On the relevance of regional collections

Biological collections are the basis of the Earth’s biodiversity knowledge and most of them are regional collections. Here we present two collections from the Federal University of Espírito Santo—Mammal Collection (UFES-MAM) and the associated Animal Tissue Collection (UFES-CTA)—which have been the main repository for mammal specimens collected in Espírito Santo, mostly georeferenced (~ 90%), and available in public databases. Thus, our objective with this essay was to point out the contributions of these collections to the knowledge of the diversity of mammals in the Atlantic Forest. At the same time, we present the contributions they return to society and the scientific community, highlighting the main obstacles and challenges those regional collections face. Despite being regional, UFES-MAM and UFES-CTA stand out nationally for having biological material from a wide variety of species—mainly rodents, marsupials, and bats—also counting on a series of primate tissues collected during the outbreak of wild yellow fever in Southeastern Brazil from 2017 to 2018. These collecting efforts contributed to 42 new mammal species records for Espírito Santo, and 25 species that had already been registered in the state but were listed only in out-of-state collections or reported in literature without voucher specimens. We hope that the information reported here are examples of good practices and increase knowledge and visibility of the rich collection that these regional collections house.

European Journal of Taxonomy: a deeper look into a decade of data

The European Journal of Taxonomy (EJT) is a decade-old journal dedicated to the taxonomy of living and fossil eukaryotes. Launched in 2011, the EJT published exactly 900 articles (31 778 pages) from 2011 to 2021. The journal has been processed in its entirety by Plazi, liberating the data therein, depositing it into TreatmentBank, Biodiversity Literature Repository and disseminating it to partners, including the Global Biodiversity Information Facility (GBIF) using a combination of a highly automated workflow, quality control tools, and human curation. The dissemination of original research along with the ability to use and reuse data as freely as possible is the key to innovation, opening the corpus of known published biodiversity knowledge, and furthering advances in science. This paper aims to discuss the advantages and limitations of retro-conversion and to showcase the potential analyses of the data published in EJT and made findable, accessible, interoperable and reusable (FAIR) by Plazi. Among others, taxonomic and geographic coverage, geographical distribution of authors, citation of previous works and treatments, timespan between the publication and treatments with their cited works are discussed. Manually counted data were compared with the automated process, the latter being analysed and discussed. Creating FAIR data from a publication results in an average multiplication factor of 166 for additional access through the taxonomic treatments, figures and material citations citing the original publication in TreatmentBank, the Biodiversity Literature Repository and the Global Biodiversity Information Facility. Despite the advances in processing, liberating data remains cumbersome and has its limitations which lead us to conclude that the future of scientific publishing involves semantically enhanced publications.

ICTIOFAUNA DE POÇAS DE MARÉ EM TERRAÇOS CONSOLIDADOS DO LITORAL AMAZÔNICO BRASILEIRO

As poças de maré são formadas pelo represamento de massas d’água durante a vazante e a sua troca ocorre ao longo de cada ciclo de marés, configurando em um ambiente explorado por várias espécies. A ictiofauna é um componente das poças de maré, algumas espécies são totalmente adaptadas (e.g. plasticidade fisológica, tamanho reduzido) e seu ciclo de vida ocorre apenas nas poças de maré. Contudo, muitas espécies utilizam as poças de maré em algumas fases do ciclo de vida para fins de alimentação, refúgio e reprodução. Considerando que os inventários são fundamentais para o conhecimento da biodiversidade, nosso estudo investigou a assembleia de peixes em poças de marés da Praia do Araçagy no período de outubro de 2016 a abril de 2017. No total, nós registramos 409 exemplares, pertencendo a 13 espécies, distribuídas em 11 famílias e sete ordens. Espécies residentes e estuarinas de importância comercial foram dominantes. INTERTIDAL FISHES OF THE CEMENTED TERRACES FROM BRAZILIAN AMAZON COAST: Tidal pools are formed by the damming of marine water during an ebb tide and their exchange occurs along each tidal cycle, configuring an environment explored by several species. The ichthyofauna is one of the components of the tide pools, with some species being fully adapted (e. g. physiological plasticity, reduced size) and their life cycles occuring uniquely on this environment. However, most species use tide pools at some stage of their life cycle for feeding, refuge and reproduction. Considering the main role of faunal inventories for the increase in biodiversity knowledge, this study investigates the fish assemblage in tide pools at Praia do Araçagy from October 2016 to April 2017. In total, were recorded 409 specimens belonging to 13 species, distributed in 11 families and seven orders. Resident and estuarine species with commercial importance were dominant.

College Students’ Knowledge and Perspective of Towards Biodiversity and its Conservation and Protection

Rich biodiversity is one of the Philippines’ greatest assets. Unfortunately, there is a continuous decline in the diversity of flora and fauna across the world. This calls for the need to educate people, especially younger generations, to value and protect biodiversity and natural resources. The study aimed to assess the students’ extent of knowledge and identify their perspectives towards biodiversity and its protection and conservation. A total of 268 randomly selected students at Aurora State College of Technology Zabali Campus were involved in the study. Survey questionnaires were used to obtain data and information which were subjected to statistical tests. The students had a moderate knowledge level on biodiversity with a mean score of 6.65 out of 10 items (SD = 1.50). Their perspective on biodiversity was leaning toward its protection and conservation, with a mean score of 7.2 out of 10 items (SD = 1.29). Factors affecting the students’ knowledge were gender (p = .003) and academic department (p = 0.003). Females and those associated with the Department of Forestry and Environmental Sciences and Department of Industrial technology were found to have more knowledge than the others. Males, on the other hand, were found to have a more positive perspective towards biodiversity. Knowledge and perspective had a weak correlation with r = 0.39. Students were not well-aware, but were in support of the Philippines’ biodiversity-related laws, which could help shape their mindset and actions towards biodiversity conservation and protection. As an implication, the college administration must revisit the curricula of all degree programs and ensure that students from each degree program are environmentally educated, emphasizing biodiversity conservation.

College Students’ Knowledge and Perspective of Towards Biodiversity and its Conservation and Protection

Rich biodiversity is one of the Philippines’ greatest assets. Unfortunately, there is a continuous decline in the diversity of flora and fauna across the world. This calls for the need to educate people, especially younger generations, to value and protect biodiversity and natural resources. The study aimed to assess the students’ extent of knowledge and identify their perspectives towards biodiversity and its protection and conservation. A total of 268 randomly selected students at Aurora State College of Technology Zabali Campus were involved in the study. Survey questionnaires were used to obtain data and information which were subjected to statistical tests. The students had a moderate knowledge level on biodiversity with a mean score of 6.65 out of 10 items (SD = 1.50). Their perspective on biodiversity was leaning toward its protection and conservation, with a mean score of 7.2 out of 10 items (SD = 1.29). Factors affecting the students’ knowledge were gender (p = .003) and academic department (p = 0.003). Females and those associated with the Department of Forestry and Environmental Sciences and Department of Industrial technology were found to have more knowledge than the others. Males, on the other hand, were found to have a more positive perspective towards biodiversity. Knowledge and perspective had a weak correlation with r = 0.39. Students were not well-aware, but were in support of the Philippines’ biodiversity-related laws, which could help shape their mindset and actions towards biodiversity conservation and protection. As an implication, the college administration must revisit the curricula of all degree programs and ensure that students from each degree program are environmentally educated, emphasizing biodiversity conservation.

Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph

OpenBiodiv is a biodiversity knowledge graph containing a synthetic linked open dataset, OpenBiodiv-LOD, which combines knowledge extracted from academic literature with the taxonomic backbone used by the Global Biodiversity Information Facility. The linked open data is modelled according to the OpenBiodiv-O ontology integrating semantic resource types from recognised biodiversity and publishing ontologies with OpenBiodiv-O resource types, introduced to capture the semantics of resources not modelled before. We introduce the new release of the OpenBiodiv-LOD attained through information extraction and modelling of additional biodiversity entities. It was achieved by further developments to OpenBiodiv-O, the data storage infrastructure and the workflow and accompanying R software packages used for transformation of academic literature into Resource Description Framework (RDF). We discuss how to utilise the LOD in biodiversity informatics and give examples by providing solutions to several competency questions. We investigate performance issues that arise due to the large amount of inferred statements in the graph and conclude that OWL-full inference is impractical for the project and that unnecessary inference should be avoided.

Building a Global Open Extensible Biodiversity Commons Network

Recent global events reinforce the need for local to global coalitions to address a variety of socio-environmental challenges such as the current COVID-19 pandemic (Cook et al. 2020) and biodiversity loss in general. Scientists reviewing data and fitness for current and future use note urgent necessary changes needed in data collection, specimen collection and preservation, infrastructure, human capacity, and standards-of-practice (Raven and Miller 2020, Morrison et al. 2017, Cook et al. 2020). Multi-faceted research questions often require cross-disciplinary collaboration. A recent paper analyzed conservation and disease mitigation research author networks and discovered that certain disciplines do not work together unless the research has outcomes that serve all groups involved (Kading and Kingston 2020). This research reinforces the finding that common goals offer a powerful way to build effective cross-disciplinary networks, speed up collaboration, and more effectively take on complex research. To move toward a Digital Extended Specimen (DES), the alliance for biodiversity knowledge is engaging in community building. The above summary when coupled with conversations from our alliance-led online consultations reinforces known threads and reveals some emerging themes about partnerships and collaborations. Our group continues to work on defining what a Digital Specimen is (or is not) and then communicating that succinctly to the worldwide community. At the same time we recognize the need for an extensible digital specimen object, we note the need for an extensible network. We note that groups need to and are motivated to solve local issues (as in for their town, or their country or continent). So, looking for and selecting common threads across these regional scales will be key to realizing and motivating effective partnerships and networks. Foremost, this includes expanding participation beyond Europe and North America. We recognize the need to form new partnerships to expand our network and learn from our new partners. For example, the Digital Humanities community would like to talk about the intersection of the humanities, social sciences, biology, and collections that can help each other to do better research. With this talk, and through participation in TDWG2021, we seek to share information and insights gathered so far about next steps and about building and sustaining the network we need to realize a biodiversity data commons and get input from those who participate in our session.

Participative Decision Making and the Sharing of Benefits: Laws, ethics, and data protection for building extended global communities

Transdisciplinary and cross-cultural cooperation and collaboration are needed to build extended, densely interconnected information resources. These are the prerequisites for the successful implementation and execution of, for example, an ambitious monitoring framework accompanying the post-2020 Global Biodiversity Framework (GBF) of the Convention on Biological Diversity (CBD; SCBD 2021). Data infrastructures that meet the requirements and preferences of concerned communities can focus and attract community involvement, thereby promoting participatory decision making and the sharing of benefits. Community acceptance, in turn, drives the development of the data resources and data use. Earlier this year, the alliance for biodiversity knowledge (2021a) conducted forum-based consultations seeking community input on designing the next generation of digital specimen representations and consequently enhanced infrastructures. The multitudes of connections that arise from extending the digital specimen representations through linkages in all “directions” will form a powerful network of information for research and application. Yet, with the power of an extended, accessible data network comes the responsibility to protect sensitive information (e.g., the locations of threatened populations, culturally context-sensitive traditional knowledge, or businesses’ fundamental data and infrastructure assets). In addition, existing legislation regulates access and the fair and equitable sharing of benefits. Current negotiations on ‘Digital Sequence Information’ under the CBD suggest such obligations might increase and become more complex in the context of extensible information networks. For example, in the case of data and resources funded by taxpayers in the EU, such access should follow the general principle of being “as open as possible; as closed as is legally necessary” (cp. EC 2016). At the same time, the international regulations of the CBD Nagoya Protocol (SCBD 2011) need to be taken into account. Summarizing main outcomes from the consultation discussions in the forum thread “Meeting legal/regulatory, ethical and sensitive data obligations” (alliance for biodiversity knowledge 2021b), we propose a framework of ten guidelines and functionalities to achieve community building and drive application: Substantially contribute to the conservation and protection of biodiversity (cp. EC 2020). Use language that is CBD conformant. Show the importance of the digital and extensible specimen infrastructure for the continuing design and implementation of the post-2020 GBF, as well as the mobilisation and aggregation of data for its monitoring elements and indicators. Strive to openly publish as much data and metadata as possible online. Establish a powerful and well-thought-out layer of user and data access management, ensuring security of ‘sensitive data’. Encrypt data and metadata where necessary at the level of an individual specimen or digital object; provide access via digital cryptographic keys. Link obligations, rights and cultural information regarding use to the digital key (e.g. CARE principles (Carroll et al. 2020), Local Context-labels (Local Contexts 2021), licenses, permits, use and loan agreements, etc.). Implement a transactional system that records every transaction. Amplify workforce capacity across the digital realm, its work areas and workflows. Do no harm (EC 2020): Reduce the social and ecological footprint of the implementation, aiming for a long-term sustainable infrastructure across its life-cycle, including development, implementation and management stages. Substantially contribute to the conservation and protection of biodiversity (cp. EC 2020). Use language that is CBD conformant. Show the importance of the digital and extensible specimen infrastructure for the continuing design and implementation of the post-2020 GBF, as well as the mobilisation and aggregation of data for its monitoring elements and indicators. Strive to openly publish as much data and metadata as possible online. Establish a powerful and well-thought-out layer of user and data access management, ensuring security of ‘sensitive data’. Encrypt data and metadata where necessary at the level of an individual specimen or digital object; provide access via digital cryptographic keys. Link obligations, rights and cultural information regarding use to the digital key (e.g. CARE principles (Carroll et al. 2020), Local Context-labels (Local Contexts 2021), licenses, permits, use and loan agreements, etc.). Implement a transactional system that records every transaction. Amplify workforce capacity across the digital realm, its work areas and workflows. Do no harm (EC 2020): Reduce the social and ecological footprint of the implementation, aiming for a long-term sustainable infrastructure across its life-cycle, including development, implementation and management stages. Balancing the needs for open access, as well as protection, accountability and sustainability, the framework is designed to function as a robust interface between the (research) infrastructure implementing the extensible network of digital specimen representations, and the myriad of applications and operations in the real world. With the legal, ethical and data protection layers of the framework in place, the infrastructure will provide legal clarity and security for data providers and users, specifically in the context of access and benefit sharing under the CBD and its Nagoya Protocol. Forming layers of protection, the characteristics and functionalities of the framework are envisioned to be flexible and finely-grained, adjustable to fulfill the needs and preferences of a wide range of stakeholders and communities, while remaining focused on the protection and rights of the natural world. Respecting different value systems and national policies, the framework is expected to allow a divergence of views to coexist and balance differing interests. Thus, the infrastructure of the digital extensible specimen network is fair and equitable to many providers and users. This foundation has the capacity and potential to bring together the diverse global communities using, managing and protecting biodiversity.

A Nano(publication) Approach Towards Big Data in Biodiversity

One of the major challenges in biodiversity informatics is the generation of machine-readable data that is interoperable between different biodiversity-related data infrastructures. Producers of such data have to comply with existing standards and to be resourceful enough to enable efficient data generation, management and availability. Conversely, nanopublications offer a decentralised approach (Kuhn et al. 2016) towards achieving data interoperability in a robust and standarized way. A nanopublication is a named RDF graph, which serves to communicate a single fact and its original source (provenance) through the use of identifiers and linked data (Groth et al. 2010). It is composed of three constituent graphs (assertion, provenance, and publication info), which are linked to one another in the nanopublication header (Kuhn et al. 2016). For instance, a nanopublication has been published to assert a species interaction in which a hairy woodpecker (Picoides villosus) ate a beetle (genus Ips), along with the license and related bibliographic citation*1. In biodiversity, nanopublications can be used to exchange information between infrastructures in a standardised way (Fig. 1) and to enable curation and correction of knowledge. They can be implemented within different workflows to formalise biodiversity knowledge in self-enclosed graphs. We have developed several nanopublication models*2 for different biodiversity use cases: species occurrences, new species descriptions, biotic interactions, and links between taxonomy, sequences and institutions. Nanopublications can be generated by various means: semi-automatic extraction from the published literature with a consequent human curation and publication; generation during the publication process by the authors via dedicated formalisation tool and published together with the article; de novo generation of a nanopublication through decentralised networks such as Nanobench (Kuhn et al. 2021). semi-automatic extraction from the published literature with a consequent human curation and publication; generation during the publication process by the authors via dedicated formalisation tool and published together with the article; de novo generation of a nanopublication through decentralised networks such as Nanobench (Kuhn et al. 2021). One of the possible uses of nanopublications in biodiversity is communicating new information in a standardised way so that it can be accessed and interpreted by multiple infrastructures that have a common agreement on how information is expressed through the use of particular ontologies, vocabularies and sets of identifiers. In addition, we envision nanopublications to be useful for curation or peer-review of published knowledge by enabling any researcher to publish a nanopublication containing a comment of an assertion made in a previously published nanopublication. With this talk, we aim to showcase several nanopublication formats for biodiversity and to discuss the possible applications of nanopublications in the biodiversity domain.

Towards Interlinked FAIR Biodiversity Knowledge: The BiCIKL perspective

The Horizon 2020 project Biodiversity Community Integrated Knowledge Library (BiCIKL) (started 1st of May 2021, duration 3 years) will build a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in biodiversity and life sciences. Together, the BiCIKL 14 partners will solidify open science practices by providing access to data, tools and services at each stage of, and along the entire biodiversity research and data life cycle (specimens, sequences, taxon names, analytics, publications, biodiversity knowledge graph) (Fig. 1, see also the BiCIKL kick-off presentation through Suppl. material 1), in compliance with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. The existing services provided by the participating infrastructures will expand through development and adoption of shared, common or interoperable domain standards, resulting in liberated and enhanced flows of data and knowledge across these domains. BiCIKL puts a special focus on the biodiversity literature. Over the span of the project, BiCIKL will develop new methods and workflows for semantic publishing and integrated access to harvesting, liberating, linking, and re-using sub-article-level data extracted from literature (i.e., specimens, material citations, sequences, taxonomic names, taxonomic treatments, figures, tables). Data linkages may be realised with different technologies (e.g., data warehousing, linking between FAIR Data Objects, Linked Open Data) and can be bi-lateral (between two data infrastructures) or multi-lateral (among multiple data infrastructures). The main challenge of BiCIKL is to design, develop and implement a FAIR Data Place (FDP), a central tool for search, discovery and management of interlinked FAIR data across different domains. The key final output of BiCIKL will the future Biodiversity Knowledge Hub (BKH), a one-stop portal, providing access to the BiCIKL services, tools and workflows, beyond the lifetime of the project.