A semantically enriched taxonomic revision of Gryonoides Dodd, 1920 (Hymenoptera, Scelionidae), with a review of the hosts of Teleasinae

Teleasinae are commonly collected scelionids that are the only known egg parasitoids of carabid beetles and therefore play a crucial role in shaping carabid populations in natural and agricultural ecosystems. We review the available host information of Teleasinae, report a new host record, and revise Gryonoides Dodd, 1920, a morphologically distinct teleasine genus. We review the generic concept of Gryonoides and provide diagnoses and descriptions of thirteen Gryonoides species and two varieties: G. glabriceps Dodd, 1920, G. pulchellus Dodd, 1920 (= G. doddi Ogloblin, 1967, syn. nov. and G. pulchricornis Ogloblin, 1967, syn. nov.), G. brasiliensis Masner & Mikó, sp. nov., G. flaviclavus Masner & Mikó, sp. nov., G. fuscoclavatus Masner & Mikó, sp. nov., G. garciai Masner & Mikó, sp. nov., G. mexicali Masner & Mikó, sp. nov., G. mirabilicornis Masner & Mikó, sp. nov., G. obtusus Masner & Mikó, sp. nov., G. paraguayensis Masner & Mikó, sp. nov., G. rugosus Masner & Mikó, sp. nov., G. uruguayensis Masner & Mikó, sp. nov. We treat Gryonoides scutellaris Dodd, 1920, as status uncertain. Gryonoides mirabilicornis Masner & Mikó, sp. nov. is the only known teleasine with tyloids on two consecutive flagellomeres, a well-known trait of Sparasionidae. An illustrated identification key to species of Gryonoides, a queryable semantic representation of species descriptions using PhenoScript, and a simple approach for making Darwin Core Archive files in taxonomic revisions accessible are provided.

Colección viva del Jardín Botánico de la Universidad de la Amazonia Florencia – Caquetá / Living collection of the Universidad de la Amazonia Botanical Garden, Florencia – Caquetá

Se presenta un listado de especies de plantas vasculares presentes en el Jardín Botánico Uniamazonia (JBUDLA), ubicado en el campus Centro en Florencia – Caquetá. Se inventarió y se actualizó el número de especies botánicas empleando el formato único para el registro de colecciones vivas, donde el objetivo principal fue documentar y dar continuidad a la ejecución del plan de manejo de las colecciones vivas del jardín Botánico Uniamazonia. La información obtenida en este inventario se sistematizó de acuerdo a lo requerido por el Instituto de investigación en Recursos Biológicos Alexander von Humboldt en la plantilla “Darwin Core”, para ser subidas al SIB Colombia y el GBIF. Se registraron un total de 1.614 individuos, pertenecientes a 251 especies, 180 géneros y 62 familias, de las cuales las de mayor riqueza fueron Fabaceae con 29 especies, Araceae con 23, Orquidaceae con 18, Arecaceae con 14, Moraceae con 10, Rubiaceae con 8 y Euphorbiaceae con 4 especies.

The fungal literature-based occurrence database for southern West Siberia (Russia)

The paper presents the initiative on literature-based occurrence data mobilisation of fungi and fungi-related organisms (literature-based occurrences, Darwin Core MaterialCitation) to develop the Fungal literature-based occurrence database for the southern West Siberia (FuSWS). The initiative on mobilisation of literature-based occurrence data started in the northern part of West Siberia in 2016. The present project extends the initiative to the southern regions and includes ten administrative territories (Tyumen Region, Sverdlovsk Region, Chelyabinsk Region, Omsk Region, Kurgan Region, Tomsk Region, Novosibirsk Region, Kemerovo Region, Altai Territory and Republic of Altai). The area occupies the central to southern part of the West Siberian Plain and extends for about 1.5 K km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River and from north to south—about 1.3 K km. The total area equals about 1.4 million km2. The initiative is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from eight organisations dedicated to the data mobilisation was created as part of the Siberian Mycological Society (informal organisation since 2019). They have compiled the almost complete bibliographic list of mycology-related papers for the southern West Siberia, including over 900 publications for the last two centuries (the earliest dated 1800). All literature sources were digitised and an online library was created to integrate bibliography metadata and digitised papers using Zotero bibliography manager. The analysis of published sources showed that about two-thirds of works contain occurrences of fungi for the scope of mobilisation. At the time of the paper submission, the database had been populated with a total of about 8 K records from 93 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available (in Russian) at the web site of the Siberian Mycological Society. The initiative will be continued in the following years to extract the records from all published sources. The paper presents the first project with the aim of literature-based occurrence data mobilisation of fungi and fungi-related organisms in the southern West Siberia. The full bibliography and a digital library of all regional mycological publications created for the first time includes about 900 published works. By the time of paper submission, nearly 8 K occurrence records were extracted from about 90 literature sources and integrated into the FuSWS database published in GBIF.

Ecological data in Darwin Core: the case of earthworm surveys

This sampling-event dataset provides primary data about species diversity, age structure, abundance (in terms of biomass and density) and seasonal activity of earthworms (Lumbricidae). The study was carried out in old-growth broad-leaved and young forests of two protected areas ("Kaluzhskiye Zaseki" Nature Reserve and Ugra National Park) of Kaluga Oblast (Russia). The published dataset provides new data about earthworm communities in European Russia. We propose a new schema according to Darwin Core for the standardisation of the soil invertebrates survey data.

A community-developed extension to Darwin Core for reporting the chronometric age of specimens

Darwin Core, the data standard used for sharing modern biodiversity and paleodiversity occurrence records, has previously lacked proper mechanisms for reporting what is known about the estimated age range of specimens from deep time. This has led to data providers putting these data in fields where they cannot easily be found by users, which impedes the reuse and improvement of these data by other researchers. Here we describe the development of the Chronometric Age Extension to Darwin Core, a ratified, community-developed extension that enables the reporting of ages of specimens from deeper time and the evidence supporting these estimates. The extension standardizes reporting about the methods or assays used to determine an age and other critical information like uncertainty. It gives data providers flexibility about the level of detail reported, focusing on the minimum information needed for reuse while still allowing for significant detail if providers have it. Providing a standardized format for reporting these data will make them easier to find and search and enable researchers to pinpoint specimens of interest for data improvement or accumulate more data for broad temporal studies. The Chronometric Age Extension was also the first community-managed vocabulary to undergo the new Biodiversity Informatics Standards (TDWG) review and ratification process, thus providing a blueprint for future Darwin Core extension development.

Birds specimens of the zoological collection of the Universidad de Nariño, Colombia

We provide a complete dataset of bird specimens of the zoological collection at the Universidad de Nariño, Colombia. For every specimen, we reviewed taxonomic identifications to species level by applying curatorial procedures, including the comparison of skins, the use of taxonomic keys and primary literature, and by confirming georeferenced locality data. We present 1249 specimens from 419 species. Most records come from ecosystems in southwestern Colombia, department of Nariño. All records are in the Darwin Core standard and have been made available through the Colombian biodiversity portal (SiB-Colombia) and the GBIF. In addition, we projected these bird occurrences in a geographic context to analyze the density, representation of ecosystems, biogeographic regions, and administrative units (municipalities). We also examine the representation of relevant species regarding their endemism, migratory, or conservation status. With this information, we want to support research and training initiatives to support ecological planning with biogeographic approaches to understand the temporal changes in bird faunas.

Open Forest Data: Digitalizing and building an online repository

Poland is characterised by a relatively high variety of living organisms attributed to terrestrial and water environments. Currently, close to 57.000 species of living organisms are described that occur in Poland (Symonides 2008), including lowland and mountain species, those attributed to oceanic and continental areas, as well as species from forested and open habitats. Poland comprehensively represents biodiversity of living organisms on a continental scale and thus, is considered to have an important role for biodiversity maintenance. The Mammal Research Institute of Polish Academy of Sciences (MRI PAS), located in Białowieża Forest, a UNESCO Heritage Site, has been collecting biodiversity data for 90 years. However, a great amount of data gathered over the years, especially old data, is gradually being forgotten and hard to access. Old catalogues and databases have never been digitalized or publicly shared, and not many Polish scientists are aware of the existence of such resources, not to mention the rest of the scientific world. Recognizing the need for an online, interoperable platform, following FAIR data principles (findable, accessible, interoperable, reusable), where biodiversity and scientific data can be shared, MRI PAS took a lead in creation of an Open Forest Data (OFD) repository. OpenForestData.pl (Fig. 1) is a newly created (2020) digital repository, designed to provide access to natural sciences data and provide scientists with an infrastructure for storing, sharing and archiving their research outcomes. Creating such a platform is a part of an ongoing development of life sciences in Poland, aiming for an open, modern science, where data are published as free-access. OFD also allows for the consolidation of natural science data, enabling the use and processing of shared data, including API (Application Programming Interface) tools. OFD is indexed by the Directory of Open Repositories (OpenDOAR) and Registry of Research Data Repositories (re3data). The OFD platform is based entirely on reliable, globally recognized open source software: DATAVERSE, an interactive database app which supports sharing, storing, exploration, citation and analysis of scientific data; GEONODE, a content management geospatial system used for storing, publicly sharing and visualising vector and raster layers, GRAFANA, a system meant for storing and analysis of metrics and large scale measurement data, as well as visualisation of historical graphs at any time range and analysis for trends; and external tools for database storage (Orthanc) and data visualisation (Orthanc plugin Osimis Web Viewer and Online 3D Viewer (https://3dviewer.net/), which were integrated with the system mechanism of Dataverse. Furthermore, according to the need for specimen description, Darwin Core (Wieczorek et al. 2012) metadata schema was decided to be the most suitable for specimen and collections description and mapped into a Dataverse additional metadata block. The use of Darwin Core is based on the same file format, the Darwin Core Archive (DwC-A) which allows for sharing data using common terminology and provides the possibility for easy evaluation and comparison of biodiversity datasets. It allows the contributors to OFD to optionally choose Darwin Core for object descriptions making it possible to share biodiversity datasets in a standardized way for users to download, analyse and compare. Currently, OFD stores more than 10.000 datasets and objects from the collections of Mammal Research Institute of Polish Academy of Sciences and Forest Science Institute of Białystok University of Technology. The objects from natural collections were digitalized, described, catalogued and made public in free-access. OFD manages seven types of collection materials: 3D and 2D scans of specimen in Herbarium, Fungarium, Insect and Mammal Collections, images from microscopes (including stereoscopic and scanning electron microscopes), morphometric measurements, computed tomography and microtomography scans in Mammal Collection, mammal telemetry data, satellite imagery, geospatial climatic and environmental data, georeferenced historical maps. 3D and 2D scans of specimen in Herbarium, Fungarium, Insect and Mammal Collections, images from microscopes (including stereoscopic and scanning electron microscopes), morphometric measurements, computed tomography and microtomography scans in Mammal Collection, mammal telemetry data, satellite imagery, geospatial climatic and environmental data, georeferenced historical maps. In the OFD repository, researchers have the possibility to share data in standardized way, which nowadays is often a requirement during the publishing process of a scientific article. Beside scientists, OFD is designed to be open and free for students and specialists in nature protection, but also for officials, foresters and nature enthusiasts. Creation of the OFD repository supports the development of citizen science in Poland, increases visibility and access to published data, improves scientific collaboration, exchange and reuse of data within and across borders.

bddashboard: An infrastructure for biodiversity dashboards in R

The bdverse is a collection of packages that form a general framework for facilitating biodiversity science in R (programming language). Exploratory and diagnostic visualization can unveil hidden patterns and anomalies in data and allow quick and efficient exploration of massive datasets. The development of an interactive yet flexible dashboard that can be easily deployed locally or remotely is a highly valuable biodiversity informatics tool. To this end, we have developed 'bddashboard', which serves as an agile framework for biodiversity dashboard development. This project is built in R, using the Shiny package (RStudio, Inc 2021) that helps build interactive web apps in R. The following key components were developed: Core Interactive Components The basic building blocks of every dashboard are interactive plots, maps, and tables. We have explored all major visualization libraries in R and have concluded that 'plotly' (Sievert 2020) is the most mature and showcases the best value for effort. Additionally, we have concluded that 'leaflet' (Graul 2016) shows the most diverse and high-quality mapping features, and DT (DataTables library) (Xie et al. 2021) is best for rendering tabular data. Each component was modularized to better adjust it for biodiversity data and to enhance its flexibility. Field Selector The field selector is a unique module that makes each interactive component much more versatile. Users have different data and needs; thus, every combination or selection of fields can tell a different story. The field selector allows users to change the X and Y axis on plots, to choose the columns that are visible on a table, and to easily control map settings. All that in real-time, without reloading the page or disturbing the reactivity. The field selector automatically detects how many columns a plot needs and what type of columns can be passed to the X-axis or Y-axis. The field selector also displays the completeness of each field. Plot Navigation We developed the plot navigation module to prevent unwanted extreme cases. Technically, drawing 1,000 bars on a single bar plot is possible, but this visualization is not human-friendly. Navigation allows users to decide how many values they want to see on a single plot. This technique allows for fast drawing of extensive datasets without affecting page reactivity, dramatically improving performance and functioning as a fail-safe mechanism. Reactivity Reactivity creates the connection between different components. The changes in input values automatically flow to the plots, text, maps, and tables that use the input, and cause them to update. Reactivity facilitates drilling down functionality, which enhances the user’s ability to explore and investigate the data. We developed a novel and robust reactivity technique that allows us to add a new component and effectively connect it with all existing components within a dashboard tab, using only one line of code. Generic Biodiversity Tabs We developed five useful dashboard tabs (Fig. 1): (i) the Data Summary tab to give a quick overview of a dataset; (ii) the Data Completeness tab helps users get valuable information about missing records and missing Darwin Core fields; (iii) the Spatial tab is dedicated to spatial visualizations; (iv) the Taxonomic tab is designed to visualize taxonomy; and (v) the Temporal tab is designed to visualize time-related aspects. Performance and Agility To make a dashboard work smoothly and react quickly, hundreds of small and large modules, functions, and techniques must work together. Our goal was to minimize dashboard latency and maximize its data capacity. We used asynchronous modules to write non-blocking code, clusters in map components, and preprocessing and filtering data before passing it to plots to reduce the load. The 'bddashboard' package modularized architecture allows us to develop completely different interactive and reactive dashboards within mere minutes.

GeoNature, Open-Source FAIR Biodiversity Data Management

Huge improvements have been made throughout the years in collecting and standardising biodiversity data (Bisby 2000, Osawa 2019, Hardisty and Roberts 2013) and in overhauling how to make information in the field of biodiversity data management more FAIR (Findable, Accessible, Interoperable, Reusable) (Simons 2021), but there is still room for improvement. Most professionals working in protected areas, conservation groups, and research organisations lack the required know-how to improve the reuse ratio of their data. The GeoNature and GeoNature-Atlas (Monchicourt 2018, Corny et al. 2019) are a set of open-source software that facilitate data collection, management, validation, sharing (e.g., via Darwin Core standard) and visualisation. It is a powerful case study of collaborative work, which includes teams from private and public sectors with at least fifteen national parks and forty other organisations currently using and contributing to the package in France and Belgium (view it on github).

Improving the Adoption and Evolution of Data Standards for Fossil Specimens

As we atomize and expand the digital representation of specimen information through data standards, it is critical to evaluate the implementation of these developments, including how well they serve discipline-specific needs. In particular, fossil specimens often present challenges because they require information to be captured that is seemingly parallel to, but not entirely aligned with, that of their extant counterparts. Previous work to evaluate data sharing practices of paleontology collections has shown an imbalance in the use of Darwin Core (DwC) (Wieczorek et al. 2012) terms and many instances of underutilized terms (Little 2018). To expand upon that broad assessment and encourage better adoption of evolving standards and data practices by fossil collections, a more in-depth review of term usage is necessary. Here we review specific DwC terms that are underutilized or that present challenges for fossil occurrence records, and we examine the subsequent impact on data discovery of paleo specimens. We conclude by sharing options for improving standards implementation within a paleo context. We see key patterns and challenges in current implementation of DwC in paleo collections, as evidenced by evaluations of the typical mappings found in occurrence records for fossil specimens, data flags applied by aggregators, and discussions within the paleo collections community. These can be organized into three broad groupings. Group 1: Some DwC terms (or classes of terms) are clear to implement, but are underutilized due to issues that are also found within the neontological community. Example: Location. In the case of terms related to the Location class, paleontology has a need for a way to deal with sensitive locality information. The sensitivity here typically relates to laws restricting the sharing of locality information to protect fossil sites versus neontological requirements to protect threatened, rare, or endangered species. The end goal of needing to fuzz locality information without completely making the specimen record undiscoverable or unusable is the same. There is a need for better education at the paleo data provider-level related to standards for recording and sharing information in this category, which could be based on existing neontological community standards. Group 2: A second group of DwC terms often seem clear to implement, but the terminology used to describe and define them might be unfamiliar to paleontologists or read as unnecessary for fossil occurrences. This uncertainty about the applicability of a term to paleo data can often result in data not being mapped or fully shared. Example: recordedBy (= collector). In these cases, a simple translation of what the definition means in verbiage that is familiar to paleontologists, or the inclusion of paleo-oriented examples in the DwC documentation, can make implementation clear. Group 3: A third group of issues relates to DwC terms, classes, and/or extensions that are more complicated in the context of fossil vs. neontological data. In some cases use of these terms is complicated for neontological data as well, but perhaps for different reasons. The terms impacted by these challenges can sometimes have the same general use, but due to the nature of fossil preservation, or because a term has a different meaning within the discipline of paleontology, additional layers of uncertainty or ambiguity are present. Examples: Resource Relationship/Interactions, Individual count, Preparations, Taxon. Review of these terms and their related classes and/or the extensions they are part of has revealed that they might require qualification, further explanation, additional vocabulary terms, or even the need for special handling instructions when data are ingested and normalized at the aggregator level. This group of issues is more complicated to resolve, but the problems are not intractable and can progress toward solutions through further discussion within the community, active participation in the standards development and review process, and development of clear guidelines. Strategically assessing these terms and generating discipline-specific guidelines to be used by the paleo community can improve the mobilization and discovery of fossil occurrence data. Documenting these paleo data practices not only helps data providers, it also increases the utility of these data within the broader research community by clearly outlining how the terms were used. Overall, this discipline-focused approach to understanding the implementation of data standards like DwC at the term level, helps to increase knowledge sharing across the paleo community, improves data quality and standards adoption, and moves these datasets towards alignment with best practices like the FAIR (Findable, Accessible, Interoperable, Reusable) data principles.