary sources. Part of the ITHAKA family.
JSTOR Plant Science
JSTOR Plant Science
Global Plants
data aggregator http://about.jstor.org/global-plants
JSTOR Plant Science (now Global Plants) is an online environment that provides access to foundational content vital to plant science - plant type specimens, taxonomic structures, scientific literature, and related materials. This new environment includes over a million type specimens, paintings, drawings, correspondence, and supporting materials. By 2013, they expect to have over 2.2 million type specimens available, making JSTOR Plant Science the largest collection of its kind in the world. These materials are now truly global in scope representing over 200 partners in 50 countries on 5 continents.
JTS
Java Topology Suite
API http://tsusiatsoftware.net/jts/main.html
API for modelling and manipulating 2-dimensional linear geometry. It provides numerous geometric predicates and functions. JTS conforms to the Simple Features Specification for SQL published by the Open GIS Consortium.
KML Keyhole Markup Language language http://code.google.com/apis/kml/ Keyhole Markup Language (KML) is an XML notation for expressing geographic annotation and visualization within Internet-based, two-dimensional maps and three-dimensional Earth browsers. KML was developed for use with Google Earth, which was originally named Keyhole Earth Viewer. It was created by Keyhole, Inc, which was acquired by Google in 2004. KML is an international standard of the Open Geospatial Consortium. Google Earth was the first program able to view and graphically edit KML files. Other projects such as Marble have also started to develop KML support.
Kurator Kurator software http://wiki.datakurator.net/web/ Kurator is a project to develop a provenance-enabled Workflow Platform and Toolkit to Curate Biodiversity Data.
LBCC
North American Lichens and Bryophytes - Sensitive Indicators of Environmental Quality and Change data aggregator, TCN http://lichenportal.org/portal/
http://bryophyteportal.org/portal/
iDigBio summary
This project will image about 2.3 million North American lichen and bryophyte specimens from more than 60 collections to address questions of how species distributions change after major environmental events, both in the past and projected into the future.
LepNet
Lepidoptera of North America Network data aggregator, TCN Lepidoptera_of_North_America_Network Digitization TCN: Lepidoptera of North America Network: Documenting Diversity in the Largest Clade of Herbivores
LibXML
LibXML standard http://xmlsoft.org/
XML C parser and toolkit developed for the Gnome project.
Libraries of Life Libraries of Life: More to specimens than meets the eye software, education http://www.libraries-of-life.org/ Augmented reality specimen cards serve as an exciting, new education and outreach tool that aim to promote engagement and accessibility to biodiversity specimens, which largely remain hidden from public view in U.S. museums, universities, field stations, and other institutions. The Libraries of Life team is a collaboration between the U.S. National Science Foundation's National Resource for Advancing Digitization of Biodiversity Collections (iDigBio) and a growing number of Thematic Collections Networks (TCNs).
LifeDesks
LifeDesks
data management No website found
No longer functional. LifeDesks was intended for teams of taxonomists to facilitate easy and fast data sharing. Individuals or teams could create taxon-based checklists and taxon pages. Taxon pages may include descriptions, photographs, maps and bibliographies. The information could be readily shared with the Encyclopedia of Life to generate their species pages.
Lifemapper
Lifemapper visualization http://www.lifemapper.org/
http://lifemapper.acis.ufl.edu/lm/map/
Lifemapper uses all of the online geospatial species occurrence data to create distribution maps and, notably, goes one step further to predict where an individual species should exist based on where it is documented to live.
LifeWatch ESFRI Landmark LifeWatch data aggregator, data management, visualization http://www.servicecentrelifewatch.eu/ The LifeWatch Service Centre serves the EU biodiversity and ecosystem research community in its work to support the understanding and rational management of our ecosystems by policy makers, resource managers, the private sector and the general public. The Service Centre deals with the provision of services to the user community so as to facilitate the use of the infrastructure, provides information and supports with a particular focus to scientists, fosters user engagement in the services' development, draws new communities of interest for the infrastructure.
LINCAOCNET
Les Insectes Comestibles d'Afrique de L'Ouest et Centrale sur Internet
data aggregator http://gbif.africamuseum.be/lincaocnet/
Global access to knowledge about life on Earth.
Lucid Lucid software http://www.lucidcentral.com/ Lucid tools are powerful and highly flexible knowledge management software applications designed to help users with identification or diagnostic tasks.
Macaulay Library The Cornell Lab of Ornithology, Macaulay Library organization http://www.macaulaylibrary.org A multimedia resource for the study of animal behavior and biodiversity, with more than 175,000 audio and 60,000 video recordings documenting the behavioral diversity of birds and other animals. The organization also provides training, expert consultation, and equipment that enable scientists, educators, and nature enthusiasts to discover and record the natural world.
MaCC The Macrofungi Collection Consortium: Unlocking a Biodiversity Resource for Understanding Biotic Interactions, Nutrient Cycling and Human Affairs data aggregator, TCN http://mycoportal.org/portal/index.php
iDigBio summary
Scientists in the U.S. have been studying these fungi for the past 150 years, resulting in a legacy of approximately 1.4 million dried scientific specimens conserved in 35 institutions in 24 states. These institutions have now joined in an effort to digitize and share online all data associated with macrofungi specimens. The resulting resource will enable a national census of macrofungi, never before attempted, and will allow researchers to better understand the diversity of these organisms and the relationship between macrofungi and the organisms with which they form intimate relationships.
Magnolia grandiFLORA Magnolia grandiFLORA: The digital herbarium for Mississippi data aggregator http://www.mississippiplants.org/ Project Magnolia grandiFLORA is an effort to digitize herbaria throughout Mississippi and to provide scientific and educational resources to the citizens of Mississippi and researchers around the world.
MaM The Mid-Atlantic Megalopolis TCN The_Mid-Atlantic_Megalopolis Digitization TCN: The Mid-Atlantic Megalopolis: Achieving a greater scientific understanding of our urban world
MaNIS Mammal Networked Information System georeferencing http://www.manisnet.org/ With support from the National Science Foundation, seventeen North American institutions and their collaborators developed the Mammal Networked Information System. The original objectives of MaNIS were to 1) facilitate open access to combined specimen data from a web browser, 2) enhance the value of specimen collections, 3) conserve curatorial resources, and 4) use a design paradigm that can be easily adopted by other disciplines with similar needs. As an NSF-funded initiative, MaNIS achieves these objectives while avoiding the need for long-term, external maintenance of the network and centralized data management.
MANTIS MantisBT software http://www.mantisbt.org/ MantisBT is a free popular web-based bug tracking system. It is written in the PHP scripting language and works with MySQL, MS SQL, and PostgreSQL databases and a webserver. MantisBT has been installed on Windows, Linux, Mac OS, OS/2, and others. Almost any web browser should be able to function as a client. It is released under the terms of the GNU General Public License (GPL).
MapWindow GIS
MapWindow GIS Open Source Project
visualization http://www.mapwindow.org/ The MapWindow GIS project includes a free and open source desktop geographic information system (GIS) with an extensible plugin architecture; a GIS ActiveX control; and C# GIS programmer library called DotSpatial.
MapReduce MapReduce software https://www-01.ibm.com/software/data/infosphere/hadoop/mapreduce/ Hadoop MapReduce is a programming model and software framework for writing applications that rapidly process vast amounts of data in parallel on large clusters of compute nodes.
MapsData MapsData data management, visualization http://www.mapsdata.co.uk/online-file-converter/ Mapsdata lets you visualize data on a map and share it with others in one easy step. You can map your customers, map economic data, map environmental data, or anything that has latitude, longitude, a coordinate, ZIP code or postcode. Provides an online converter, converting files to KML, or batch conversion of postcodes, UTM and other co-ordinate formats.
MBB
Moss Bug Base nomenclature, taxonomy http://rameau.snv.jussieu.fr/cgi-bin/coleorrhyncha.pl The MBB – Moss Bug Base is a taxonomic database of extant and fossil taxa of Coleorrhyncha. It contains information on taxonomy (accepted names and synonyms), nomenclature, bibliography and distribution as basis for further studies on these insects. It is intended to add information on host relationships for extant taxa and on stratigraphy for fossil taxa in future releases.
Mendeley
Mendeley literature https://www.mendeley.com/ Mendeley is a combination of a desktop application and a website which helps you manage, share and discover both content and contacts in research.
MIBBI
Minimum Information for Biological and Biomedical Investigations
standards http://mibbi.sourceforge.net/
MIBBI is managed by a mix of community representatives and invited domain experts. The Portal exists to promote extant projects to the wider community (and each other) and to link to relevant resources. The Foundry is a project to synthesize reporting guidelines from various communities into a suite of orthogonal standards. Discussion lists, teleconferences, open-access development and meetings ensure openness and accountability.
MiCC The Microfungi Collections Consortium: A Networked Approach to Digitizing Small Fungi with Large Impacts on the Function and Health of Ecosystems data aggregator, TCN http://www.microfungi.org/
iDigBio summary
The Microfungi Collections Consortium (MiCC) is a collaborative effort among 38 US institutions to digitize specimen label data from 2.3 million North American microfungi specimens and make these data available online to the broader community through the MyCoPortal website.
MOBOT
Missouri Botanical Garden
institution http://www.missouribotanicalgarden.org/
Oldest botanical garden in continuous operation and a National Historic Landmark. Home to Tropicos.
ModestR
ModestR software, visualization http://www.ipez.es/ModestR/
ModestR is a software tool aimed to provide academic community (particularly people involved in Ecology and biodiversity management) with a powerful but easy-to-use tool for working with species distribution maps and taxonomic data.
MOL
Map of Life visualization http://www.mol.org/
http://www.mappinglife.org/
Map of Life aims to support effective and global biodiversity education, monitoring, research and decision-making by assembling and integrating a wide range of knowledge about species distributions and their dynamics over time. This website aims to be a complete resource for convergent evolution. It allows exploration of the ways that similar adaptive solutions have repeatedly evolved from unrelated starting points and identifies hundreds of examples of convergence.
Morphbank Morphbank :: Biological Imaging data aggregator http://www.morphbank.net/index.php Morphbank :: Biological Imaging is a continuously growing database of images that scientists use for international collaboration, research and education. Images deposited in Morphbank :: Biological Imaging document a wide variety of research including: specimen-based research in comparative anatomy, morphological phylogenetics, taxonomy and related fields focused on increasing our knowledge about biodiversity. The project receives its main funding from the Biological Databases and Informatics program of the National Science Foundation (Grant DBI-0446224). Morphbank :: Biological Imaging was established in 1998 by a Swedish-Spanish-American group of entomologists and is currently housed at the School of Computational Science (SCS) at Florida State University. The project has grown immensely since its beginnings and presently includes a team of 15 biologists, computer scientists, and information scientists who are working on developing the software. Morphbank :: Biological Imaging is dedicated to using open-source software and is a Fair Use Web Site. The software used in the current Morphbank :: Biological Imaging system includes PHP, ImageMagick, MySQL, Apache, Java, and JavaScript.
Morphobank Morphobank: Homology of phenotypes over the web data aggregator http://morphobank.org/ MorphoBank is a web application providing an online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). One can think of MorphoBank as two databases in one: one that permits researchers to upload images and affiliate data with those images (labels, species names, etc.) and a second database that allows researchers to upload morphological data and affiliate it with phylogenetic matrices. In both cases, MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived.
MorphoSource MorphoSourc data aggregator http://morphosource.org/ MorphoSource is a project-based data archive that allows researchers to store and organize, share, and distribute their own 3D data. Furthermore any registered user can immediately search for and download 3D morphological data sets that have been made accessible through the consent of data authors.
Morphster
Morphster ontology http://ribs.csres.utexas.edu/morphster/
Ontology management tool. Morphster.org's goal is to develop a demonstration prototype of a service-oriented architecture enabling and supporting morphologically based phylogenetic studies.
MHC
The Macroalgal Herbarium Consortium: Accessing 150 Years of Specimen Data to Understand Changes in the Marine/Aquatic Environment data aggregator, TCN http://macroalgae.org
iDigBio summary
Macroalgae are the foundation of marine, estuarine and freshwater benthic ecosystems providing food, substrata and protection for a myriad of other aquatic organisms. Many macroalgal species are sensitive to environmental change. The data provided through the portal will allow researchers and the public at large determine how macroalgal biodiversity and our aquatic ecosystems have changed over the past 150 years as a result of climate change, bioinvasions, and a wide range of human activity.
mx mx data management http://mx.phenomix.org/index.php/Main_Page
http://mx.phenomix.org/index.php/Features
Succeeded by TaxonWorks. mx (preferred reference all lowercase) is a Ruby-based platform that consists of a Ruby on Rails (RoR) application and various supporting gems/libraries. Initially conceived and developed as a collaborative web-based content management system for biosystematists mx now has a wide range of functionality much of which can broadly categorized under the umbrella of biodiversity informatics. Runs web-based, can run locally as well.
MySQL
MySQL data management http://www.mysql.com/
Open Source relational database
NameBank
ClassificationBank
NameBank
ClassificationBank
nomenclature, taxonomy http://ubio.org/
NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. NameBank defines and serves nomenclatural concepts as XML objects.
ClassificationBank is a "taxonomic concept server" focused on accurately representing subjective taxonomic opinion in the form of classifications and checklists. These classifications may vary considerably in both scope and precision. ClassificationBank draws upon NameBank elements to form the uBio Taxonomic Name Server.
National Biodiversity Data Center National Biodiversity Data Center data aggregator http://www.biodiversityireland.ie/ The National Biodiversity Data Centre is a national organisation that collates, manages and analyses and disseminates data on Ireland’s biodiversity.
NatureServe NatureServe community, data aggregator http://www.natureserve.org/ NatureServe's mission is to provide the scientific basis for effective conservation action. A Network Connecting Science with Conservation.
NCSA The National Center for Supercomputing Applications cloud computing http://www.ncsa.illinois.edu/ The National Center for Supercomputing Applications (NCSA), located at the University of Illinois at Urbana-Champaign, provides powerful computers and expert support that help thousands of scientists and engineers across the country improve our world. With the computing power available at NCSA, researchers simulate how galaxies collide and merge, how proteins fold and how molecules move through the wall of a cell, how tornadoes and hurricanes form, and other complex natural and engineered phenomena.
NEOMAP
Neogene Mammal Mapping Portal visualization http://www.ucmp.berkeley.edu/neomap/use.html NEOMAP is an initial stage in a distributed database system for paleomammalogy, designed to link different, free-standing databases (Miocene Mammal Mapping Project [MIOMAP] and FAUNMAP) by a common access portal. These two linked datasets now provide point-occurrence data for all published late-Oligocene through Holocene mammals in the USA, and for many Quaternary localities in Canada. Interactively search for, retrieve, and analyze data from the MIOMAP and FAUNMAP databases, either separately or in concert.
NEON National Ecological Observatory Network data management, data repository, project http://www.neonscience.org/ NEON is a continental-scale ecological observation system for examining critical ecological issues. It is designed to gather and synthesize data on the impacts of climate change, land use change and invasive species on natural resources and biodiversity. Data will be collected from 106 sites (60 terrestrial, 36 aquatic and 10 aquatic experimental) across the U.S. (including Alaska, Hawaii and Puerto Rico) using instrument measurements and field sampling. The sites have been strategically selected to represent different regions of vegetation, landforms, climate, and ecosystem performance. NEON will combine site-based data with remotely sensed data and existing continental-scale data sets (e.g., satellite data) to provide a range of scaled data products that can be used to describe changes in the nation’s ecosystem through space and time.
NeotomaDB Neotoma Database data aggregator http://www.neotomadb.org/ Neotoma Paleoecology Database and Community is an online hub for data, research, education, and discussion about paleoenvironments.
NESCent National Evolutionary Synthesis Center organization http://www.nescent.org/ The National Evolutionary Synthesis Center (NESCent) is a nonprofit science center dedicated to cross-disciplinary research in evolution. NESCent is jointly operated by Duke University, The University of North Carolina at Chapel Hill, and North Carolina State University, and is sponsored by the National Science Foundation. NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries.
NEVP Mobilizing New England Vascular Plant Specimen Data to Track Environmental Change data aggregator, TCN http://nevp.org/,br.iDigBio summary NEVP will provide data to support studies of the nature and consequences of environmental change in the New England region over the last three centuries. This project will digitally capture specimen data and images from about 1.3 million vascular plant specimens housed in 15 large to small herbaria located across the region and then share online the resulting images and data.
NIBA Network Integrated Biocollections Alliance community http://digbiocol.wordpress.com/ Succeeded by BCoN. An alliance that developed the strategic plan from which the National Science Foundation's Advancing Digitization of Biological Collections (ADBC) was launched.
NIMBUS Nimbus Platform and Infrastructure cloud computing http://www.nimbusproject.org/ An integrated set of tools that deliver the power and versatility of infrastructure clouds to scientific users. Nimbus Platform allows you to combine Nimbus, OpenStack, Amazon, and other clouds. Nimbus Infrastructure is an open source EC2/S3-compatible Infrastructure-as-a-Service implementation specifically targeting features of interest to the scientific community such as support for proxy credentials, batch schedulers, best-effort allocations, and others.
NLP Natural Language Processing computer science, software, standard https://en.wikipedia.org/wiki/Natural_language_processing Natural language processing (NLP) is a field of computer science, artificial intelligence, and computational linguistics concerned with the interactions between computers and human (natural) languages.
Notes from Nature
Notes from Nature citizen science, transcription https://www.notesfromnature.org/ Transcription of museum records using a Zooniverse citizen science platform.
NSCA Natural Science Collections Alliance community http://www.nscalliance.org The Natural Science Collections Alliance is a Washington, D.C.-based nonprofit association that supports natural science collections, their human resources, the institutions that house them, and their research activities for the benefit of science and society. Members are part of an international community of museums, botanical gardens, herbariums, universities and other institutions that house natural science collections and utilize them in research, exhibitions, academic and informal science education, and outreach activities.
NSF
National Science Foundation Federal Agency http://www.nsf.gov/ National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering.
NSII National Specimen Information Infrastructure data aggregator http://www.nsii.org.cn/ Biodiversity e-Science Infrastructure in China. Chinese Academy of Sciences.
OBIS Ocean Biogeographic Information System data aggregator http://www.iobis.org/ OBIS allows users to search marine species datasets from all of the world's oceans.
OBO Foundry
OBO Foundry community, data repository, ontology http://www.obofoundry.org/ The OBO Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles.
OCR Optical Character Recognition software https://en.wikipedia.org/wiki/Optical_character_recognition Optical Character Recognition, or OCR, is a technology that enables you to convert different types of documents, such as scanned paper documents, PDF files or images captured by a digital camera into editable and searchable data.
OCRopus
OCRopus software http://code.google.com/p/ocropus/
Document analysis and OCR system, featuring pluggable layout analysis, pluggable character recognition, statistical natural language modeling, and multi-lingual capabilities.
ODBC Open Database Connectivity language https://en.wikipedia.org/wiki/Open_Database_Connectivity ODBC is a standard C interface for accessing database management systems (DBMS). The designers of ODBC aimed to make it independent of database systems and operating systems. An application can use ODBC to query data from a DBMS, regardless of the operating system or DBMS it uses. ODBC accomplishes DBMS independence by using an ODBC driver as a translation layer between the application and the DBMS. The application uses ODBC functions, and the driver passes the query to the DBMS.
OA
Open Annotation
Open Annotation Data Model data management, standard http://www.openannotation.org/spec/core/ The Open Annotation Core Data Model specifies an interoperable framework for creating associations between related resources, annotations, using a methodology that conforms to the Architecture of the World Wide Web. Open Annotations can easily be shared between platforms, with sufficient richness of expression to satisfy complex requirements while remaining simple enough to also allow for the most common use cases, such as attaching a piece of text to a single web resource.
Open Atrium
Atrium
Open Atrium software http://www.openatrium.com/
https://www.drupal.org/project/openatrium
Intranet and team collaboration portal package based on Drupal.
openModeller
openModeller
software http://openmodeller.sourceforge.net/ openModeller provides a flexible, robust, cross-platform environment to carry out ecological niche modeling experiments.
Open Refine
Open Refine software http://openrefine.org/ Formerly Google Refine, a free, open source, powerful tool for working with messy data.
OpenStack Open Stack Cloud Manager cloud computing http://www.openstack.org/ OpenStack is an IaaS cloud computing project by Rackspace Cloud and NASA. Currently more than 120 companies have joined the project among which are Citrix Systems, Dell, AMD, Intel, Canonical, SUSE Linux, HP, and Cisco. It is free open source software released under the terms of the Apache License. OpenStack integrates code from NASA's Nebula platform as well as Rackspace's Cloud Files platform.
Open Tree of Life Open Tree of Life API, data aggregator http://opentreeoflife.org/
http://opentreeoflife.github.io/
Open Tree of Life aims to construct a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data.
OpenUp!
Opening up Europe’s natural history heritage for Europeana
data aggregator http://open-up.eu/
Project which would provide this multimedia content with specific biological and multilingual functionality to a wide European cultural audience through EUROPEANA was proposed.
OpenZoom
OpenZoom software https://github.com/openzoom No longer being maintained or supported.
Oracle
Oracle data management http://www.oracle.com/technetwork/database/enterprise-edition/downloads/index.html
Commercial high end data management system.
ORCiD ORCiD identifier http://orcid.org/ ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized.
ORNIS Ornithological Information System data aggregator http://www.ornisnet.org/home Superceeded by VertNet. Over 5 million bird specimens are housed in North American collections, documenting the composition, distribution, ecology, and systematics of the world's estimated 10,000-16,000 bird species. Millions of additional observational records are held in diverse data sets. ORNIS addresses the urgent call for increased access to these data in an open and collaborative manner, and involves development of a suite of online software tools for data analysis and error-checking. This project, funded by the National Science Foundation, expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Improved access to avian data sets will allow predictive uses to reveal patterns and processes of evolutionary and ecological phenomena that have not been apparent heretofore. Along with similar infrastructures for other vertebrate groups, it also will enable detailed and synthetic knowledge of the earth's biodiversity for tracking climate change, emerging diseases (e.g., West Nile Virus), and other conservation challenges for species in the 21st century.
OWL Web Ontology Language language http://en.wikipedia.org/wiki/Web_Ontology_Language The Web Ontology Language (OWL) is a family of knowledge representation languages for authoring ontologies.
PaleoCore
PaleoCore: Towards a Data Standard for Paleoanthropology data aggregator, standards http://paleocore.org/ PaleoCore is an initiative to develop data standards and digital infrastructure for paleoanthropology. PaleoCore addresses the common scientific challenge of merging results from independent research programs.
PaleoDb
Paleobiology Database
data aggregator http://paleodb.org
Provide global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.
PaleoNICHES
Digitizing Fossils to Enable New Syntheses in Biogeography - Creating a PALEONICHES
data aggregator, TCN http://www.digitalatlasofancientlife.org/
iDigBio summary
The Paleoniches project will digitize nearly 450,000 specimens belonging to 900 species from several museums throughout the U.S. and will focus on three different time periods in the history of life: the Ordovician, Pennsylvanian, and Neogene. We will create on line digital atlases illustrating and describing these fossils and providing maps showing where they can be found and an 'app' so these atlases can be used on handheld devices out in the field.
PaleoPortal The Paleontology Portal education http://www.paleoportal.org/ This site is a resource for anyone interested in paleontology, from the professional in the lab to the interested amateur scouting for fossils to the student in any classroom. Many resources are gathered into this single entry "portal" to paleontological information on the Internet.
PEN Partner to Existing Network ADBC, TCN https://www.nsf.gov/pubs/2015/nsf15576/nsf15576.htm/ Proposals to partner with and further the efforts of ongoing NSF-funded TCNs. The new partners must increase the number of specimens digitized in the ongoing project and fill gaps not addressed by the specimens in the existing TCN.
Pensoft Pensoft publishing http://pensoft.net/ Pensoft is an independent academic publishing company, well known worldwide for its innovations in the field of semantic publishing, as well as for its cutting-edge publishing tools and workflows. Pensoft publishes notable biodiversity journals such as Biodiversity Data Journal, BioRisk, MycoKeys, PhytoKeys and Zookeys.
PeriodO PeriodO gazetteer http://perio.do/ A gazetteer of period definitions of historical, art-historical, and archaeological periods for linking and visualizing data.
PhenoBlast PhenoBlast data aggregator http://aquila.bio.nyu.edu/cgi-bin/rnaidb/browse/phenoblast.cgi A database of phenotypic signatures, providing access to results from the RNAi Database interference studies in Caenorhabditis elegans.
Phenoscape Phenoscape software http://phenoscape.org A scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions. In other words, making descriptive observations amenable to large-scale computation so that they can be subjected to computational data integration and knowledge discovery techniques in ways similarly powerful as the traditional techniques used for numeric, quantitative observations.
Photoshop Adobe Photoshop software http://www.adobe.com/products/photoshop.html Highly sophisticated image editing software, the gold standard from Adobe. Latest version (2016) is Adobe Photoshop CC.
Photosimile Photosimile hardware, software http://ortery.com/products/photosimile5000-professional-multi-row-360-degree-photography-device.php A 28" x 28" x 28" daylight-balanced photography studio that includes a compatible Canon Rebel SLR camera and powerful system control software, Photosimile 5000 facilitates the creation of professional still photos, 360-degree, hemispherical and full spherical product animations.

Driven by software, the system allows users to control all camera and studio settings. This is a fully automated, precise image capture and efficient image processing tool.

Phylocode Phylocode taxonomy https://www.ohio.edu/phylocode/ The PhyloCode is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny. The PhyloCode will go into operation in a few years, but the exact date has not yet been determined.
Phylojive Phylogeny Javascript Information Visualiser and Explorer visualization http://phylojive.acis.ufl.edu/PhyloJive/
https://github.com/TRIN/phyloJIVE
The growing catalogue of online biodiversity data sources has reached a scale where data integration and mashups can be truly useful. Information about species is being aggregated at national and international scales. PhyloJIVE (Phylogeny Javascript Information Visualiser and Explorer) is one such mashup placing biodiversity web-services into an evolutionary context.
Phylolink Phylolink visualization http://phylolink.ala.org.au/ Phylolink is a collection of tools through which biodiversity can be explored from a phylogenetic (or tree of life) perspective. At the core of these tools is the ability to easily intersect a phylogenetic tree with species occurrence records, environmental data, and species character information. The result is powerful ways of combining data to generate flexible and customisable visualisations, profiles and metrics for biodiversity. Phylolink builds upon PhyloJIVE, which was developed by CSIRO, the Taxonomy Research and Information Network (TRIN), and the Centre for Australian National Biodiversity Research (CANBR).
Picturae Picturae digitization https://picturae.com/uk/ Mass digitization of herbarium sheets, negatives, 2D sheets etc.
Planting Science
Planting Science education http://www.plantingscience.org/
Learning and research resource, bringing together students, plant scientists, and teachers from across the nation.
PLANTS Database
USDA-NRCS PLANTS Database
nomenclature http://plants.usda.gov
Provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. It includes names, plant symbols, checklists, distributional data, species abstracts, characteristics, images, crop information, automated tools, onward Web links, and references.
Plazi
Plazi
literature, publisher http://plazi.org/ Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. Maintains a digital taxonomic literature repository to enable archiving of taxonomic treatments. Participates in the development of new models for publishing taxonomic treatments in order to maximize interoperability with other relevant cyberinfrastructure components (e.g., name servers, biodiversity resources, etc.). Advocates and educates about the vital importance of maintaining free and open access to scientific discourse and data
PlutoF
PlutoF
cloud computing, data repository http://plutof.ut.ee/
Provides cloud database and computing services for the taxonomical, ecological, phylogenetical, etc. research. PlutoF enables users to create, manage, share, analyse and publish biology-related databases and projects.
PNW Herbaria
Consortium of Pacific Northwest Herbariabr> data aggregator http://www.pnwherbaria.org/
The ultimate goal of the Consortium of Pacific Northwest Herbaria is to provide the scientific community, land management agencies, conservation organizations, and the interested public with a single online access point to the wealth of existing and emerging information about the Pacific Northwest flora.
PostGIS
PostGIS data management http://postgis.net/ Adds support for geographic objects to the PostgreSQL object-relational database. Required to implement map server and other spatial applications/libraries in PostgreSQL.
PostgreSQL
PostgreSQL data management http://www.postgresql.org
Open Source relational database.
prefixcommons prefixcommons identifier http://www.prefixcommons.org/
https://github.com/prefixcommons
Harmonizing identifier prefixes and namespace paths across the lifesciences
pro-iBiosphere pro-iBiosphere data aggregator, project http://www.pro-ibiosphere.eu Ended in 2014. Coordination and policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability and Dissemination - Biodiversity information constitutes an important source of knowledge for many disciplines. For example, it is fundamental to supporting conservation and for understanding the potential impacts of climate change. External and internal factors call for an urgent modernization of the production and accessibility of these data, information and knowledge. These external factors include the need for biodiversity data to support decisions for regional and taxon focused conservation. Internal factors are a consequence of the opportunities of the digital revolution, and the need to reconcile the escalating volume of data with the requirement to curate it by a fixed number of taxonomists. The pro-iBiosphere project has been launched for a period of two years (September 1st, 2012 to August 31st, 2014), with the goal of addressing technical and semantic interoperability challenges and preparing the ground for the creation of a system for intelligent management of biodiversity knowledge which will improve the present system of taxonomic literature.
PROJ.4
PROJ.4 - Cartographic Projections Library visualization https://github.com/OSGeo/proj.4/wiki
Cartographic Projections library for PostgreSQL. Required to implement map server and other spatial applications/libraries in PostgreSQL.
Psyl'list Psyl'list data aggregator http://www.hemiptera-databases.com/psyllist/ Psyl'list is an online database dedicated to jumping plant lice. The aim of this ongoing project is primarily to make up for the absence of world catalogue for Psylloidea, in organizing taxonomic data and providing easy access to the published taxonomic data that is already available but scattered in the literature. Informations about geographical distribution and host-plants are partly available for some species and will be complemented continuously.
Python Python language https://www.python.org/ Python is a widely used high-level, general-purpose, interpreted, dynamic programming language that lets you work quickly and integrate systems more effectively.
QGIS
Quantum GIS visualization http://www.qgis.org/en/site/ Open source GIS.
R R Project for Statistical Computing software https://www.r-project.org/ R is a free software language and environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
Raintree
Tropical Plant Database
data aggregator http://www.rain-tree.com/plants.htm
Provides accurate and factual information on the important plants of the Amazon Rainforest. Last updated 2013.
RDA Research Data Alliance organization https://rd-alliance.org/ The Research Data Alliance (RDA) builds the social and technical bridges that enable open sharing of data. The RDA vision is researchers and innovators openly sharing data across technologies, disciplines, and countries to address the grand challenges of society.
RDF Resource Description Framework language http://www.w3.org/RDF/ RDF is a standard model for data interchange on the Web. RDF has features that facilitate data merging even if the underlying schemas differ, and it specifically supports the evolution of schemas over time without requiring all the data consumers to be changed. RDF extends the linking structure of the Web to use URIs to name the relationship between things as well as the two ends of the link (this is usually referred to as a triple). Using this simple model, it allows structured and semi-structured data to be mixed, exposed, and shared across different applications. This linking structure forms a directed, labeled graph, where the edges represent the named link between two resources, represented by the graph nodes. This graph view is the easiest possible mental model for RDF and is often used in easy-to-understand visual explanations.
Recorder 6
Recorder 6 data management http://jncc.defra.gov.uk/default.aspx?page=4592
Tool for those entering, collating and exchanging records of species and habitats. Fast and accurate import of data from a variety of sources and different formats, flexible reporting framework, and mapping facilities to enter, view and query data.
Re:discovery Re:discovery Software data management, software http://www.rediscov.com/ Re:discovery is a museum and archival collections management software package that documents and maintains object and digitally-based collections. An internet component allows institutions to share their collections with the public. Re:discovery may be used by archivists, registrars, collections managers, curators, archaeologists, slide librarians, educators, and researchers. It is currently in use at close to 500 sites in the United States and Canada.
Redmine Redmine software http://www.redmine.org/ Redmine is a flexible project management web application. Written using the Ruby on Rails framework, it is cross-platform and cross-database.
ReFindit ReFindit API, literature, taxonomy http://refindit.org/ ReFindit provides an easy search function, based on a simple interface, which also collates and sorts the results from the search engines for presentation to the user to read and with the option to refine the results presented or submit a new search.
REST REpresentational State Transfer standard http://en.wikipedia.org/wiki/Representational_state_transfer Representational state transfer (REST) is a style of software architecture for distributed hypermedia systems such as the World Wide Web. The REST architectural style was developed in parallel with HTTP/1.1, based on the existing design of HTTP/1.0. The largest implementation of a system conforming to the REST architectural style is the World Wide Web. REST exemplifies how the Web's architecture emerged by characterizing and constraining the macro-interactions of the four components of the Web, namely origin servers, gateways, proxies, and clients, without imposing limitations on the individual participants. As such, REST essentially governs the proper behavior of participants.
ridigbio ridigbio language https://github.com/iDigBio/ridigbio An interface to iDigBio's API
RMCA
Royal Museum for Central Africa
institution http://www.africamuseum.be
As a research institute, the RMCA leads several scientific projects. Some 85 scientists and 150 students and trainees conduct research on an ever-changing continent of countless communities, lush forests, stark deserts, and unrivalled wildlife.
ROpenSci ROpenSci data analysis, software, visualization https://ropensci.org/ rOpenSci creates R packages that allow access to data repositories through the R statistical programming environment.
RStudio RStudio software https://www.rstudio.com/ A powerful and productive user interface for R. It's free and open source, and works great on Windows, Mac, and Linux.
SCAN Symbiota Collections of Arthropods Network data aggregator, TCN http://scan1.acis.ufl.edu/
iDigBio summary
The Symbiota Collections of Arthropods Network (SCAN) brings together 10 diverse arthropod collections at universities and museums throughout the Southwest to create a virtual network of ground dwelling arthropods which are notably responsive to temporal and spatial environmental changes.
Scratchpads Scratchpads software http://scratchpads.eu/ Scratchpads is a social networking tool to build, share, and publish information on the diversity of life. It is part of the EU funded ViBRANT project, and the NERC funded e-Monocot project. As part of these initiatives a new version of the Scratchpads will be released in January 2012.
SEINET
Southwest Environmental Information Network
data aggregator http://swbiodiversity.org/seinet/
Gateway to distributed data resources of interest to the environmental research community in Arizona and beyond.
SEPASAL
Survey of Economic Plants for Arid and Semi-Arid Lands
data aggregator http://www.kew.org/ceb/sepasal/
Database and enquiry service about useful "wild" and semi-domesticated plants of tropical and subtropical drylands, developed and maintained at the Royal Botanic Gardens, Kew.
SERNEC
SouthEast Regional Network of Expertise and Collections
The Key to the Cabinets: Building and Sustaining a Research Database for a Global Biodiversity Hotspot
data aggregator, TCN http://sernec.appstate.edu/
iDigBio summary
The current project will allow the SERNEC group to make data available for over 3 million specimens using the latest photography and information capture tools and to engage citizen scientists and students to assist in transcribing and georeferencing this large dataset. The research generated through this project can help regional planners, land managers and communities to manage their natural resources in our ever-changing environment.
SiB
Sistema de información sobre Biodiversidad de Colombia data aggregator http://www.sibcolombia.net/web/sib/home The SIB is a country initiative which aims to provide free access to information on biological diversity in Colombia for building a sustainable society.
SilverCollection SilverCollection data management, software http://www.silverbiology.com/products/silvercollection/ SilverCollection is an interactive web portal for herbaria and other biological collections. It is a cliet-specific customized application for online access to specimen data and images.
SilverLining
Silver Lining Systems hardware http://silverlining-systems.com/ Silver Lining Systems delivers both complete servers and the fabric technologies to design or build your own scale-out fabric-connected infrastructure.
SOAP Simple Object Access Protocol protocol http://en.wikipedia.org/wiki/SOAP SOAP is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks. It relies on Extensible Markup Language (XML) for its message format, and usually relies on other Application Layer protocols, most notably Hypertext Transfer Protocol (HTTP) and Simple Mail Transfer Protocol (SMTP), for message negotiation and transmission. SOAP can form the foundation layer of a web services protocol stack, providing a basic messaging framework upon which web services can be built.
Spark Apache Spark cluster computing http://spark.apache.org/ Apache Spark™ is a fast and general engine for large-scale data processing.
SPARQL
SPARQL language http://www.w3.org/TR/rdf-sparql-query/ SPARQL is an RDF query language, that is, a query language for databases, able to retrieve and manipulate data stored in Resource Description Framework format.
Species 2000
Species 2000 taxonomy http://sp2000.org/
Species 2000 is a "federation" of database organisations working closely with users, taxonomists, and sponsoring agencies. Its goal is to create a validated checklist of all the world's species (plants, animals, fungi and microbes) by bringing together an array of global species databases covering each of the major groups of organisms. The programme in partnership with the Integrated Taxonomic Information system (ITIS) of North America currently produces the Catalogue of Life, which is used by the Global Biodiversity Information Facility (GBIF), and Encyclopedia of Life (EoL) as the taxonomic backbone to their web portals.
speciesLink speciesLink data aggregator http://splink.cria.org.br speciesLink is a distributed system that integrates information in real-time primary data from scientific collections. The system was developed thanks to the support of institutions: FAPESP, GBIF, JRS Foundation, MCT, CNPq, FINEP and CRIA . The goal of the network is to link species integrate specie and specimen data available in natural history museums, herbaria and culture collections, making it openly and freely available on the Internet. Tools are being developed to help interoperability, integration, visualization, and data cleaning.
Specify Specify data management http://specifysoftware.org/content/welcome-specify-6 The NSF-funded Specify Software Project offers Specify 6.5 and allied applications for museum and herbarium research data processing. Specify 6 handles specimen information for computerizing collection holdings, for tracking specimen and tissue management transactions, and for mobilizing species occurrence data to the Internet. Specify runs on Windows, Mac OS X, and Linux computers; it is free and open source licensed. Specify 6.5 was released in September, 2013.
SPNHC
Society for the Preservation of Natural History Collections organization
http://www.spnhc.org/
The Society for the Preservation of Natural History Collections [SPNHC] is an international society whose mission is to improve the preservation, conservation and management of natural history collections to ensure their continuing value to society. SPNHC takes a leading role in promoting collections care issues to the academic community, governments, and the general public. Our members are dedicated to training and mentoring the next generation of collections professionals.
SQL Structured Query Language language http://en.wikipedia.org/wiki/SQL SQL is a programming language designed for managing data in relational database management systems (RDBMS). Originally based upon relational algebra and tuple relational calculus, its scope includes data insert, query, update and delete, schema creation and modification, and data access control. SQL became a standard of the American National Standards Institute (ANSI) in 1986, and of the International Organization for Standards (ISO) in 1987. Since then the standard has been enhanced several times with added features. However, issues of SQL code portability between major RDBMS products still exist due to lack of full compliance with, or different interpretations of the standard.
SQLite SSQLite data management, software https://www.sqlite.org/ SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine. SQLite is the most widely deployed database engine in the world. The source code for SQLite is in the public domain.
STEM Science, Technology, Engineering, and Mathematics Coalition community http://www.stemedcoalition.org/ The Science, Technology, Engineering, and Mathematics (STEM) Education Coalition works to support STEM programs for teachers and students at the U. S. Department of Education, the National Science Foundation, and other agencies that offer STEM related programs. The STEM Education Coalition represents all sectors of the technological workforce, from knowledge workers, to educators, to scientists, engineers, and technicians. The participating organizations of the STEM Education Coalition are dedicated to ensuring quality STEM education at all levels.
SYMBIOTA
Symbiota Software Project
data aggregator, data management http://symbiota.org
The Symbiota Software Project is working toward building a library of webtools to aid biologists in establishing specimen-based virtual floras and faunas. Symbiota web tools strive to integrate biological community knowledge and data in order to synthesize a network of databases and tools that will aid in increasing our overall environmental comprehension.
SYNTHESYS
Synthesis of Systematics Resources
project http://www.synthesys.info/
4 year project which began in September 2009 comprises 20 European natural history museums, Universities and botanic gardens. It aims to create an integrated European infrastructure for researchers in the natural sciences. SYNTHESYS is split into three activities: Access, Networking and Joint Research Activities.
SysTax
SysTax data management http://www.biologie.uni-ulm.de/systax/index.html
SysTax database system comprises: concept-based botanical and zoological systematics, literature, Botanic Gardens, Herbaria, and Zoological Collections, addresses, multimedia data (pictures, sound files and video sequences).
TACC Texas Advanced Computing Center cloud computing, organization http://www.tacc.utexas.edu/ The Texas Advanced Computing Center (TACC) at The University of Texas at Austin is one of the leading centers of computational excellence in the United States. The center's mission is to enable discoveries that advance science and society through the application of advanced computing technologies.
TAPIR TDWG Access Protocol for Information Retrieval protocol http://www.tdwg.org/activities/tapir/ Largely superseded by IPT. TAPIR specifies a standardized, stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure. TAPIR combines and extends features of the BioCASe and DiGIR protocols to create a new and more generic means of communication between client applications and data providers using the Internet. TapirDotNET implements the TAPIR protocol (stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure). TapirLink Implements the TAPIR protocol (stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure). Only tabular (denormalized) data can be served.
Taxonworks Taxonworks data management, software http://taxonworks.org/
https://github.com/SpeciesFileGroup/TaxonWorks
TaxonWorks is a long-term effort of the Species File Group to facilitate biodiversity informatics.
TCN
Thematic Collections Network project https://www.idigbio.org/content/thematic-collections-networks A network of collaborative institutions with a strategy for digitizing information that addresses a particular research theme. Funded by the National Science Foundation's Advancing Digitization of Biological Collections (ADBC) program. TCNs are responsible for conducting the digitization of collections. TCNs are charged with defining and delineating subprojects for technology development or content generation; identifying deliverable goals, metrics for assessment, and specific needs for community support; providing technical support; and strengthening communications and outreach to other collections.
TDWG Biodiversity Information Standards Taxonomic Database Working Group organization http://www.tdwg.org/ TDWG is a not for profit scientific and educational association that is affiliated with the International Union of Biological Sciences. TDWG was formed to establish international collaboration among biological database projects. TDWG promoted the wider and more effective dissemination of information about the world's heritage of biological organisms for the benefit of the world at large. Biodiversity Information Standards (TDWG) now focuses on the development of standards for the exchange of biological/biodiversity data.
Tesseract
Tesseract OCR https://github.com/tesseract-ocr/
OCR engine developed at HP (1985-1995), one of the top 3 engines in the 1995 UNLV Accuracy test.
The Field Book Project The Field Book Project data aggregator http://www.mnh.si.edu/rc/fieldbooks/ The Field Book Project's overall mission is to create one online location for scholars and others to visit when searching for field books and other field research materials. Funded by the Council for Library and Information Resources (CLIR), the Project is a joint initiative between the Smithsonian National Museum of Natural History and the Smithsonian Institution Archives.
TNRS Taxonomic Name Resolution Service nomenclature http://tnrs.iplantcollaborative.org/
Service that receives taxonomic names, and reports back the best name according to an authoritative source, in this case TROPICOS. The ability to 'reconcile' alternative names for the same species and return a preferred name can 'normalize' taxonomy in biodiversity databases that currently use different names.
TOLKIN The Tree of Life Knowledge and Information Network data management http://www.tolkin.org/ TOLKIN is an information management and analytical web application to provide informatics support for phylodiversity and biodiversity research projects. As a web-based application, TOLKIN is able to support collaborative projects by providing shared access to a variety of data on voucher specimens, taxonomy, bibliography, morphology, DNA samples, and sequences.
TORCH Texas Oklahoma Regional Consortia of Herbaria community http://www.torcherbaria.org/ The Texas Oklahoma Regional Consortium of Herbaria was developed to advocate for and to organize herbaria in Texas and Oklahoma.
tranScriptorium tranScriptorium transcription http://transcriptorium.eu/ tranScriptori
Transkribus Transkribus software, transcription https://transkribus.eu/Transkribus/ Transkribus is a comprehensive Transcription and Recognition Platform (TRP) consisting of an expert tool (Transkribus), a webinterface (http://transkribus.eu/) and several cloud services. The main objective of Transkribus is to support users who are engaged in the transcription of printed or handwritten documents, namely humanities scholars, archives, volunteers - and computer scientists.
TreeBASE
TreeBASE data aggregator http://www.treebase.org
Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. Relational database designed to manage and explore information on phylogenetic relationships.
Trifacta Trifacta data management, software, visualization https://www.trifacta.com/ Trifacta is a platform for preparing data for analysis.
TROPICOS TROPICOS nomenclature, database http://www.tropicos.org/ Tropicos was originally created for internal research but has since been made available to the world's scientific community. All of the nomenclatural, bibliographic, and specimen data accumulated in the Missouri Botanical Garden's electronic databases during the past 25 years are publicly available here. This system has over 1.2 million scientific names and 3.9 million specimen records.
TRY Plant Trait Database data aggregator https://www.try-db.org/TryWeb/Home.php Plant traits - morphological, anatomical, biochemical, physiological or phenological features of individuals or their component organs or tissues - are a key to understanding and predicting the adaptation of ecosystems in the face of biodiversity loss and global change. To improve the empirical data basis for such projections, in 2007 the TRY project was initiated, aimed at bringing together the different plant trait databases worldwide.
TTD
Tri-Trophic TCN
Tri-Trophic Databasing
Plants, Herbivores, and Parasitoids: A Model System for the Study of Tri-trophic Associations
data aggregator, TCN http://tcn.amnh.org/
iDigBio summary
This Thematic Collection Network (TCN) focused on one of the major herbivorous insect clades, the Hemiptera (aphids, scales, hoppers, cicadas, and true bugs), their host plants, and their parasitoids in a Tri-Trophic Databasing and imaging project.
TurboScan TurboScan software https://play.google.com/store/apps/details?id=com.piksoft.turboscan&hl=en
https://itunes.apple.com/us/app/turboscan-quickly-scan-multipage/id342548956?mt=8
TurboScan turns your iPhone or Android device into a full-featured and powerful scanner for documents, receipts, notes, photos, whiteboards, and other text.
uBio Universal Biological Indexer and Organizer nomenclature, taxonomy http://www.ubio.org
uBio is an initiative within the science library community to join international efforts to create and utilize a comprehensive and collaborative catalog of known names of all living (and once-living) organisms. The Taxonomic Name Server (TNS) catalogs names and classifications to enable tools that can help users find information on living things using any of the names that may be related to an organism.
UFBI University of Florida Biodiversity Institute organization http://news.ufl.edu/2002/11/07/biodiversity/ Established at the Florida Museum of Natural History (FLMNH) and located on the University of Florida (UF) campus, the mission of the Biodiversity Institute is to expand the research and outreach capacity of the FLMNH. The Institute creates a cross-disciplinary research facility where scientists, educators, students, and policy-makers develop research and educational collaborations. It will meet the challenge of understanding biodiversity in a rapidly changing world by accelerating research and distribution of validated information, thereby improving the ability to respond to environmental issues and challenges. The Institute is expected to create additional synergy and efficiencies through the hiring of key positions and the implementation of policies that create collaboration and holistic problem solving.
UNITE
UNITE data aggregator http://unite.ut.ee/
UNITE is a unified system for the DNA based fungal species linked to the classification. Molecular key for fungi, fungal rDNA ITS sequence database.
Universal Chalcidoidea Database
Universal Chalcidoidea Database data aggregatortaxonomy http://www.nhm.ac.uk/research-curation/research/projects/chalcidoids/database/
Allows users to find the current valid taxon for genus- and species-group names; browse valid families, genera, and species, with synonyms; list chalcidoid parasitoids of an associate family, genus, or species; list taxa associated with a valid chalcidoid genus or species; list chalcidoid taxa recorded from regions, countries, or states; and browse images and videos of chalcidoids.
USVH United States Virtual Herbarium project community, data aggregator http://usvirtualherbarium.org/ The mission of the United States Virtual Herbarium (USVH) is to provide, using digital technologies, integrated access to all the plant specimen information in the museums and herbaria of the United States of America and, by so doing, better inform scientific research in areas of national and global significance, promote adoption of internationally recognized biological data management standards, and encourage interest in plant diversity.
VACS
Developing a Centralized Digital Archive of Vouchered Animal Communication Signals data aggregator, TCN iDigBio summary VACS will digitize and make accessible media recordings associated with physical voucher specimens, broadly organized around the research theme of understanding the evolution and ecology of communication signals.
VASCAN
Vascular Plants of Canada
data aggregator http://data.canadensys.net/vascan/
Comprehensive database of all vascular plants reported in Canada, Greenland (Denmark) and Saint Pierre and Miquelon (France). VASCAN is literature-based, though recent additions are sometimes specimen-based.
Vernon Systems Vernon Systems data management http://www.vernonsystems.com/
Vernon Systems Limited develops two collections management systems for museums and galleries: Vernon CMS, a world leading desktop system for medium-to-large organisations, and eHive, a hosted web-based system for small museums, individual collectors and consortia.
VertNet Vertebrate Network data aggregator http://vertnet.org/ VertNet is a growing collaboration of natural history collections designed to fulfill the critical need for high quality biodiversity data. It provides an integrated, globally accessible, and sustainable infrastructure via a cloud-based architecture to create a fast, cost-effective, and scalable data platform. This infrastructure represents a new model for data publishing that maintains the fundamental capacity for curation of data at the source, while leveraging the advantages of cloud-based computing technologies. VertNet is the umbrella organization for MaNIS, HerpNET, ORNIS, and FishNet2.
ViBRANT
Virtual Biodiversity Research and Access Network for Taxonomy project http://vbrant.eu/
Virtual Biodiversity Research and Access Network for Taxonomy (ViBRANT) is a European Union FP7 funded project starting in December 2010 that will support the development of virtual research communities involved in biodiversity science. Our goal is to provide a more integrated and effective framework for those managing biodiversity data on the Web.

ViBRANT provides: 1) A virtual research environment (Scratchpads) where users can safely store, share and manage their research information.
2) Analytical services for users to build identification keys and phylogenetic trees.
3) A publication platform for users to automatically compile biodiversity science manuscripts from their research database.
4) A portal for users to centrally access publicly accessible biodiversity research information and literature.
4) Training, helping research communities to use these tools and services. 5) A standards compliant technical architecture that can be sustained by biodiversity research community.

VIVO
VIVO
software http://vivoweb.org
Open source semantic web application to enable the discovery of research and scholarship across disciplines at that institution and beyond.
VMWare VMWare cloud computing http://www.vmware.com/ A company providing virtualization software founded in 1998 and based in Palo Alto, California, USA. The company was acquired by EMC Corporation in 2004, and operates as a separate software subsidiary. The company is most notable for its hypervisors virtual machine managers (VMM), one of many hardware virtualization techniques that allow multiple operating systems, termed guests, to run concurrently on a host computer.
WCSP
World Checklist of Selected Plant Families
nomenclature http://apps.kew.org/wcsp/
International collaborative programme that provides the latest peer reviewed and published opinions on the accepted scientific names and synonyms of selected plant families.
Windows Azure Windows Azure cloud computing http://www.microsoft.com/windowsazure/ Windows Azure and SQL Azure enable users to build, host, and scale applications in Microsoft datacenters. They require no up-front expenses, no long term commitment, and enable users to pay only for the resources used.
WeDigBio Worldwide Engagement for Digitizing Biocollections citizen science, transcription https://www.wedigbio.org/ Worldwide Engagement for Digitizing Biocollections, or WeDigBio, is a 4-day event that engages participants online and onsite in digitizing natural history collections.

Onsite events are hosted by museums, herbaria, universities, and other institutions and enable face to face meetups where participants engage with local collections.

WISFlora Flora of Wisconsin, Consortium of Wisconsin Herbaria data aggregator http://wisflora.herbarium.wisc.edu/ A collaborative effort between the herbaria of the UW-Madison (WIS) and the UW-Steven's Point (UWSP), along with most of the other herbaria located in the state of Wisconsin. It contains information on each of the more than 2600 vascular plant species that occurs in Wisconsin, including photos, distribution maps, specimen records, and more.
WoRMS World Register of Marine Species data aggregator, nomenclature, taxonomy http://www.marinespecies.org/ With WoRMS aims to provide the most authoritative list of names of all marine species globally, ever published.
WSDL Web Services Description Language language http://www.w3.org/TR/wsdl WSDL is an XML format for describing network services as a set of endpoints operating on messages containing either document-oriented or procedure-oriented information. The operations and messages are described abstractly, and then bound to a concrete network protocol and message format to define an endpoint. Related concrete endpoints are combined into abstract endpoints (services). WSDL is extensible to allow description of endpoints and their messages regardless of what message formats or network protocols are used to communicate.
Xen Xen Project cloud computing http://www.xenproject.org/ The Xen hypervisor, the powerful open source industry standard for virtualization, offers a powerful, efficient, and secure feature set for virtualization of x86, x86_64, IA64, ARM, and other CPU architectures. It supports a wide range of guest operating systems including Windows, Linux, Solaris, and various versions of the BSD operating systems. Xen powers most public cloud services and many hosting services, such as Amazon Web Services, Rackspace Hosting, and Linode.
XML Extensible Markup Language language http://www.w3.org/XML/ Extensible Markup Language (XML) is a simple, very flexible text format derived from SGML (ISO 8879). Originally designed to meet the challenges of large-scale electronic publishing, XML is also playing an increasingly important role in the exchange of a wide variety of data on the Web and elsewhere.
XSEDE Extreme Science and Engineering Discovery Environment cloud computing https://www.xsede.org/home The Extreme Science and Engineering Discovery Environment (XSEDE) is the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world. It is a single virtual system that scientists can use to interactively share computing resources, data, and expertise. Scientists and engineers around the world use these resources and services things like supercomputers, collections of data, and new tools. XSEDE, and the experts who lead the program, will make these resources easier to use and help more people use them. The five-year, $121-million project is supported by the National Science Foundation. It replaces and expands on the NSF TeraGrid project. More than 10,000 scientists used the TeraGrid to complete thousands of research projects, at no cost to the scientists. That same sort of work only in more detail, generating more new knowledge and improving our world in an even broader range of fields continues with XSEDE.
YAMZ YAMZ Metadictionary metadata http://www.yamz.net/ The YAMZ Metadictionary is an open vocabulary of metadata terms from all domains and from all parts of "metadata speech".
Zenodo Zenodo Biodiversity Literature Repository literature, data repository https://zenodo.org Zenodo is an open dependable home for the long-tail of science, enabling researchers to share and preserve any research outputs in any size, any format and from any science.
Zoomify Zoomify software http://www.zoomify.com/ A popular web-based image viewer that allows easy panning and zooming.
Zooniverse
Zooniverse transcription https://www.zooniverse.org/ The Zooniverse is home to the internet's largest, most popular and most successful citizen science projects.