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

Pharmaceutical compounding of orphan active ingredients in Belgium : how community and hospital pharmacists can address the needs of patients with rare diseases

Background: Pharmaceutical compounding of orphan active ingredients can offer cost-effective treatment to patients when no other drug product is available for a rare disease or during periods of drug product shortages. Additionally, it allows customized therapy for patients with rare diseases. However, standardized compounding formulas and procedures, and monographs are required to ensure the patients' safety. Results: Standardized formulas and compounding procedures were developed for seven orphan active ingredients (L-arginine, sodium benzoate, sodium phenylbutyrate, L-carnitine, chenodesoxycholic acid, primaquine phosphate, pyridoxal phosphate) and one non-orphan molecule (sodium perchlorate) regularly compounded by hospital pharmacists for extemporaneous use. The stability of these formulations was evaluated over 3months at refrigerated (5 degrees C) and standard storage conditions (25 degrees C/60%RH) using HPLC-based assays and a suitable shelf life was assigned to the formulations. Additionally, suitable analytical methods for quality control of formulations of pyridoxal phosphate and sodium perchlorate were developed as monographs for these components were not available in the European Pharmacopeia or United States Pharmacopeia. Conclusions: Availability of compounding formulas and protocols, as well as stability information, for orphan active ingredients can improve patients' access to treatment for rare diseases. Such data were collected for seven orphan active ingredients to treat patients with rare diseases when no other treatment is available. More efforts are needed to develop standardized formulas and compounding procedures for additional orphan active ingredients whose clinical efficacy is well-known but which are not available as products with a marketing authorization. Additionally, a legal framework at EU level is required to enable the full potential of pharmaceutical compounding for orphan active ingredients

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

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)

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

ANTIGUA PILA BAUTISMAL [Material gráfico]

FOTO PAPEL DE PILA BAUTISMALPILA DONDE BAUTIZARON A LOS MENCEYES GUANCHES. ADQUIRIDA POR EL COLECCIONISTA EN TENERIFE.Copia digital. Madrid : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 201

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

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_{<it>α </it>}value of 77.6% and an SOV_{<it>α </it>}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