Search

Technological advancements in biological monitoring have facilitated the study of insect communities at unprecedented spatial scales. The progress allows more comprehensive coverage of the diversity within a given area while minimizing disturbance and reducing the need for extensive human labour. Compared with traditional methods, these novel technologies offer the opportunity to examine biological patterns that were previously beyond our reach. However, to address the pressing scientific inquiries of the future, data must be easily accessible, interoperable and reusable for the global research community. Biodiversity information standards and platforms provide the necessary infrastructure to standardize and share biodiversity data. This paper explores the possibilities and prerequisites of publishing insect data obtained through novel monitoring methods through GBIF, the most comprehensive global biodiversity data infrastructure. We describe the essential components of metadata standards and existing data standards for occurrence data on insects, including data extensions. By addressing the current opportunities, limitations, and future development of GBIF's publishing framework, we hope to encourage researchers to both share data and contribute to the further development of biodiversity data standards and publishing models. Wider commitments to open data initiatives will promote data interoperability and support cross-disciplinary scientific research and key policy indicators. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, the field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based methods in large-scale monitoring, and to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, we provide three recommendations for how to improve and harmonize efforts in biodiversity assessment and monitoring via metabarcoding: (i) we should adopt the use of synthetic spike-ins, which will act as positive controls and internal standards; (ii) we should consider using several markers through a multiplex polymerase chain reaction (PCR) approach; and (iii) we should commit to the publication and transparency of all protocol-associated metadata in a standardized fashion. For (i), we provide a ready-to-use recipe for synthetic cytochrome c oxidase spike-ins, which enable between-sample comparisons. For (ii), we propose two gene regions for the implementation of multiplex PCR approaches, thereby achieving a more comprehensive community description. For (iii), we offer guidelines for transparent and unified reporting of field, wet-laboratory and dry-laboratory procedures, as a key to making comparisons between studies. Together, we feel that these three advances will result in joint quality and calibration standards rather than the current laboratory-specific proof of concepts. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well-being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within-species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (N e ). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large-scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long-term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally., (© 2022 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behlaf of Cambridge Philosophical Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Background: The increasing availability of multi-omics data is leading to regularly revised estimates of existing biodiversity data. In particular, the molecular data enable novel species to be characterized and the information linked to those already observed to be increased with new genomics data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy-to-use IT tools have become a key point to design future research. The more users are able to access biodiversity-related information, the greater the ability of the scientific community to expand its knowledge in this area., Results: In this article we focus on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool that can retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. We use 3 case studies to show how an efficient organization of the available data can lead to obtaining new information that is fundamental as a starting point for new research. Using this approach highlights the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad-spectrum studies such as metagenomics., Conclusions: ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim of helping researchers to improve experimental designs and highlight the main gaps in the coverage of available data., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

Genomic data are being produced and archived at a prodigious rate, and current studies could become historical baselines for future global genetic diversity analyses and monitoring programs. However, when we evaluated the potential utility of genomic data from wild and domesticated eukaryote species in the world's largest genomic data repository, we found that most archived genomic datasets (86%) lacked the spatiotemporal metadata necessary for genetic biodiversity surveillance. Labor-intensive scouring of a subset of published papers yielded geospatial coordinates and collection years for only 33% (39% if place names were considered) of these genomic datasets. Streamlined data input processes, updated metadata deposition policies, and enhanced scientific community awareness are urgently needed to preserve these irreplaceable records of today's genetic biodiversity and to plug the growing metadata gap., Competing Interests: Competing interest statement: L.L., M.R.G., C.R., R.J.T., and E.D.C. serve on the steering committee for the Genomics Observatories Metadatabase without compensation., (Copyright © 2021 the Author(s). Published by PNAS.)

The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA mi Tags; and (iii) 16S-V4 V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode data sets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables. Ocean Barcode Atlas is a freely-available web service at: http://oba.mio.osupytheas.fr/ocean-atlas/., (© 2021 John Wiley & Sons Ltd.)

The increasing amount of publicly available research data provides the opportunity to link and integrate data in order to create and prove novel hypotheses, to repeat experiments or to compare recent data to data collected at a different time or place. However, recent studies have shown that retrieving relevant data for data reuse is a time-consuming task in daily research practice. In this study, we explore what hampers dataset retrieval in biodiversity research, a field that produces a large amount of heterogeneous data. In particular, we focus on scholarly search interests and metadata, the primary source of data in a dataset retrieval system. We show that existing metadata currently poorly reflect information needs and therefore are the biggest obstacle in retrieving relevant data. Our findings indicate that for data seekers in the biodiversity domain environments, materials and chemicals, species, biological and chemical processes, locations, data parameters and data types are important information categories. These interests are well covered in metadata elements of domain-specific standards. However, instead of utilizing these standards, large data repositories tend to use metadata standards with domain-independent metadata fields that cover search interests only to some extent. A second problem are arbitrary keywords utilized in descriptive fields such as title, description or subject. Keywords support scholars in a full text search only if the provided terms syntactically match or their semantic relationship to terms used in a user query is known., Competing Interests: The authors have declared that no competing interests exist.

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology., (© 2020 John Wiley & Sons Ltd.)

Interdisciplinary collaborations and data sharing are essential to addressing the long history of human-environmental interactions underlying the modern biodiversity crisis. Such collaborations are increasingly facilitated by, and dependent upon, sharing open access data from a variety of disciplinary communities and data sources, including those within biology, paleontology, and archaeology. Significant advances in biodiversity open data sharing have focused on neontological and paleontological specimen records, making available over a billion records through the Global Biodiversity Information Facility. But to date, less effort has been placed on the integration of important archaeological sources of biodiversity, such as zooarchaeological specimens. Zooarchaeological specimens are rich with both biological and cultural heritage data documenting nearly all phases of human interaction with animals and the surrounding environment through time, filling a critical gap between paleontological and neontological sources of data within biodiversity networks. Here we describe technical advances for mobilizing zooarchaeological specimen-specific biological and cultural data. In particular, we demonstrate adaptations in the workflow used by biodiversity publisher VertNet to mobilize Darwin Core formatted zooarchaeological data to the GBIF network. We also show how a linked open data approach can be used to connect existing biodiversity publishing mechanisms with archaeoinformatics publishing mechanisms through collaboration with the Open Context platform. Examples of ZooArchNet published datasets are used to show the efficacy of creating this critically needed bridge between biological and archaeological sources of open access data. These technical advances and efforts to support data publication are placed in the larger context of ZooarchNet, a new project meant to build community around new approaches to interconnect zoorchaeological data and knowledge across disciplines., Competing Interests: The authors have declared no competing interests exist.

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals., (© 2017 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

Microbial data and metadata are scattered throughout the scientific literature, databases and unpublished lab notes and thereby often are difficult to access. Hot spots of (meta)data are internal descriptions of culture collections and initial descriptions of novel taxa in primary literature. Here we describe three exemplary mobilization projects which yielded metadata published through the prokaryotic metadatabase BacDive. The Reichenbach collection of myxobacteria includes information on 12,535 typewritten index cards which were digitized. A total of 37,156 data points were extracted by text mining. In the second mobilization project, Analytical Profile Index (API) tests on paper forms were targeted. Overall 6820 API tests were digitized, which provide physiological data of 4524 microbial strains. Thirdly, the extraction of metadata from 523 new species descriptions of the International Journal of Systematic and Evolutionary Microbiology, yielding 35,651 data points, is described. All data sets were integrated and published in BacDive. Thereby these metadata not only became accessible and searchable but were also linked to strain taxonomy, isolation source, cultivation condition, and molecular biology data., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information's (NCBI's) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

In taxonomy, precision of species collection data is a cornerstone for advancing research and its diverse applications. Despite the widespread recognition of the significance of these data, researchers have frequently neglected some important details in published taxonomic studies. Historically, fungal studies leaned heavily on the morphological delineation of taxa. In contrast, taxonomic methods currently employ a synthesis of a diverse combination of morpho-molecular markers, chemical attributes and both ecological and geographic data. Even with these new methods, mycologists value the data derived from old fungal records as essential guides for current and future studies. Therefore, this underscores the importance of careful documentation of data on habits and habitats in parallel with fungal collection. While collecting specimens of fungi, it is important to record metadata such as sampling location, habitat (host/substrate), season (date or specific season) and physical and morphological information on the specimen itself. These datasets will provide a rich source of information for the taxonomy, ecology and conservation of fungal resources. Understanding fungal distribution patterns and the possible explanations for these patterns is a real challenge for conserving biodiversity, and the lack of data-recording of specimens creates substantial obstacles. Accurate fungarium data are a basic source for understanding fungal distribution and patterns of richness and assessing red-listed and invasive species. This paper explores the importance of additions to fungal data recording, emphasising fungal hosts and geographic locations. We also discuss the significant roles of seemingly insignificant details in fungal data recording to enhance the understanding of researchers about the ecological relationships of fungal species. [ABSTRACT FROM AUTHOR]

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Copyright of ABI Technik is the property of De Gruyter and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration. In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications. To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. This mapping, combined with the development of the MIxS-DwC extension, enables the incorporation of MIxS core terms into DwC-compliant metadata records, facilitating seamless data exchange between MIxS and DwC user communities. Through the implementation of this translation layer, data produced in either MIxS- or DwC-compliant formats can now be efficiently brokered, breaking down silos and fostering closer collaboration between the biodiversity and omics communities. To ensure its sustainability and lasting impact, TDWG and GSC have both signed a Memorandum of Understanding (MoU) on creating a continuous model to synchronize their standards. These achievements mark a significant step forward in enhancing data sharing and utilization across domains, thereby unlocking new opportunities for scientific discovery and advancement. [ABSTRACT FROM AUTHOR]

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome‐scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data‐sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever. [ABSTRACT FROM AUTHOR]

Aim: Species occurrence records are essential to understanding Earth's biodiversity and addressing global environmental issues, but do not always reflect actual locations of occurrence. Certain geographical coordinates are assigned repeatedly to thousands of observation/collection records. This may result from imperfect data management and georeferencing practices, and can greatly bias the inferred distribution of biodiversity and associated environmental conditions. Nonetheless, these 'biodiverse' coordinates are often overlooked in taxon‐centric studies, as they are identifiable only in aggregate across taxa and datasets, and it is difficult to determine their true circumstance without in‐depth, focused investigation. Here we assess highly recurring coordinates in biodiversity data to determine artificial hotspots of occurrences. Location: Global. Taxon: Land plants, birds, mammals, insects. Methods: We identified highly recurring coordinates across plant, bird, insect and mammal records in the Global Biodiversity Information Facility, the largest aggregator of biodiversity data. We determined which are likely artificial hotspots by examining metadata from over 40 million records, assessing spatial distributions of associated datasets, contacting data managers and reviewing literature. These results were compiled into the Artificial Hotspot Occurrence Inventory (AHOI). Results: Artificial biodiversity hotspots generally comprised geopolitical and grid centroids. The associated uncertainty ranged from several square kilometres to millions. Such artificial biodiversity hotspots were most prevalent in plant records. For instance, over 100,000 plant occurrence records were assigned the centroid coordinates of Brazil, and points that have at least 1000 associated occurrences comprised over 9 million records. In contrast, highly recurring coordinates in animal data more often reflected actual sites of observation. Main conclusions AHOI can be used to (i) improve accuracy of biodiversity assessments; (ii) estimate uncertainty associated with records from artificial hotspots and make informed decisions on whether to include them in scientific studies; and (iii) identify problems in biodiversity informatics workflows and priorities for improvement. [ABSTRACT FROM AUTHOR]

Elusive flaws are identified in techniques widely adopted to organize the Material Examined sections in taxonomic publications, mostly regarding the usage of the term ibidem and the nesting of information such as country and states. Logical errors are identified that prevent objective retrieval of the original information and can hinder or block its interpretation, even in case-by-case analyses. It is demonstrated that the free usage of ibidem in the sense of “same as previous except as follows” compromises the interpretation of data, characterizing bad practice. Solutions are proposed for the precise usage of both the term ibidem and the nesting technique. A new technique for organizing, compressing, and presenting information, called grid-setting, is described and evaluated. Its most notable practical effect is that the Material Examined section becomes literally a coded data sheet, which can be accurately converted back to spreadsheet format. In addition, the grid-setting technique was able to generate texts up to 30% shorter than those edited with the best-known traditional techniques. The new ideas and fixes are incorporated into a new software, flexible enough to process varied and unlimited data into largely user-defined texts, which remain nevertheless universal in their format and logical interpretation.

Fair and equitable benefit sharing of genetic resources is an expectation of the Nagoya Protocol. Although the Nagoya Protocol does not yet formally apply to Digital Sequence Information ("DSI"), discussions are currently underway regarding to include such data through ongoing Convention on Biological Diversity ("CBD") negotiations. While Indigenous Peoples and Local Communities ("IPLC") expect the value generated from genomic data to be subject to benefit sharing arrangements, a range of views are currently being expressed by Nation States, IPLC and other stakeholders. The use of DSI gives rise to unique considerations, creating a gray area as to how it should be considered under the Nagoya Protocol's Access and Benefit Sharing ("ABS") principles. One way for benefit sharing to be enhanced is through the connection of data to proper provenance information. A significant development is the use of digital labeling systems to ensure that the origin of samples is appropriately disclosed. The Traditional Knowledge and Biocultural Labels initiative offers a practical option for data provided to genomic databases. In particular, the BioCultural Labels ("BC Labels") are a mechanism for Indigenous communities to identify and maintain provenance, origin and authority over biocultural material and data generated from Indigenous land and waters held in research, cultural institutions and data repositories. This form of cultural metadata adds value to the research endeavor and the creation of Indigenous fields within databases adds transparency and accountability to the research environment. [ABSTRACT FROM AUTHOR]

Background: Tremendous amounts of data generated from microbiome research studies during the last decades require not only standards for sampling and preparation of omics data but also clear concepts of how the metadata is prepared to ensure re-use for integrative and interdisciplinary microbiome analysis. Results: In this Commentary, we present our views on the key issues related to the current system for metadata submission in omics research, and propose the development of a global metadata system. Such a system should be easy to use, clearly structured in a hierarchical way, and should be compatible with all existing microbiome data repositories, following common standards for minimal required information and common ontology. Although minimum metadata requirements are essential for microbiome datasets, the immense technological progress requires a flexible system, which will have to be constantly improved and re-thought. While FAIR principles (Findable, Accessible, Interoperable, and Reusable) are already considered, international legal issues on genetic resource and sequence sharing provided by the Convention on Biological Diversity need more awareness and engagement of the scientific community. Conclusions: The suggested approach for metadata entries would strongly improve retrieving and re-using data as demonstrated in several representative use cases. These integrative analyses, in turn, would further advance the potential of microbiome research for novel scientific discoveries and the development of microbiome-derived products. [ABSTRACT FROM AUTHOR]

Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines' status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the 'Philippines' biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location-highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon. [ABSTRACT FROM AUTHOR]

The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million‐tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client‐side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on relatively old mobile devices.The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species.The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in, and supporting multiple applications including exhibition kiosks and digital art.After 10 years of work, our tree of life explorer is now broadly complete, it has attracted nearly 1.5 million online users, and is backed by a novel long‐term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree. [ABSTRACT FROM AUTHOR]

Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-scale syntheses may be compromised if metabarcoding workflows differ from each other. There are ongoing efforts to improve standardization for the reporting of inventory data. However, harmonization at the stage of generating metabarcode data has yet to be addressed. A modular framework for harmonized data generation offers a pathway to navigate the complex structure of terrestrial metazoan biodiversity. Here, through our collective expertise as practitioners, method developers, and researchers leading metabarcoding initiatives to inventory terrestrial biodiversity, we seek to initiate a harmonized framework for metabarcode data generation, with a terrestrial arthropod module. We develop an initial set of submodules covering the 5 main steps of metabarcode data generation: (i) sample acquisition; (ii) sample processing; (iii) DNA extraction; (iv) polymerase chain reaction amplification, library preparation, and sequencing; and (v) DNA sequence and metadata deposition, providing a backbone for a terrestrial arthropod module. To achieve this, we (i) identified key points for harmonization, (ii) reviewed the current state of the art, and (iii) distilled existing knowledge within submodules, thus promoting best practice by providing guidelines and recommendations to reduce the universe of methodological options. We advocate the adoption and further development of the terrestrial arthropod module. We further encourage the development of modules for other biodiversity fractions as an essential step toward large-scale biodiversity synthesis through harmonization. [ABSTRACT FROM AUTHOR]

Recordings of bat echolocation and social calls are used for many research purposes from ecological studies to taxonomy. Effective use of these relies on identification of species from the recordings, but comparative recordings or detailed call descriptions to support identification are often lacking for areas with high biodiversity. The ChiroVox website (www.chirovox.org) was created to facilitate the sharing of bat sound recordings together with their metadata, including biodiversity data and recording circumstances. To date, more than 30 researchers have contributed over 3,900 recordings of nearly 200 species, making ChiroVox the largest open-access bat call library currently available. Each recording has a unique identifier that can be cited in publications; hence the acoustic analyses are repeatable. Most of the recordings available through the website are from bats whose species identities are confirmed, so they can be used to determine species in recordings where the bats were not captured or could not be identified. We hope that with the help of the bat researcher community, the website will grow rapidly and will serve as a solid source for bat acoustic research and monitoring. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Presence-only biodiversity data are increasingly relied on in biodiversity, ecology, and conservation research, driven by growing digital infrastructures that support open data sharing and reuse. Recent reviews of open biodiversity data have clearly documented the value of data sharing, but the extent to which the biodiversity research community has adopted open data practices remains unclear. We address this question by reviewing applications of presence-only primary biodiversity data, drawn from a variety of sources beyond open databases, in the indexed literature. We characterize how frequently researchers access open data relative to data from other sources, how often they share newly generated or collated data, and trends in metadata documentation and data citation. Our results indicate that biodiversity research commonly relies on presence-only data that are not openly available and neglects to make such data available. Improved data sharing and documentation will increase the value, reusability, and reproducibility of biodiversity research. [ABSTRACT FROM AUTHOR]

Entomology collections, along with natural history collections in general, are crucial for research in understanding biological diversity and the impact of humans on landscapes and climate. However, much of the metadata associated with these collections is not available in a digital format, making it difficult for researchers to access and analyze. Digitizing metadata and preserving specimens is necessary to make these collections accessible and prevent data loss. Additionally, there is a need for continued collecting and preservation of scientific specimens, as new technologies alone cannot replace the value of physical specimens. The future of entomological collections relies on the support and advocacy of entomologists and the inclusion of diverse perspectives and knowledge. [Extracted from the article]

Background and objectives: The environmental effects of static gear fishing include habitat-level effects such as permanent changes to the physical environment and the structure of the benthic and epibenthic communities. Ecosystems subjected to prolonged exposure to pressure from static gear may undergo permanent changes and may never regain their prior 'unfished' state even if the fishing pressure is removed entirely. These long-term changes to physical structure of benthic habitats have implications for benthic biodiversity and ecosystem functioning. Despite this, the understanding of habitat and static fishing gear interactions is limited- with most studies focusing on the impact of mobile fishing gear. The rise of ecosystem-based fisheries management (EBFM), where managers and decision-makers manage target species within their environmental context while protecting essential ecosystem services and components, has led to an increased demand for ecosystem-level reference points. A systematic review could provide clarification on the short and long-term impacts of commercial static gear fishing on benthic community diversity. Methods: This review will examine primary studies on the relationship between static fishing gear, intensity, and benthic biodiversity to answer the primary question 'How do different types of static fishing gear affect benthic species richness and abundance?'. A structured search will be conducted in English. The search terms used to find relevant data to answer the research question were chosen specifically for this review and were generated using the R package litsearchr. Captured articles will be screened against pre-defined eligibility criteria. The internal and external validity of remaining studies will be classified using a pre-defined framework. Studies meeting validity will be used for data extraction. Data to be extracted includes data on study design, intervention, study results, habitat and geographical context. Outcome data (such as sample sizes, means and measures of variation such as confidence intervals, standard deviations, and standard errors) will also be extracted. Information on effect modifiers will also be collected where available as well as metadata on study methodologies and general article identifiers. Data will be used for both narrative and quantitative synthesis techniques. [ABSTRACT FROM AUTHOR]

Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity. Fungi are everywhere, yet we have only named and described a minute fraction of the fungal world. In this Review, Lofgren and Stajich review the state of fungal diversity research, highlighting recent technological advancements and how changing viewpoints in taxonomy and systematics can be integrated to advance research and preserve biodiversity. [ABSTRACT FROM AUTHOR]

The World Checklist of Vascular Plants (WCVP) is a comprehensive list of scientifically described plant species, compiled over four decades, from peer-reviewed literature, authoritative scientific databases, herbaria and observations, then reviewed by experts. It is a vital tool to facilitate plant diversity research, conservation and effective management, including sustainable use and equitable sharing of benefits. To maximise utility, such lists should be accessible, explicitly evidence-based, transparent, expert-reviewed, and regularly updated, incorporating new evidence and emerging scientific consensus. WCVP largely meets these criteria, being continuously updated and freely available online. Users can browse, search, or download a user-defined subset of accepted species with corresponding synonyms and bibliographic details, or a date-stamped full dataset. To facilitate appropriate data reuse by individual researchers and global initiatives including Global Biodiversity Information Facility, Catalogue of Life and World Flora Online, we document data collation and review processes, the underlying data structure, and the international data standards and technical validation that ensure data quality and integrity. We also address the questions most frequently received from users. Measurement(s) Vascular Plant • Species Technology Type(s) digital curation Sample Characteristic - Organism Tracheophyta Sample Characteristic - Location global Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.15035046 [ABSTRACT FROM AUTHOR]

Several recent papers have highlighted best practices, defined metadata standards and proposed checklists for reproducibility of species distribution models (SDMs). A new paper by Zurell et al. (2020) formalizes, extends and implements many of these ideas in a standardized protocol for reporting SDMs called ODMAP (Overview, Data, Model, Assessment, Prediction). ODMAP has the potential to revolutionize species distribution modeling, not through the development of new methods, but rather by providing a long overdue system to document, communicate and reproduce methods. ODMAP could lead to improved basic and applied science outcomes by increasing comprehension and transparency, and by guiding implementation of best practices. However, the impact that ODMAP has on SDMs depends in large part on the extent to which journals, reviewers and funding agencies encourage its use and whether mentors introduce it to the next generation of biodiversity scientists. Important next steps include formalizing mechanisms for the broader research community to participate in future development of ODMAP and related standards for best practices in biodiversity modeling. [ABSTRACT FROM AUTHOR]

Species and habitats are the subjects of legislation that mandates reporting of information on ecosystem conditions. Improvements in sensors, sampling platforms, information systems, and collaborations among experts and information users now enables more effective and up-to-date information to meet regional and national needs. Specifically, advances in environmental DNA (eDNA)-based assessments of biodiversity, community science data, various underwater imaging devices, and environmental, behavioral, and physiology observations from animal telemetry provide new opportunities to address multiple requirements for reporting status and trends, including insights into life in the deep ocean. Passive and active acoustic sensors help monitor marine life, boat traffic, and noise pollution. Satellites provide repeated, frequent, and long-term records of many relevant variables from global to local scales and, when combined with numerical computer simulations, allow planning for future scenarios. Metadata standards facilitate the transfer of data from machine to machine, thus streamlining assessments and forecasting and providing knowledge directly to the public. The Marine Biodiversity Observation Network (MBON) facilitates this exchange of information on life in the sea. The collaborative efforts of the Central and Northern California Ocean Observing System (CeNCOOS) of the US Integrated Ocean Observing System and its partners provide an example of a regional MBON process for information delivery. This includes linking policy and management needs, prioritizing observing data from various platforms and methods, streamlining data handling practices, and delivering information for management such as for the Monterey Bay National Marine Sanctuary and the California Current Large Marine Ecosystem, with iterative process adaptation. [ABSTRACT FROM AUTHOR]

Single-cell RNA sequencing (scRNA-seq) provides an unprecedented view of cellular diversity of biological systems. However, across the thousands of publications and datasets generated using this technology, we estimate that only a minority (<25%) of studies provide cell-level metadata information containing identified cell types and related findings of the published dataset. Metadata omission hinders reproduction, exploration, validation, and knowledge transfer and is a common problem across journals, data repositories, and publication dates. We encourage investigators, reviewers, journals, and data repositories to improve their standards and ensure proper documentation of these valuable datasets. Most Gene Expression Omnibus (GEO) depositions of single-cell mRNA sequencing data do not include cell-level metadata generated by typical analysis pipelines; this Essay maintains that this omission greatly hinders reproduction, exploration, validation, and knowledge transfer and is a common problem across journals, data repositories, and publication dates. [ABSTRACT FROM AUTHOR]

The present dataset contains information about aquatic macroinvertebrates and environmental variables collected before and after the implementation of a small "run-of-river" hydropower plant on the Saldur stream, a glacier-fed stream located in the Italian Central-Eastern Alps. Between 2015 and 2019, with two sampling events per year, we collected and identified 34,836 organisms in 6 sampling sites located within a 6 km stretch of the stream. Given the current boom of the hydropower sector worldwide, and the growing contribution of small hydropower plants to energy production, data here included may represent an important – and long advocated – baseline to assess the effects that these kinds of powerplants have on the riverine ecosystem. Moreover, since the Saldur stream is part of the International Long Term Ecological Research network, this dataset also constitutes part of the data gathered within this research programme. All samples are preserved at Eurac Research facilities. Measurement(s) Abundance of benthic macroinvertebrates • Physical and chemical water parameters • biodiversity assessment objective Technology Type(s) Surber sampler • Multiparameter probe • material sampling process Sample Characteristic - Organism Aquatic benthic macroinvertebrates Sample Characteristic - Environment englacial stream Sample Characteristic - Location Province of Bolzano-Bozen • Central Eastern Alps • Italy Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.14046554 [ABSTRACT FROM AUTHOR]

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 19 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. [ABSTRACT FROM AUTHOR]

Species of Acanthobothrium have been documented as parasites of the spiral intestine of elasmobranchs. Results of a metadata analysis indicate that 114 species of elasmobranchs have been reported as hosts of 200 species of Acanthobothrium. The metadata analysis revealed that 3.7% of species of sharks and 14.9% of species of rays that have been reported as hosts to date; some species are parasitized by more than one species of Acanthobothrium. This work provides a Category designation, as proposed by Ghoshroy and Caira (2001), for each species of Acanthobothrium. These Category designations are a tool to facilitate comparisons among members of Acanthobothrium for descriptions of new species in the future. [ABSTRACT FROM AUTHOR]

Biodiversity informatics depends on digital access to credible information about species. Many online resources host species' data, but the lack of categorisation for these resources inhibits the growth of this entire field. To explore possible solutions, we examined the (now retired) Biodiversity Information Projects of the World (BIPW) dataset created by the Biodiversity Information Standards (TDWG); this project, which ran from 2007-2015 (officially removed from the TDWG website in 2018) was an attempt at organising the Web's biodiversity databases into an indexed list. To do this, we applied a simple classification scheme to score databases within BIPW based on nine data categories, to characterise trends and current compositions of this biodiversity einfrastructure. Primarily, we found that of 600 databases investigated from BIPW, only 315 (~53%) were accessible at the time of this writing, underscoring the precarious nature of the biodiversity information landscape. Many of these databases are still available, but suffer accessibility issues such as link rot, thus putting the information they contain in danger of being lost. We propose that a community-driven database of biodiversity databases with an accompanying ontology could facilitate efficient discovery of relevant biodiversity databases and support smaller databases - which have the greatest risk of being lost. [ABSTRACT FROM AUTHOR]

The zoologist Dr. José Santiago Lima-Verde (1945-2019) made a number of major contributions to the field of animal biology in the northeastern Brazil, in particular through his research with snakes. While employed as a professor at Escola Superior de Agricultura de Mossoró, currently the Universidade Federal Rural do Semi-Árido, Prof. Lima-Verde established a herpetological collection which remained forgotten for a number of decades. In the present study, we describe the revitalization of this collection, which included the updating of the identification of the species and the compilation of the metadata on the collection, which is now named the Coleção Herpetológica Lima-Verde. We catalogued 80 specimens representing 30 species, including 23 species of snakes, five lizards, and two amphisbaenians. One third (30%) of the specimens had information on dates and sites, with the majority of these specimens being collected in the Brazilian State of Rio Grande do Norte during the 1970's. We also catalogued 315 eggs of seven snake species, from 22 clutches laid in captivity. The collection presents unpublished data and will constitute a reference for future herpetological research on the species found in western region of State of Rio Grande do Norte. Our findings reinforce the importance of zoological collections for the understanding of patterns of biodiversity, and we would recommend the creation of more regional scientific collections and the broader recognition of their value as a basic source of biological data. [ABSTRACT FROM AUTHOR]

O acesso aos dados de pesquisa permite o desenvolvimento de pesquisas adicionais, fornece informações para subsidiar decisões e contribui para a transparência na ciência. Este estudo analisa a comunicação científica dos conjuntos de dados relacionados à temática biodiversidade, sob a perspectiva do uso dos metadados ao longo do fluxo de informação científica. Para tanto, será realizada a análise comparativa entre os padrões de metadados internacionalmente recomendados e as evidências de uso dos metadados nos registros de conjuntos de dados de pesquisa. Trata-se de uma pesquisa qualitativa e descritiva, com estratégia de coleta de dados bibliográfica e documental, considerando como fontes os artigos da literatura científica e os registros de metadados dos conjuntos de dados relativos à biodiversidade extraídos em repositórios de acesso livre. As buscas por evidências de uso dos metadados serão guiadas pelo método chamado recuperação de informação realizada pouco-a-pouco (bit-at-a-time ou berry picking). Para coleta e análise adota-se a revisão sistematizada e a meta-síntese. Como resultado, espera-se delinear o panorama de uso dos metadados no registro dos dados de pesquisa sobre biodiversidade. Além disso, há a expectativa de que seja possível também identificar práticas internalizadas na gestão, comunicação e governança desses dados. Making data accessible allows further research, provides information for decision-making and contributes to transparency in science. This paper presents an ongoing study about the scientific communication of the global biodiversity data sets, analyzed under the perspective of metadata use throughout the scientific information flow. The proposed methodology aims to establish a baseline by identifying the internationally recommended metadata standards and compare it with existent metadata evidences. This study is grounded in a qualitative and descriptive research of metadata evidences that will be guided by the berry picking method. Furthermore, the systematic review and meta-synthetic analysis were defined as methods to collect and analyze metadata evidences extracted from scientific articles and metadata records related to biodiversity research data sets of public repositories. The expected outcome is to outline metadata use in biodiversity data sets in a comparative analysis view to recommended standards. It is also expected to identify practices that have been adopted in the management, communication and governance of biodiversity research data. [ABSTRACT FROM AUTHOR]

People are one of the best known and most stable entities in the biodiversity knowledge graph. The wealth of public information associated with people and the ability to identify them uniquely open up the possibility to make more use of these data in biodiversity science. Person data are almost always associated with entities such as specimens, molecular sequences, taxonomic names, observations, images, traits and publications. For example, the digitization and the aggregation of specimen data from museums and herbaria allow us to view a scientist's specimen collecting in conjunction with the whole corpus of their works. However, the metadata of these entities are also useful in validating data, integrating data across collections and institutional databases and can be the basis of future research into biodiversity and science. In addition, the ability to reliably credit collectors for their work has the potential to change the incentive structure to promote improved curation and maintenance of natural history collections. [ABSTRACT FROM AUTHOR]

Understanding how the plants and animals that live in the sea floor vary in their spatial patterns of diversity and abundance is fundamental to gaining insight into the role of biodiversity in maintaining ecosystem functioning in coastal ecosystems, as well as advancing the modelling of species distributions under realistic assumptions. Yet, it is virtually unknown how the relationships between abundance patterns and different biotic and environmental processes change depending on spatial scales, which is mainly due to a lack of data. Within the project Spatial Organization of Species Distributions: Hierarchical and Scale-Dependent Patterns and Processes in Coastal Seascapes at the National Institute for Water and Atmospheric Research (NIWA) in New Zealand we collected multi-scale and high-resolution data on macrobenthic biodiversity. We found 146 species dominated by bivalves, polychaetes, and crustaceans (>500 µ m) that live hidden in marine sandflats and collected point measurements of important environmental variables (sediment grain-size distributions, chlorophyll a concentration, organic content, and visible sandflat parameters) in three large intertidal harbours (Kaipara, Tauranga, and Manukau). In each harbour we sampled 400 points for macrobenthic community composition and abundances, as well as the full set of environmental variables. Using an elaborate sampling design, we were able to cover scales from 30 cm to a maximal extent of 1 km. All data and extensive metadata are available from the data publisher PANGAEA via the persistent identifier 10.1594/PANGAEA.903448 (Kraan et al., 2019). [ABSTRACT FROM AUTHOR]

Leguminosae includes six subfamilies, where the traditionally recognised subfamily Mimosoideae was accepted as a distinct clade included within the recircumscribed subfamily Caesalpinioideae, called informally as Mimosoid clade. The representatives of the tribes Acacieae and Ingeae can be differentiated principally in terms of the patterns of their stamens, being free in Acacieae and monadelphous in Ingeae. The floristic survey of Acacieae and Ingeae in the Environmental Protection Area Serra Branca included analysis of specimens collected from June 2011 to September 2012. The analyses were supplemented with dried collections from the following herbaria: ALCB, HRB and HUEFS. Ten species were cataloged, distributed among four genera of Ingeae: Calliandra Benth. (1 sp.), Chloroleucon (Benth.) Britton & Rose ex Record (1 sp.), Enterolobium Mart. (1 sp.), Pithecellobium Mart. (1 sp.); and one genus of Acacieae: Senegalia Raf. (6 spp.). The most representative species were Calliandra aeschynomenoides Benth. associated with sandy and stony soils and Chloroleucon foliolosum (Benth.) G.P.Lewis and Senegalia bahiensis (Benth.) Seigler & Ebinger growing on sandy-clay soils. The taxonomic treatment includes a key for the identification, descriptions, illustrations, photos, data of the geographical distribution phenological data and comments about the species. [ABSTRACT FROM AUTHOR]

Systematic reviews (SRs) and systematic mapping aim to maximize transparency and comprehensiveness while minimizing subjectivity and bias. These are time‐consuming and complex tasks, so SRs are considered resource intensive, but published estimates of systematic‐review resource requirements are largely anecdotal. We analyzed all Collaboration for Environmental Evidence (CEE) SRs (n = 66) and maps (n = 20) published from 2012 to 2017 to estimate the average number of articles retained at each review stage. We also surveyed 33 experienced systematic reviewers to collate information on the rate at which those stages could be completed. In combination, these data showed that the average CEE SR takes an estimated 164 d (full‐time equivalent) (SD 23), and the average CEE systematic map (SM) (excluding critical appraisal) takes 211 d (SD 53). While screening titles and abstracts is widely considered time‐consuming, metadata extraction and critical appraisal took as long or longer to complete, especially for SMs. Given information about the planned methods and evidence base, we created a software tool that predicts time requirements of a SR or map with evidence‐based defaults as a starting point. Our results shed light on the most time‐consuming stages of the SR and mapping processes, will inform review planning, and can direct innovation to streamline processes. Future predictions of effort required to complete SRs and maps could be improved if authors provide more details on methods and results. Article impact statement: We provide data on the effort needed to complete systematic literature reviews and maps and new software to help users apply our findings. [ABSTRACT FROM AUTHOR]

Information on species distribution is recognized as a crucial input for biodiversity conservation and management. To that end, considerable resources have been dedicated towards increasing the quantity and availability of species occurrence data, boosting their use in species distribution modeling and online platforms for their dissemination. Currently, those platforms face the challenge of bringing biology into modeling by making informed decisions that result in meaningful models, based on limited occurrence and ecological data. Here we describe BioModelos, a modeling approach supported by an online system and a core team of modelers, whereby a network of experts contributes to the development of species distribution models by assessing the quality of occurrence data, identifying potentially limiting environmental variables, establishing species’ accessible areas and validating modeling predictions qualitatively. Models developed through BioModelos become freely and publicly available once validated by experts, furthering their use in conservation applications. Our approach has been implemented in Colombia since 2013 and it currently consist of a network of nearly 500 experts that collaboratively contribute to enhance the knowledge on the distribution of a growing number of species and it has aided the development of several decision support products such as national risk assessments and biodiversity compensation manuals. BioModelos is an example of operationalization of an essential biodiversity variable at a national level through the implementation of a research infrastructure that enhances the value of open access species data. [ABSTRACT FROM AUTHOR]

Recent changes in institutional cyberinfrastructure and collections data storage methods have dramatically improved accessibility of specimen-based data through the use of digital databases and data aggregators. This analysis of digitized fish collections in the U.S. demonstrates how information from data aggregators, in this case iDigBio, can be extracted and analyzed. Data from U.S. institutional fish collections in iDigBio were explored through a strictly programmatic approach using the ridigbio package and fishfindR web application. iDigBio facilitates the aggregation of collections data on a purely voluntary fashion that requires collection staff to consent to sharing of their data. Not all collections are sharing their data with iDigBio, but the data harvested from 38 of the 143 known fish collections in the U.S. that are in iDigBio account for the majority of fish specimens housed in U.S. collections. In the 22 years since publication of the last survey providing information on these 38 collections, 1,219,168 specimen records (lots), 15,225,744 specimens, 3,192 primary types, and 32,868 records of secondary types have been added. This is an increase of 65.1% in the number of cataloged records and an increase of 56.1% in the number of specimens. In addition to providing specimen-based data for research, education, and various outreach activities, data that are accessible via data aggregators can be used to develop accurate, up-to-date reports of information on institutional collections. Such reports present collections data in an organized and accessible fashion and can guide targeted efforts by collections personnel to meet discipline-specific needs and make data more transparent to downstream users. Data from this survey will be updated and published regularly in a dynamic web application that will aid collections staff in communicating collections value while simultaneously giving stakeholders a way to explore collections holdings as they relate to the institutions in which they are housed. It is through this resource that collections will be able to leverage their data against those of similar collections to aid in the procurement of financial and institutional support. [ABSTRACT FROM AUTHOR]

The Biodiversity Heritage Library (BHL) will soon upload its 60 millionth page of open access biodiversity literature onto the BHL website and the BHL's Internet Archive Collection. The BHL's massive repository of free knowledge includes content that is available nowhere else online, as well as accessible versions of content that are locked behind paywalls elsewhere. If we are to continue to expand our understanding of life on Earth, we must ensure that the foundation of biodiversity knowledge provided by BHL is discoverable by the tools we rely on to navigate the ever-expanding internet. These tools - search engines and their algorithms - preferentially deliver (and rank) content with good metadata and persistent identifiers (PIDs). In modern online publishing, PID assignment and linking happens at the point of publication: DOIs (Digital Object Identifiers) for publications, ORCIDs (Open Researcher and Contributor IDs) for people, and RORs (Research Organization Registry IDs) for organisations. The DOI system provided by Crossref (the DOI registration agency for scholarly content) delivers reciprocal citations, enabling convenient clicking from article to article, and citation tracking, enabling authors and institutions to track the impact and reach of their research output. Publications that lack PIDs, which include the vast majority of legacy literature, are hard to find and sit outside the linked network of scholarly research. This makes it nearly impossible to determine whether they are being cited, let alone viewed, mentioned, shared or liked. At TDWG 2020, Page 2020, Kearney 2020, Richard 2020 (and 2019, Page 2019b, Page 2019a, Kearney 2019b, Kearney 2019a and 2018, Kearney 2018), we emphasised the need to bring the historic biodiversity literature into the modern linked network of scholarly research. In October 2020, BHL launched a new working group to do exactly this. The BHL Persistent Identifier Working Group (Team #RetroPID) brings together expertise from across BHL's global community. Over the past year, we have worked tirelessly to make it easier to find, cite, link, share and track the content on BHL, adding article-level metadata to journals and retrospectively assigning DOIs (#RetroPIDs). Most importantly, we have developed the tools and documentation that will enable the entire BHL community to take contributed content from "just" accessible to persistently discoverable. This paper will detail our efforts to retrofit the historic literature (a square peg) into the modern PID system (a round hole) and will present both the achievements and the challenges of this important work. [ABSTRACT FROM AUTHOR]