64 research outputs found
IRMNG 2006–2016: 10 Years of a Global Taxonomic Database
IRMNG, the Interim Register of Marine and Nonmarine Genera, was commenced in 2006 as an initiative of the Australian OBIS Node (OBIS Australia) following an analysis of the taxonomic names management needs of the Ocean Biogeographic Information System (OBIS). The main objectives were to produce a hierarchical classification of all life, both extant and fossil, to at least generic level (and to species as data were readily available) and to provide a tool to distinguish marine from nonmarine, and extant from fossil taxa. Over its first 10 years of operation IRMNG has acquired almost 487,000 of an estimated 510,000 published genus names (including both valid names and synonyms) in addition to almost 1.8 million species names, of which 1.3 million are considered valid. Throughout this time IRMNG data have been available for public query via a dedicated web interface based at CSIRO in Australia, as well as being supplied as bulk downloads for use by a range of global biodiversity projects. Over the period 2014-2016 responsibility for the system has been passed to the Data Centre Division of the Flanders Marine Institute (VLIZ) in Belgium, which is continuing the maintenance and development of IRMNG at its new web location, www.irmng.org. With its present estimated holdings of >95% of all published genus names (plus associated authorities and years of publication) across all taxonomic domains, including fossil as well as extant taxa, within an internally consistent taxonomic hierarchy, IRMNG is at present uniquely placed to provide an overview of “all life” to at least generic level, to permit the discovery of trends in publication of genera through time, to provide preliminary information on the marine vs. nonmarine and extant vs. fossil status of the taxa concerned, and to generate lists of both unique and non-unique names (homonyms sensu lato) for the benefit of users of biodiversity data
Marine biodiversity discovery: the metrics of new species descriptions
Based on the World Register of Marine Species (WoRMS), there are currently c. 242,000 known valid marine species living in the world's oceans and marine biota continue to be discovered and named steadily at a current average of 2,332 new species per year. The “average” newly described marine species is a benthic crustacean, annelid, or mollusc between 2 and 10 mm in size, living in the tropics at depths of 0–60 m, and represented in the description by 7–19 specimens. It is described after a shelf life of 13.5 years in an article with two to three authors in a journal with an IF <1, published by an academic institution or society or a small commercial publisher. It is highly likely that the description is not accompanied by molecular data and that its authors do not work in an institution in a region of the world where the new species comes from. At the current pace of discovery and characterization, it will take several hundred years to describe the remaining 1–2 million unknown marine species. With increased facilitation of access to literature, marine taxonomy will increasingly rely on retired professionals and citizen scientists. The barriers to new marine species descriptions are in part technological (access to habitats that are difficult to sample) and educational (training to generate and use molecular barcodes), but mostly institutional (funding of taxonomic work) and regulatory (restrictions imposed by access and benefit sharing legislation)
Fishing for data and sorting the catch : assessing the data quality, completeness and fitness for use of data in marine biogeographic databases
Being able to assess the quality and level of completeness of data has become indispensable in marine biodiversity research, especially when dealing with large databases that typically compile data from a variety of sources. Very few integrated databases offer quality flags on the level of the individual record, making it hard for users to easily extract the data that are fit for their specific purposes. This article describes the different steps that were developed to analyse the quality and completeness of the distribution records within the European and international Ocean Biogeographic Information Systems (EurOBIS and OBIS). Records are checked on data format, completeness and validity of information, quality and detail of the used taxonomy and geographic indications and whether or not the record is a putative outlier. The corresponding quality control (QC) flags will not only help users with their data selection, they will also help the data management team and the data custodians to identify possible gaps and errors in the submitted data, providing scope to improve data quality. The results of these quality control procedures are as of now available on both the EurOBIS and OBIS databases. Through the Biology portal of the European Marine Observation and Data Network (EMODnet Biology), a subset of EurOBIS records-passing a specific combination of these QC steps-is offered to the users. In the future, EMODnet Biology will offer a wide range of filter options through its portal, allowing users to make specific selections themselves. Through LifeWatch, users can already upload their own data and check them against a selection of the here described quality control procedures
Erratum to: Analysing the content of the European Ocean Biogeographic Information System (EurOBIS): available data, limitations, prospects and a look at the future
Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences
The Ocean Biogeographic Information System (OBIS) is the world's most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.Fil: De Pooter, Daphnis. Flanders Marine Institute; BélgicaFil: Appeltans, Ward. UNESCO-IOC; BélgicaFil: Bailly, Nicolas. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Bristol, Sky. United States Geological Survey; Estados UnidosFil: Deneudt, Klaas. Flanders Marine Institute; BélgicaFil: Eliezer, Menashè. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Fujioka, Ei. University Of Duke. Nicholas School Of Environment. Duke Marine Lab; Estados UnidosFil: Giorgetti, Alessandra. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Goldstein, Philip. University of Colorado Museum of Natural History, OBIS; Estados UnidosFil: Lewis, Mirtha Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Lipizer, Marina. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Mackay, Kevin. National Institute of Water and Atmospheric Research; Nueva ZelandaFil: Marin, Maria Rosa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Moncoiffé, Gwenaëlle. British Oceanographic Data Center; Reino UnidoFil: Nikolopoulou, Stamatina. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Provoost, Pieter. UNESCO-IOC; BélgicaFil: Rauch, Shannon. Woods Hole Oceanographic Institution; Estados UnidosFil: Roubicek, Andres. CSIRO Oceans and Atmosphere; AustraliaFil: Torres, Carlos. Universidad Autonoma de Baja California Sur; MéxicoFil: van de Putte, Anton. Royal Belgian Institute for Natural Sciences; BélgicaFil: Vandepitte, Leen. Flanders Marine Institute; BélgicaFil: Vanhoorne, Bart. Flanders Marine Institute; BélgicaFil: Vinci, Mateo. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Wambiji, Nina. Kenya Marine and Fisheries Research Institute; KeniaFil: Watts, David. CSIRO Oceans and Atmosphere; AustraliaFil: Klein Salas, Eduardo. Universidad Simon Bolivar; VenezuelaFil: Hernandez, Francisco. Flanders Marine Institute; Bélgic
Recommendations for the standardisation of open taxonomic nomenclature for image-based identifications
This paper recommends best practice for the use of open nomenclature (ON) signs applicable to image-based faunal analyses. It is one of numerous initiatives to improve biodiversity data input to improve the reliability of biological datasets and their utility in informing policy and management. Image-based faunal analyses are increasingly common but have limitations in the level of taxonomic precision that can be achieved, which varies among groups and imaging methods. This is particularly critical for deep-sea studies owing to the difficulties in reaching confident species-level identifications of unknown taxa. ON signs indicate a standard level of identification and improve clarity, precision and comparability of biodiversity data. Here we provide examples of recommended usage of these terms for input to online databases and preparation of morphospecies catalogues. Because the processes of identification differ when working with physical specimens and with images of the taxa, we build upon previously provided recommendations for specific use with image-based identifications
MolluscaBase – announcing a World Register of all Molluscs
Resumen de comunicación oral en congresoThe Mollusca, second largest phylum on Earth, lack a global listing of valid names or even precise figures for the number of Recent species. The launching of MolluscaBase is intended to fill this gap, expanding the contents of the World Register of Marine Species (WoRMS) to include all marine, freshwater and terrestrial molluscs, recent and fossil. The WoRMS database, hosted at the Flanders Marine Institute (VLIZ) at Oostende, had more than 1,000,000 unique visitors in 2013 and provides the taxonomic backbone for initiatives such as Encyclopedia of Life, Catalogue of Life, and others. It currently contains more than 44,000 valid species names of Recent marine Mollusca, which are estimated to represent approximately 95% of all valid species. There is no similar global list of the freshwater and terrestrial Mollusca. It is estimated that there are about 23,000 species of land snails/slugs and about 5,000 freshwater gastropods and bivalves. The number of named fossil Mollusca is not known, but is in the same order of magnitude as that of Recent species. MolluscaBase is intended as an authoritative taxonomic database, relying only on published sources and built by taxonomic editors who are active malacologists and respond to feedback from users. Like in WoRMS, the contents should include Taxonomic hierarchy, Current name and synonymy, Literature sources, Distributions (using countries as the basic unit for land-based distributions), Fossil range (expressed in terms of the international chronostratigraphic chart) and other taxon attributes. This initiative is supported by LifeWatch, the E-Science European Infrastructure for Biodiversity and Ecosystem Research. In a first move, MolluscaBase should build on the existing WoRMS contents incorporating the contents of existing initiatives like CLEMAM (Checklist of European MArine Molusca), FreshGEN (Freshwater Gastropods of the European Neogene) and Fauna Europaea. The long term goal of filling the gaps in non-marine and fossil components of MolluscaBase needs your support! If you are a taxonomist, specializing in any group of non-marine or extinct molluscs, and wish to become a contributor to MolluscaBase, please let us know and contact the WoRMS team at [email protected], or the corresponding author, to find your possible role in MolluscaBase!Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech
Analysing the content of the European Ocean Biogeographic Information System (EurOBIS): available data, limitations, prospects and a look at the future
Learning biophysically-motivated parameters for alpha helix prediction
<p>Abstract</p> <p>Background</p> <p>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.</p> <p>Results</p> <p>Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Q<sub><it>α </it></sub>value of 77.6% and an SOV<sub><it>α </it></sub>value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.</p> <p>Conclusion</p> <p>The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.</p
The World Amphipoda Database: history and progress
We provide an overview of the World Amphipoda Database (WAD), a global species database that is part of the World Register of Marine Species (WoRMS). Launched in 2013, the database contains entries for over 10,500 accepted species names. Edited currently by 31 amphipod taxonomists, following WoRMS priorities, the WAD has at least one editor per major group. All accepted species are checked by the editors, as is the authorship available for all of the names. The higher classification is documented for every species and a type species is recorded for every genus name. This constitutes five of the 13 priorities for completion, set by WoRMS. In 2015, five LifeWatch grants were allocated for WAD activities. These included a general training workshop in 2016, together with data input for the superfamily Lysianassoidea and for a number of non-marine groups. Philanthropy grants in 2019 and 2021 covered more important gaps across the whole group. Further work remains to complete the linking of unaccepted names, original descriptions, and environmental information. Once these tasks are completed, the database will be considered complete for 8 of the 13 priorities, and efforts will continue to input new taxa annually and focus on the remaining priorities, particularly the input of type localities. We give an overview of the current status of the order Amphipoda, providing counts of the number of genera and species within each family belonging to the six suborders currently recognized
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