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Unlabelled: Biodiversity studies are relying increasingly on primary biodiversity records (PBRs) for modelling and analysis. Because biodiversity data are frequently 'harvested'-i.e. not collected by the researcher for that particular study, but obtained from data aggregators such as the Global Biodiversity Information Facility-researchers need to be aware of strengths and weaknesses of their data before they venture into further analysis. R is becoming a lingua franca of data exploration and analysis. Here, we describe an R package, bdvis, which facilitates efforts to understand the gaps and strengths of PBR data with quick and useful visualization functions., Availability and Implementation: The full code of the R package bdvis, along with instructions on how to install and use it, is available via CRAN - The Comprehensive R Archive Network (http://cran.r-project.org/web/packages/bdvis/index.html) and in the corresponding author's main GitHub repository: http://www.github.com/vijaybarve/bdvis The source code is licensed under CC0 CONTACT: vijay.barve@gmail.com., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Unlabelled: We present a REST web service to assess the geospatial quality of primary biodiversity data. It enables access to basic and advanced functions to detect completeness and consistency issues as well as general errors in the provided record or set of records. The API uses JSON for data interchange and efficient parallelization techniques for fast assessments of large datasets., Availability and Implementation: The Geospatial Data Quality API is part of the VertNet set of APIs. It can be accessed at http://api-geospatial.vertnet-portal.appspot.com/geospatial and is already implemented in the VertNet data portal for quality reporting. Source code is freely available under GPL license from http://www.github.com/vertnet/api-geospatial, Contact: javier.otegui@gmail.com or rguralnick@flmnh.ufl.edu, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2016. Published by Oxford University Press.)

The planet is experiencing an ongoing global biodiversity crisis. Measuring the magnitude and rate of change more effectively requires access to organized, easily discoverable, and digitally-formatted biodiversity data, both legacy and new, from across the globe. Assembling this coherent digital representation of biodiversity requires the integration of data that have historically been analog, dispersed, and heterogeneous. The Integrated Publishing Toolkit (IPT) is a software package developed to support biodiversity dataset publication in a common format. The IPT's two primary functions are to 1) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and 2) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. Here we discuss the key need for the IPT, how it has developed in response to community input, and how it continues to evolve to streamline and enhance the interoperability, discoverability, and mobilization of new data types beyond basic Darwin Core records. We close with a discussion how IPT has impacted the biodiversity research community, how it enhances data publishing in more traditional journal venues, along with new features implemented in the latest version of the IPT, and future plans for more enhancements.

In order to effectively understand and cope with the current 'biodiversity crisis', having large-enough sets of qualified data is necessary. Information facilitators such as the Global Biodiversity Information Facility (GBIF) are ensuring increasing availability of primary biodiversity records by linking data collections spread over several institutions that have agreed to publish their data in a common access schema. We have assessed the primary records that one such publisher, the Spanish node of GBIF (GBIF.ES), hosts on behalf of a number of institutions, considered to be a highly representative sample of the total mass of available data for a country in order to know the quantity and quality of the information made available. Our results may provide an indication of the overall fitness-for-use in these data. We have found a number of patterns in the availability and accrual of data that seem to arise naturally from the digitization processes. Knowing these patterns and features may help deciding when and how these data can be used. Broadly, the error level seems low. The available data may be of capital importance for the development of biodiversity research, both locally and globally. However, wide swaths of records lack data elements such as georeferencing or taxonomical levels. Although the remaining information is ample and fit for many uses, improving the completeness of the records would likely increase the usability span for these data.

Unlabelled: In any data quality workflow, data publishers must become aware of issues in their data so these can be corrected. User feedback mechanisms provide one avenue, while global assessments of datasets provide another. To date, there is no publicly available tool to allow both biodiversity data institutions sharing their data through the Global Biodiversity Information Facility network and its potential users to assess datasets as a whole. Contributing to bridge this gap both for publishers and users, we introduce BIoDiversity DataSets Assessment Tool, an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections., Availability and Implementation: The online application is accessible at http://www.unav.es/unzyec/mzna/biddsat/ and is supported by all major browsers. The source code is licensed under the GNU GPLv3 license (http://www.gnu.org/licenses/gpl-3.0.txt) and is available at https://github.com/jotegui/BIDDSAT.

The establishment of protected areas is one of the main tools used for biodiversity conservation, one of the components of environmental management. Although the theoretical framework for protected areas has been long known and discussed, there are few data about their practical effectiveness as a means to preserve biodiversity. Through the analysis of information from the Global Biodiversity Information Facility (GBIF), we have looked for any relationship between the protection status and the general species richness (i.e., number of all living species, taken as a surrogate for biodiversity) in the Spanish Pyrenees. We found that higher protection levels were associated to higher richness of non-endangered species. However, additional reliability tests have shown that for endangered species, the amount of currently available data may still be insufficient for effective management. To avoid this lack of reliability, enhancing public access to biodiversity data or improving sampling effort is mandatory. [ABSTRACT FROM AUTHOR]

We characterize the primary biodiversity data records that have been made public for retrieval for the Pyrenean region. Such data, spanning more than a hundred years, have been collected by many institutions and individual researchers and digitized in databases, some of which have been shared through the Global Biodiversity Information Facility platform by using a standard format, Darwin Core. The datasets are not homogeneous in extent, coverage, taxonomy, or accuracy. Differences arising from taxonomic depth or group, georeferencing precision, age of collection, and other features result in biases and gaps that may influence the fitness for use of such data. Knowledge of patterns found in the data may help researchers and managers operating in the Pyrenees to estimate the reliability of available information and to assess what uses for the data are acceptable. [ABSTRACT FROM AUTHOR]