A hackathon is an event where people engage in rapid and collaborative engineering over a relatively short period of time such as 24 or 48 hours. They are often run using agile software development practices, such as sprint-like design wherein computer programmers and others involved in software development, including graphic designers, interface designers, product managers, project managers, domain experts, and others collaborate intensively on engineering projects, such as software engineering.
Ebbe Schmidt Nielsen was a Danish entomologist influential in systematics and Lepidoptera research, and an early proponent of biodiversity informatics. The journal Invertebrate Systematics was established with significant contributions from Nielsen, and he assisted in the founding of the Global Biodiversity Information Facility (GBIF). Nielsen wrote several books, published over eighty scientific papers, and was highly regarded within the scientific community. Following his death, the GBIF organised the Ebbe Nielsen Prize in his memory, awarded annually to promising researchers in the field of biodiversity informatics. The moth Pollanisus nielseni is named after Nielsen.
The Global Biodiversity Information Facility (GBIF) is an international organisation that focuses on making scientific data on biodiversity available via the Internet using web services. The data are provided by many institutions from around the world; GBIF's information architecture makes these data accessible and searchable through a single portal. Data available through the GBIF portal are primarily distribution data on plants, animals, fungi, and microbes for the world, and scientific names data.
Biodiversity informatics is the application of informatics techniques to biodiversity information, such as taxonomy, biogeography or ecology. It is defined as the application of Information technology technologies to management, algorithmic exploration, analysis and interpretation of primary data regarding life, particularly at the species level organization. Modern computer techniques can yield new ways to view and analyze existing information, as well as predict future situations. Biodiversity informatics is a term that was only coined around 1992 but with rapidly increasing data sets has become useful in numerous studies and applications, such as the construction of taxonomic databases or geographic information systems. Biodiversity informatics contrasts with "bioinformatics", which is often used synonymously with the computerized handling of data in the specialized area of molecular biology.
C-squares is a system of spatially unique, location-based identifiers (geocodes) for areas on the surface of the earth, represented as cells from a latitude- and longitude-based Discrete Global Grid at a hierarchical set of resolution steps, obtained by progressively subdividing 10×10 degree World Meteorological Organization squares; the term "c-square" is also available for use to designate any component cell of the grid. Individual cell identifiers incorporate literal values of latitude and longitude in an interleaved notation, together with additional digits that support intermediate grid resolutions of 5, 0.5, 0.05 degrees, etc.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
A taxonomic database is a database created to hold information on biological taxa – for example groups of organisms organized by species name or other taxonomic identifier – for efficient data management and information retrieval. Taxonomic databases are routinely used for the automated construction of biological checklists such as floras and faunas, both for print publication and online; to underpin the operation of web-based species information systems; as a part of biological collection management ; as well as providing, in some cases, the taxon management component of broader science or biology information systems. They are also a fundamental contribution to the discipline of biodiversity informatics.
Plazi is a Swiss-based international non-profit association supporting and promoting the development of persistent and openly accessible digital bio-taxonomic literature. Plazi is cofounder of the Biodiversity Literature Repository and is maintaining this digital taxonomic literature repository at Zenodo to provide access to FAIR data converted from taxonomic publications using the TreatmentBank service, enhances submitted taxonomic treatments by creating a version in the XML format Taxpub, and educates about the importance of maintaining open access to scientific discourse and data. It is a contributor to the evolving e-taxonomy in the field of Biodiversity Informatics.
Dryad is an international open-access repository of research data, especially data underlying scientific and medical publications. Dryad is a curated general-purpose repository that makes data discoverable, freely reusable, and citable. The scientific, educational, and charitable mission of Dryad is to provide the infrastructure for and promote the re-use of scholarly research data.
Dotmatics is an R&D scientific software company used by scientists in the R&D process that help them be more efficient in their efforts to innovate. Founded in 2005, the company's primary office is in Boston with 14 offices around the globe. In March 2021, Dotmatics joined forces with Insightful Science through a merger. In April 2022, the two companies consolidated under the Dotmatics brand. Dotmatics' software is used by 2 million scientists and researchers and 10,000 customers.
iNaturalist is a social network of naturalists, citizen scientists, and biologists built on the concept of mapping and sharing observations of biodiversity across the globe. iNaturalist may be accessed via its website or from its mobile applications. As of 21 September 2022, iNaturalist users had contributed approximately 115,651,000 observations of plants, animals, fungi, and other organisms worldwide, and around 245,700 users were active in the previous 30 days.
The Ebbe Nielsen Prize was an international science award made annually between 2002 and 2014 by the Global Biodiversity Information Facility (GBIF), to recognize a researcher who had made substantial contributions to the field of biodiversity informatics. The prize was established in memory of prominent entomologist and biodiversity informatics proponent Ebbe Nielsen, who died of a heart attack in the U.S.A. en route to the 2001 GBIF Governing Board meeting.
Richard Lawrence Pyle, Ph.D. is a scuba diver and ichthyologist working on Hawaii.
PrecisionFDA is a secure, collaborative, high-performance computing platform that has established a growing community of experts around the analysis of biological datasets in order to advance precision medicine, inform regulatory science, and enable improvements in health outcomes. This cloud-based platform is developed and served by the United States Food and Drug Administration (FDA). PrecisionFDA connects experts, citizen scientists, and scholars from around the world and provides them with a library of computational tools, workflow features, and reference data. The platform allows researchers to upload and compare data against reference genomes, and execute bioinformatic pipelines. The variant call file (VCF) comparator tool also enables users to compare their genetic test results to reference genomes. The platform's code is open source and available on GitHub. The platform also features a crowdsourcing model to sponsor community challenges in order to stimulate the development of innovative analytics that inform precision medicine and regulatory science. Community members from around the world come together to participate in scientific challenges, solving problems that demonstrate the effectiveness of their tools, testing the capabilities of the platform, sharing their results, and engaging the community in discussions. Globally, precisionFDA has more than 5,000 users.
The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database which attempts to cover published genus names for all domains of life from 1758 in zoology up to the present, arranged in a single, internally consistent taxonomic hierarchy, for the benefit of Biodiversity Informatics initiatives plus general users of biodiversity (taxonomic) information. In addition to containing over 490,000 published genus name instances as at March 2020, the database holds over 1.7 million species names, although this component of the data is not maintained in as current or complete state as the genus-level holdings. IRMNG can be queried online for access to the latest version of the dataset and is also made available as periodic snapshots or data dumps for import/upload into other systems as desired.
Nomenclator Zoologicus is one of the major compendia in the field of zoological nomenclature, compiled by Sheffield Airey Neave and his successors and published in 9 volumes over the period 1939–1994, under the auspices of the Zoological Society of London; a tenth, electronic-only volume was also produced before the project ceased. It contains over 340,000 published name instances with their authorities and details of their original publication, certain nomenclatural notes and cross references, and an indication of the taxonomic group to which each is assigned. An electronic (digitised) version of volumes 1-10 was released online by the uBio project, based at the Marine Biological Laboratory, Woods Hole, in 2004–2005.
Bionomia is a database and database entry tool which permits the name strings of collectors, and of taxonomists who determine specimen data, to be assigned to the unique person who collected or identified the specimen. If the person is living, this is done via their ORCID iD, and if dead, via their Wikidata identifier. It thereby resolves ambiguity where two or more collectors have similar names; or where one collector has worked under two names, or a single name written in two or more ways. The specimen data associated with, and used by, Bionomia are the aggregated GBIF data.
Anthony J. J. ("Tony") Rees is a British-born software developer, data manager and biologist resident in Australia since 1986, and previously a data manager with CSIRO Marine and Atmospheric Research. He is responsible for developing a number of software systems currently used in science data management, including c-squares, Taxamatch, and IRMNG, the Interim Register of Marine and Nonmarine Genera. He has also been closely involved with the development of other biodiversity informatics initiatives including the Ocean Biogeographic Information System (OBIS), AquaMaps, and the iPlant Taxonomic Name Resolution Service (TNRS).
The Biodiversity Literature Repository (BLR) is a biodiversity dedicated community created in November 11, 2013, in Zenodo, the open science repository at CERN and part of the European project OpenAIRE. The goal of BLR is to provide a long-term, stable, open repository that allows deposition of bio-taxonomic articles enhanced with custom metadata and links to data extracted from therein and deposited in BLR. As of April 25, 2021, this includes 94,443 taxonomic treatments and 293,457 figures from 48,993 articles which are made findable, accessible, interoperable and reusable FAIR data. Most of the data is uploaded on a continuous basis by Plazi using its TreatmentBank service based on their Plazi workflow, and Pensoft Publishers using BLR as repository for data published in their journals. The largest single re-user of data is the Global Biodiversity Information Facility (GBIF), using data from within 33,623 processed articles.
Vince Smith is a British entomologist and biodiversity informatician at the Natural History Museum, London.
