BCO-DMO Quick Guide

BCO-DMO, a repository funded by the National Science Foundation (NSF), supports the oceanographic research community’s data needs throughout the entire data life cycle. This guide describes the services available from BCO-DMO from proposal to preservation and highlights phases where researchers engage significantly with the office.Curating and providing open access to research data is a collaborative process. This process may be thought of as a life cycle with data passing through various phases. Each phase has its own associated actors, roles, and critical activities. Good data management practices are necessary for all phases, from proposal to preservation.NSF #143557

Towards Capturing Provenance of the Data Curation Process at Domain-specific Repositories

Presented at AGU Fall Meeting, American Geophysical Union, Washington, D.C., 10 – 14 Dec 2018Data repositories often transform submissions to improve understanding and reuse of data by researchers other than the original submitter. However, scientific workflows built by the data submitters often depend on the original data format. In some cases, this makes the repository’s final data product less useful to the submitter. As a result, these two workable but different versions of the data provide value to two disparate, non-interoperable research communities around what should be a single dataset. Data repositories could bridge these two communities by exposing provenance explaining the transform from original submission to final product. A subsequent benefit of this provenance would be the transparent value-add of domain repository data curation. To improve its data management process efficiency, the Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification defined by the Frictionless Data project (https://frictionlessdata.io). Recently, BCO-DMO has been using the Frictionless Data Package Pipelines Python library (https://github.com/frictionlessdata/datapackage-pipelines) to capture the data curation processing steps that transform original submissions to final data products. Because these processing steps are stored using a declarative language they can be converted to a structured provenance record using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). PROV-O abstracts the Frictionless Data elements of BCO-DMO’s workflow for capturing necessary curation provenance and enables interoperability with other external provenance sources and tools. Users who are familiar with PROV-O or the Frictionless Data Pipelines can use either record to reproduce the final data product in a machine-actionable way. While there may still be some curation steps that cannot be easily automated, this process is a step towards end-to-end reproducible transforms throughout the data curation process. In this presentation, BCO-DMO will demonstrate how Frictionless Data Package Pipelines can be used to capture data curation provenance from original submission to final data product exposing the concrete value-add of domain-specific repositories.NSF #143557

Biological & Chemical Oceanography Data Management Office : a domain-specific repository for oceanographic data from around the world [poster]

Presented at AGU Ocean Sciences, 11 - 16 February 2018, Portland, ORThe Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a domain-specific digital data repository that works with investigators funded under the National Science Foundation’s Division of Ocean Sciences and Office of Polar Programs to manage their data free of charge. Data managers work closely with investigators to satisfy their data sharing requirements and to develop comprehensive Data Management Plans, as well as to ensure that their data will be well described with extensive metadata creation. Additionally, BCO-DMO offers tools to find and reuse these high-quality data and metadata packages, and services such as DOI generation for publication and attribution. These resources are free for all to discover, access, and utilize. As a repository embedded in our research community, BCO-DMO is well positioned to offer knowledge and expertise from both domain trained data managers and the scientific community at large. BCO-DMO is currently home to more than 9000 datasets and 900 projects, all of which are or will be submitted for archive at the National Centers for Environmental Information (NCEI). Our data holdings continue to grow, and encompass a wide range of oceanographic research areas, including biological, chemical, physical, and ecological. These data represent cruises and experiments from around the world, and are managed using community best practices, standards, and technologies to ensure accuracy and promote re-use. BCO-DMO is a repository and tool for investigators, offering both ocean science data and resources for data dissemination and publication.NSF #143557

Capturing Provenance of Data Curation at BCO-DMO

Presented at USGS Data Management Working Group, 9, November 2020At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easier for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.NSF #192461

Capturing Provenance of Data Curation at BCO-DMO

Presented at Data Curation Network, May 15, 2020At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easer for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.NSF #192461

Using peer review to support development of community resources for research data management

This work is licensed under a Creative Commons 1.0 Public Domain Dedication. The definitive version was published in Journal of eScience Librarianship 6 (2017): e1114, doi:10.7191/jeslib.2017.1114.To ensure that resources designed to teach skills and best practices for scientific research data sharing and management are useful, the maintainers of those materials need to evaluate and update them to ensure their accuracy, currency, and quality. This paper advances the use and process of outside peer review for community resources in addressing ongoing accuracy, quality, and currency issues. It further describes the next step of moving the updated materials to an online collaborative community platform for future iterative review in order to build upon mechanisms for open science, ongoing iteration, participation, and transparent community engagement.DataONE is supported by US National Science Foundation Awards 08- 30944 and 14-30508, William Michener, Principal Investigator; Matthew Jones, Patricia Cruse, David Vieglais, and Suzanne Allard, Co-Principal Investigators

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

Ba3Ga3N5 - A Novel Host Lattice for Eu2+ - Doped Luminescent Materials with Unexpected Nitridogallate Substructure

The alkaline earth nitridogallate Ba3Ga3N5 was synthesized from the elements in a sodium flux at 760°C utilizing weld shut tantalum ampules. The crystal structure was solved and refined on the basis of single-crystal X-ray diffraction data. Ba3Ga3N5 (space group C2/c (No. 15), a = 16.801(3), b = 8.3301(2), c = 11.623(2) Å, β = 109.92 (3)°, Z = 8) contains a hitherto unknown structural motif in nitridogallates, namely, infinite strands made up of GaN4 tetrahedra, each sharing two edges and at least one corner with neighboring GaN4 units. There are three Ba2+ sites with coordination numbers six or eight, respectively, and one Ba2+ position exhibiting a low coordination number 4 corresponding to a distorted tetrahedron. Eu2+ - doped samples show red luminescence when excited by UV irradiation at room temperature. Luminescence investigations revealed a maximum emission intensity at 638 nm (FWHM =2123 cm−1). Ba3Ga3N5 is the first nitridogallate for which parity allowed broadband emission due to Eu2+ - doping has been found. The electronic structure of both Ba3Ga3N5 as well as isoelectronic but not isostructural Sr3Ga3N5 was investigated by DFT methods. The calculations revealed a band gap of 1.53 eV for Sr3Ga3N5 and 1.46 eV for Ba3Ga3N5

The Galactic Center Black Hole Laboratory

The super-massive 4 million solar mass black hole Sagittarius~A* (SgrA*) shows flare emission from the millimeter to the X-ray domain. A detailed analysis of the infrared light curves allows us to address the accretion phenomenon in a statistical way. The analysis shows that the near-infrared flare amplitudes are dominated by a single state power law, with the low states in SgrA* limited by confusion through the unresolved stellar background. There are several dusty objects in the immediate vicinity of SgrA*. The source G2/DSO is one of them. Its nature is unclear. It may be comparable to similar stellar dusty sources in the region or may consist predominantly of gas and dust. In this case a particularly enhanced accretion activity onto SgrA* may be expected in the near future. Here the interpretation of recent data and ongoing observations are discussed.Comment: 30 pages - 7 figures - accepted for publication by Springer's "Fundamental Theories of Physics" series; summarizing GC contributions of 2 conferences: 'Equations of Motion in Relativistic Gravity' at the Physikzentrum Bad Honnef, Bad Honnef, Germany, (Feb. 17-23, 2013) and the COST MP0905 'The Galactic Center Black Hole Laboratory' Granada, Spain (Nov. 19 - 22, 2013

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function