Biodiversity Information Science and Standards

Biodiversity Information Science and Standards 7: e94188 DOI: 10.3897/biss.7.94188 Authors: Steven Baskauf, Jennifer Girón Duque, Matthew Nielsen, Neil Cobb, Randy Singer, Katja Seltmann, Zachary Kachian, Mervin Pérez, Donat Agosti, Anna Klompen Abstract: The Audubon Core vocabulary terms subjectPart and subjectOrientation are used to describe the depicted part of an organism and its orientation in an image. We describe the criteria and process for developing controlled vocabularies for these two terms. The vocabularies take the form of Simple Knowledge Organization System (SKOS) concept schemes and their terms are categorized using SKOS collections to allow users to select from particular sets of values appropriate for particular organism groups and their parts. We also report the results of implementation testing used to determine the usability of the proposed terms with actual images of living organisms and preserved specimens. HTML XML PDF

Biodiversity Information Science and Standards 6: e90026 DOI: 10.3897/biss.6.90026 Authors: Anne Thessen, Dmitry Mozzherin, David Shorthouse, David Patterson Abstract: The majority of biodiversity data is not findable, accessible, integratable, or reusable, partially because of a lack of metadata. Taxonomic names as metadata are useful, but not sufficient because these names may be updated as knowledge progresses. There is a great need for tools and services that can scale up to create and maintain metadata for the vast and varied long tail of dark data. Here we examine the use of GNFinder as a tool for creating and maintaining metadata using mentions of taxa in text from publications corresponding to data sets deposited in Dryad. Most studied taxa were mentioned in the publication using a properly formed scientific name, with a few exceptions for studies that only used vernacular names and only mentioned taxa in the corresponding files. GNFinder had a high F1 Score (0.86) representing a balance between precision (0.91) and recall (0.82). GNFinder had lower performance when a name string was an irregular abbreviation, had unexpected capitalization or punctuation, or contained a qualifier (like aff. or cf.). Approximately 14% of the name strings identified in text published from 1996 to 2012 were outdated and updated to a current, valid name. Automated metadata creation and maintenance at scale using GNFinder can make it easier to find biodiversity publications as demonstrated by the Biodiversity Heritage Library and HathiTrust. HTML XML PDF

Biodiversity Information Science and Standards 6: e95668 DOI: 10.3897/biss.6.95668 Authors: Anahita Kazem, Birgitta Koenig-Ries, Henrique Pereira, Jonathan Chase Abstract: Our goal is to mobilize global species abundance and assemblage information, via a dedicated and openly accessible data repository and web portal. Preservation of raw observational data is a complement to the modelled geographic projections that are the focus of related projects such as the EBV Data Portal, which provides access to EBV (Essential Biodiversity Variables) raster datasets. Key to this effort is an emphasis on the use of standardized terms to ensure interoperability with other services, as well as annotation of (meta)data fields and values to aid discoverability and create a product that adheres to the FAIR data principles, requesting data to be Findable, Accessible, Interoperable, and Reusable (Wilkinson et al. 2016). For example, retrieval and storage of globally unique, persistent and resolvable identifiers for core aspects of the data such as taxon names and geospatial locations can serve not only to underpin more advanced search functionality for portal users, but also facilitate future efforts to link open data within online knowledge networks. However addressing social challenges may be equally important in determining the success of the portal. Where do we fit within the biodiversity data landscape and how can we incentivize researchers to submit datasets? What is our data policy? How should we retain provenance and ensure visibility for data providers? Sometimes the choice of a technical solution can itself lower social barriers, for example by providing an intuitive graphical interface to ease upload of the detailed methodological metadata characteristic of these event-based datasets, or by blurring geographic coordinates in order to reduce the risk that threatened species are located. We will present our plans for the web platform currently under construction, and welcome comment on them, to ensure that the portal meets the needs of a diverse range of potential stakeholders. HTML XML PDF

Biodiversity Information Science and Standards 6: e95683 DOI: 10.3897/biss.6.95683 Authors: Pavel Stoev, Zdravko Hubenov, Anna Ganeva, Gergin Blagoev, Boris Barov Abstract: Bulgaria is a medium-sized country located in the eastern part of the Balkan Peninsula. It hosts a rich mycota, flora and fauna, and quite well preserved natural and semi-natural ecosystems. This is mostly due to the country's geographic position between the temperate and subtropical zones, the complex geological history, and the big topographic variety. The high species diversity and endemism determine the high conservation value of Bulgarian biodiversity.The Bulgarian flora consist of more than 4,100 species, including more than 45 species of ferns, 250 species of mosses, and 2,800 higher plant species. The animals established in the country belong to 28 phyla and 75 classes. Vertebrates (858 species) comprise 2.7% of the Bulgarian fauna: 242 fishes and fish-like taxa; 24 amphibians; 40 reptiles; 452 birds; and 101 mammal species. Invertebrates account for more than 31,000 species. Over the past 25 years the number of known animals in the country has increased by over 4,500 species: from 29,000 in 1996 to 33,545 species in 2020. The total number of endemic animals is about 1,400 (4.2%). In some groups, the percentage of endemism is very high (95.5% of snails from the family Hydrobiidae and 71% of Clausiliidae; 53.6% of Diplopoda; 50.0% of terrestrial Isopoda). The richest endemic areas in Bulgaria are mostly in the mountains: Rila Mt.- 268, Pirin Mt. - 220, Western Stara Planina Mt. - 184, Western Rhodopes Mts - 183, and the Central Stara Planina Mt. – 181. Molecular data for Bulgarian animals is still insufficient, although Bulgaria ranks among the top 10 European countries in the proportion of the DNA-barcoded animal taxa; sequence coverage of animal specimens in Barcode of Life data System (BOLD) amounts to approximately 36,000 sequences from more than 7,100 Barcode index numbers (BINs).Bulgaria is part of large-scale initiatives of the European research infrastructure such as the Distributed System of Scientific Collections (DiSSCo) and the MOBILISE COST Action, with mass digitization of museum collections currently underway.Legislation to protect nature in Bulgaria dates back to the end of the 19th century and covers forestry (1890), the protection of certain species (1890's) and hunting (1897). Organized civil movements resulted in the establishment of the Union of Nature Protection (1928), the designation of several nature reserves (1933), and the first National Park (1934). More specific regulation followed with Ordinance for the Protection of Nature (1936). The Red Data Book of Bulgaria was published as early as 1984 (vol. 1, Plants) and 1985 (vol. 2, Animals), with a second updated edition in 2011. Bulgaria is also among the first countries to prepare a National Strategy for Biodiversity Protection (1993, adopted in 1998) following the Convention on Biological Diversity (CBD) process. Since then, several national plans for protection of biodiversity have been adopted including assessments of the threats, objectives, and measures for their achievement. According to recent references, such as the Red Data Book (Beshkov 2011) and the Article 17 reports of 2014 and 2020, the main threats to biodiversity in Bulgaria at the beginning of the 21st century have been human induced degradation: fragmentation and loss of habitats; industrial, agricultural and household waste pollution; direct exploitation of biological resources; genetic ingression and invasive alien species; and global climate change effects. A set of drivers for the loss of biodiversity is related to agriculture and land management, including the whole spectrum from intensification to the abandonment of traditional land, and wetland management practices. HTML XML PDF

Biodiversity Information Science and Standards 6: e95689 DOI: 10.3897/biss.6.95689 Authors: Jessica Allen, R. Troy McMullin Abstract: Community science-generated biodiversity data can provide essential information for understanding species distributions, behaviors and conservation statuses. However, their utility can be limited due to high uncertainty and variability in quality, especially for small taxonomically difficult organisms like fungi and insects. One important set of community-generated data that are increasingly used by scientists are Research Grade (RG) iNaturalist observations. These observations are aggregated into the Global Biodiversity Information Facility database. Here we assessed the accuracy of RG lichen observations in iNaturalist. Lichens are mutualistic symbioses formed between fungi and a photosynthetic partner, either algae or cyanobacteria that occur in every terrestrial ecosystem on the planet (Brodo et al. 2001). They are sensitive indicators of environmental health, especially air quality, and provide essental food and nesting material for animals, along with performing many other ecosystem services (Allen and Lendemer 2021, Brodo et al. 2001, Nimis et al. 2002). We examined hundreds of observations and determined if the identification was correct, if it was not possible to identify the observation given the data provided, or if the identification was incorrect. Identification accuracy of selected species varied widely, from zero observations with enough information for correct identification (e.g., Rhizocarpon geographicum and Cladonia chlorophaea) to 100% correct identifications (e.g., Cetradonia linearis and Physconia subpallida, McMullin and Allen 2022). Most frequently, species that require microscopic examination or chemical tests for accurate identification were unable to be verified versus those that require only macromorphology. We provide a series of suggestions for best practices to improve the quality of RG observations and thus the utility of community-generated observation data for taxonomically difficult organisms. HTML XML PDF