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Abstract Developing a predictive science of the biosphere depends heavily on the rapidly expanding biodiversity data that are commonly stored in biodiversity databases. Despite the proliferation of biodiversity databases, their independent operation has limited data discovery, comparison, and synthesis. Therefore, the biodiversity informatics community has called for improved alignment among these efforts to better catalog Earth's biodiversity. The primary challenges are incomplete knowledge of existing databases and incongruent taxonomic systems and data schemas. Addressing these issues will require development of a database registry, means to compare database contents, taxonomic harmonization, and tools that enable users to merge disparate databases based on their needs, all within a community of practice that enables people of various skill levels and roles to participate. We believe that synthesis and integration, driven by a growing and thriving community, will be the next stage of biodiversity informatics and will help unlock the full potential of biodiversity information.more » « less
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Abstract Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here, we conduct a literature review estimating temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation rate. We find that code is rarely published (only 6% of papers), with little improvement over time. We also found there may be incentives to publish code: Publications that share code have tended to be low‐impact initially, but accumulate citations faster, compensating for this deficit. Studies that additionally meet other Open Science criteria, open‐access publication, or data sharing, have still higher citation rates, with publications meeting all three criteria (code sharing, data sharing, and open access publication) tending to have the most citations and highest rate of citation accumulation.more » « less
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Romanach, Stephanie S. (Ed.)Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This otherwise simple validation is complicated by the difficulty of matching political division names to the correct geospatial object. Spelling errors, abbreviations, alternative codes, and synonyms in multiple languages present daunting name disambiguation challenges. The inability to resolve political division names reduces usable data, and analysis of erroneous observations can lead to flawed results. Here, we present the Geographic Name Resolution Service (GNRS), an application for correcting, standardizing, and indexing world political division names. The GNRS resolves political division names against a reference database that combines names and codes from GeoNames with geospatial object identifiers from the Global Administrative Areas Database (GADM). In a trial resolution of political division names extracted from >270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In assessing geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled the detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a significant data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and is accessible via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows.more » « less
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