Science for Environment Policy features a policy brief explaining the biases around biodiversity databases in their latest issue 331, from 6 June 2013. "Biodiversity databases: language and location help explain biases" features a new study arguing that low numbers of English speakers, large distances from the database host and low security acting as key barriers to data collection and among the main reasons for the underrepresentation of some countries in biodiversity databases.

Source: Amano T., Sutherland W.J. (2013) Four barriers to the global understanding of biodiversity conservation: wealth, language, geographical location and security. Proceedings of the Royal Society B. 280: 20122649. doi: 10.1098/rspb.2012.2649

Ecosystem functioning, or the role which organisms play in an ecosystem, is becoming increasingly important in marine ecological and conservation. To facilitate such studies an international team of scientists lead by S. Faulwetter from the Hellenic Centre for Marine Research (HMRC) present the Polytraitsdatabase that aims to provide re-usable, and accessible data on marine bristle worms. The paper describing the new database was published in the innovative Biodiversity Data Journal, a pioneer in the publication of integrated biological data.

Benthic organisms participate in a number of biological processes in world water basins. Their functional diversity is an important community property demonstrating the role organisms have in the ecosystem and helping to understand how the community reacts to environmental changes. Polychaetes, or bristle worms, are marine worms famous for their peculiar shapes and often vivid coloration. More than 10,000 species are described in the class worldwide, most of which living in the shelf zone of the seas and oceans, burrowing in the sediment or swimming among the plankton.

At present, the Polytraits database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 species, all referenced by literature sources. All data on these engaging organisms can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable. The new database presents a rich and easy to use collection, which cover morphological, reproductive and behavioural characteristics of polychaetes, as well as information on environmental preferences in an attempt to facilitate ecological research and conservation studies.

The researchers also provide a leading-edge approach to accessing, integrating and re-using the data. Through programming interfaces, the life-cycle information is automatically integrated into the Polychaetes Scratchpads, together with other data on polychaetes. Scratchpads are easy to use, adaptable, and provide powerful tools for managing biodiversity data. This taxon-centric virtual research environment allows browsing the taxonomic classification and retrieving various kinds of relevant information for each taxon, among which are also the collected biological traits.

Furthermore, the data are also accessible through Encyclopedia of Life's TraitBank which currently features over 3 million records related to more than 250 attributes for 272,720 taxa, including the Polytraits data. TraitBank serves as a provider for aggregated species trait data. All data uploaded there are archived and integrated with trait information from other sources to address issues of standardization of scientific data. This is the first complex database for marine organisms to be published in such an innovative way and demonstrates yet another example of collaboration between the data publisher Pensoft and Encyclopedia of Life.

The German working group on vegetation databases is dedicated to building, maintaining, linking and analysing electronic archives of vegetation plot data and provides the national repository "VegetWeb", hosted by the German Federal Agency for Nature Conservation (BfN). The 12th workshop will be hosted by the new German Centre for Integrative Biodiversity Research (iDiv) in Leipzig, Germany. The central mission of iDiv is to promote theory-driven experiments and synthesis as well as data-driven theory. The concept of iDiv encompasses the detection of biodiversity, understanding its emergence, exploring its consequences for ecosystem functions and services, and developing strategies to safeguard biodiversity under global change. In this context, the combined synthesis of species abundance and distribution data together with information on species characteristics is seen as a high potential to advance our understanding of community assembly and plant diversity patterns. For this reason, important databases have already become part of iDiv's data research platforms, such as the German Vegetation Reference Database (GVRD), the plant trait databases TRY and BIOLFLOR and the Chorology Database Halle (CDH) on plant distribution data. In this workshop, we seek to explore the potentials of such databases for future research, with a specific focus on vegetation databases.
Further Information: http://www.botanik.uni-greifswald.de/idiv_meeting_2013.html

Washington – The Environmental Protection Agency has launched a tool that aims to provide easier access to chemical safety and health data.

Washington — A new database from OSHA offers access to safety profiles and information on workplace chemicals.

Washington – A new database from the Center for Progressive Reform spotlights state criminal cases and advocacy campaigns against employers that have failed to comply with worker safety laws.

Longmeadow, MA – More than 1,000 worker deaths have occurred during the first seven months of 2015, according to the U.S. Worker Fatality Database.

Washington — The Department of Transportation is changing how users access the Drug and Alcohol Testing Management Information System.

Washington — The Environmental Protection Agency has developed a mobile app that allows users to easily search an online database of more than 400 disinfectant products that can help prevent and reduce the spread of SARS-CoV-2 – the coronavirus that causes COVID-19.

Washington – NIOSH has made one of its injury databases available to the public, allowing users to create national estimates on a variety of nonfatal occupational injuries.

New York — Legislation recently introduced in New York City would establish a database on workplace deaths, and employers could be fined up to $2,500 per violation for not reporting data.

BGS updates national CO2 storage database  Agg-Net

Update released for BGS open-source database software, ETL Helper  British Geological Survey

Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs.

Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.

Interoperability of crystallographic data with other disciplines is essential for the smooth and rapid progress of structure-based science in the computer age. Within crystallography and closely related subject areas, there is already a high level of conformance to the generally accepted FAIR principles (that data be findable, accessible, interoperable and reusable) through the adoption of common information exchange protocols by databases, publishers, instrument vendors, experimental facilities and software authors. Driven by the success within these domains, the IUCr has worked closely with CODATA (the Committee on Data of the International Science Council) to help develop the latter's commitment to cross-domain integration of discipline-specific data. The IUCr has, in particular, emphasized the need for standards relating to data quality and completeness as an adjunct to the FAIR data landscape. This can ensure definitive reusable data, which in turn can aid interoperability across domains. A microsymposium at the IUCr 2023 Congress provided an up-to-date survey of data interoperability within and outside of crystallography, expounded using a broad range of examples.

In recent years, there is a significant interest from the crystallographic and materials science communities to have access to raw diffraction data. The effort in archiving raw data for access by the user community is spearheaded by the International Union of Crystallography (IUCr) Committee on Data. In materials science, where powder diffraction is extensively used, the challenge in archiving raw data is different to that from single crystal data, owing to the very nature of the contributions involved. Powder diffraction (X-ray or neutron) data consist of contributions from the material under study as well as instrument specific parameters. Having raw powder diffraction data can be essential in cases of analysing materials with poor crystallinity, disorder, micro structure (size/strain) etc. Here, the initiative and progress made by the International Centre for Diffraction Data (ICDDR) in archiving powder X-ray diffraction raw data in the Powder Diffraction FileTM (PDFR) database is outlined. The upcoming 2025 release of the PDF-5+ database will have more than 20 800 raw powder diffraction patterns that are available for reference.

An exhaustive search for missing symmetry was performed for 223 076 entries in the ICSD (2023-2 release). Approximately 0.65% of them can be described with higher symmetry than reported. Out of the identified noncentrosymmetric entries, ∼74% can be described by centrosymmetric space groups; this has implications for compatible physical properties. It is proposed that the information on the correct space group is included in the ICSD.

The International Tables Symmetry Database (https://symmdb.iucr.org/), which is part of International Tables for Crystallography, is a collection of individual databases of crystallographic space-group and point-group information with associated programs. The programs let the user access and in some cases interactively visualize the data, and some also allow new data to be calculated `on the fly'. Together these databases and programs expand upon and complement the symmetry information provided in International Tables for Crystallography Volume A, Space-Group Symmetry, and Volume A1, Symmetry Relations between Space Groups. The Symmetry Database allows users to learn about and explore the space and point groups, and facilitates the study of group–subgroup relations between space groups, with applications in determining crystal-structure relationships, in studying phase transitions and in domain-structure analysis. The use of the International Tables Symmetry Database in all these areas is demonstrated using several examples.

This article presents a web-based framework to build a database without in-depth programming knowledge given a set of CIF dictionaries and a collection of CIFs. The framework consists of two main elements: the public site that displays the information contained in the CIFs in an ordered manner, and the restricted administrative site which defines how that information is stored, processed and, eventually, displayed. Thus, the web application allows users to easily explore, filter and access the data, download the original CIFs, and visualize the structures via JSmol. The modulated structures open database B-IncStrDB, the official International Union of Crystallography repository for this type of material and available through the Bilbao Crystallographic Server, has been re-implemented following the proposed framework.

The Drinking Water Treatability Database presents an overview of different contaminants and possible treatment processes to remove them from drinking water.  

Empowering Enterprises with AI-Driven Insights

Customers looking for recycling equipment can now browse through objective reviews before making a purchase.

The acquisition of the premium domain name OpportunityZones.com was completed in September.

Robert Daly serves as a database solutions architect at Amazon Web Services.

Prospect Wallet Revamps 50 million B2B Database for Unmatched Accuracy and Responsiveness

Ispirer Systems and Gemini collaboration accelerates post-migration refinement by up to 80%.

Details are now available of the Netskills course on 'Database Design and SQL' to be held on Tuesday 13th June 2006 at the University of Bath are now available. This course is an ideal warm up for the Institutional Web Management Workshop. [2006-04-27]

RiceProteomeDB (RPDB): a user-friendly database for proteomics data storage, retrieval, and analysis  Nature.com

In this espisode we take a closer look at relational database systems and the concepts behind them. We start by discussing the relational paradigm, its concepts and ramifications, and go on to architectural aspects.

Recording Venue: Skype Guest: Martin Fowler and Pramod Sadalage In this episode, we talk with Pramod Sadalage and Martin Fowler about database evolution and agile database development. We discuss the basic challenges for working with a database in an agile development culture and how to include database design and most of all, database evolution, in […]

Recording Venue: Skype Guest: Michael Hunger Michael Hunger of Neo Technology, and a developer on the Neo4J database, joins Robert to discuss graph databases. Graph databases fall within the larger category of NoSQL databases but they are not primarily a solution to problems of scale. They differentiate themselves from RDBMS in offering a data model built […]