Latest Articles from Research Ideas and Outcomes Latest 19 Articles from Research Ideas and Outcomes https://riojournal.com/ Thu, 28 Mar 2024 11:14:08 +0200 Pensoft FeedCreator https://riojournal.com/i/logo.jpg Latest Articles from Research Ideas and Outcomes https://riojournal.com/ Permits, contracts and their terms for biodiversity specimens https://riojournal.com/article/114366/ Research Ideas and Outcomes 10: e114366

DOI: 10.3897/rio.10.e114366

Authors: Edmund Schiller, Karin Wiltschke-Schrotta, Eva Häffner, Jutta Buschbom, Frederik Leliaert, Breda Zimkus, John Dickie, Suzete Gomes, Chris Lyal, Daniel Mulcahy, Alan Paton, Gabi Droege

Abstract: We present two different typologies of legal/contractual information in the context of natural history objects: the Biodiversity Permit/Contract Typology categorises permits and contracts, and the Typology of Legal/Contractual Terms for Biodiversity Specimens categorises the terms within permits and contracts. The Typologies have been developed under the EU-funded SYNTHESYS+ project with the participation of experts from outside the consortium. The document further addresses a possible technical integration of these typologies into the Distributed System of Scientific Collections (DiSSCo). The implementation in the DiSSCo data model is outlined and a concrete use case is presented to show how conditions, e.g. the Typology of Legal/Contractual Terms, can be introduced into the DiSSCo Electronic Loans and Visits System (ElViS). Finally, we give an outlook on the next steps to develop the typologies into a standard that supports compliance with legal and contractual obligations within the wider community of natural science collections.

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Project Report Wed, 10 Jan 2024 10:27:53 +0200
Sharing taxonomic expertise between natural history collections using image recognition https://riojournal.com/article/79187/ Research Ideas and Outcomes 8: e79187

DOI: 10.3897/rio.8.e79187

Authors: Michael Greeff, Max Caspers, Vincent Kalkman, Luc Willemse, Barry Sunderland, Olaf Bánki, Laurens Hogeweg

Abstract: Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise.

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Research Idea Tue, 1 Mar 2022 10:02:21 +0200
Palaeontology Collection Policy https://riojournal.com/article/62808/ Research Ideas and Outcomes 7: e62808

DOI: 10.3897/rio.7.e62808

Authors: Björn Kröger, Anniina Kuusijärvi, Leena Myllys, Pasi Sihvonen, Gunilla Ståhls-Mäkelä, Henry Väre, Markku Oinonen, Aino Juslén, Leif Schulman, Marko-Tapio Hyvärinen

Abstract: The Paleontological Collection (PalCo) is one of partial collections of the Finnish Museum of Natural History Luomus. General principles and guidelines for the collections are defined in the General Collection Policy of Luomus. The PalCo Policy is subordinate to the General Collection Policy of Luomus, clarifying its content with reference to the special characteristics of the paleontological collections. The PalCo includes fossil plant, invertebrate and vertebrate specimens worldwide in scope and from all geologic ages to support Finnish research and educational projects. The coverage emphasizes Paleozoic and Quaternary specimens from Finland, the Baltic countries and Scandinavia. The PalCo Policy defines the purpose of the collections, the objectives, the distribution of responsibilities for collection management and maintenance in the organisation, and the principles of collection accumulation, preservation, accessibility and use.

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Policy Brief Fri, 19 Feb 2021 11:30:00 +0200
The Genomic Resources Collection Policy of the Finnish Museum of Natural History https://riojournal.com/article/61664/ Research Ideas and Outcomes 7: e61664

DOI: 10.3897/rio.7.e61664

Authors: Gunilla Ståhls, Alexandre Aleixo, Marko-Tapio Hyvärinen, Anniina Kuusijärvi, Leena Myllys, Henry Väre, Pasi Sihvonen, Arto Luttinen, Björn Kröger, Markku Oinonen, Leif Schulman, Aino Juslén

Abstract: The Genomic Resources Collection is a separate, independently managed part of the natural history collections of the Finnish Museum of Natural History Luomus specifically intended for consumptive research. The GRC policy deals with the materials that are archived for the very purpose of enabling the study of biological diversity at the genome level, DNA extractions of animal, fungal and plant specimens, and animal tissue samples stored deep-frozen for purposes of future DNA extraction. The GRC policy defines the purpose of the collections, the objectives and content of the procedures and activities related to them, the distribution of responsibilities for collection management and maintenance in Luomus, and the principles of collection accumulation, preservation and accessibility.The aim of the GRC is to store and loan genomic samples for research purposes. In taxonomic coverage the collection overlaps with all the taxonomically delimited specimen collections managed by the Zoology and Botany Units, but is distinguished as being directed to preserve the genomic (DNA) information irrespective of the phenotypic variation that are the focus of specimen collections. The GRC includes both Finnish and foreign samples, all legally and ethically obtained, mostly linked to a specimen voucher in the taxonomic collections. The GRC samples are documented and trackable in Luomus collections management system. In accordance with the Universities Act, the GRC belongs to the national natural science collections of Luomus. For their part, the GRC collection implement the mission of Luomus, which is to be “responsible for the preservation, accumulation and exhibition of the national natural history collections and for research and education relating to them”.

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Policy Brief Mon, 11 Jan 2021 11:35:00 +0200
White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA) https://riojournal.com/article/62361/ Research Ideas and Outcomes 6: e62361

DOI: 10.3897/rio.6.e62361

Authors: Niels Raes, Ana Casino, Hilary Goodson, Sharif Islam, Dimitrios Koureas, Edmund Schiller, Leif Schulman, Laura Tilley, Tim Robertson

Abstract: The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure (RI) is presently in its preparatory phase. DiSSCo is developing a new distributed RI to operate as a one-stop-shop for the envisaged European Natural Science Collection (NSC) and all its derived information. Through mass digitisation, DiSSCo will transform the fragmented landscape of NSCs, including an estimated 1.5 billion specimens, into an integrated knowledge base that will provide interconnected evidence of the natural world. Data derived from European NSCs underpin countless discoveries and innovations, including tens of thousands of scholarly publications and official reports annually (supporting legislative and regulatory processes on sustainability, environmental change, land use, societal infrastructure, health, food, security, etc.); base-line biodiversity data; inventions and products essential to bio-economy; databases, maps and descriptions of scientific observations; educational material for students; and instructive and informative resources for the public. To expand the user community, DiSSCo will strengthen capacity building across Europe for maximum engagement of stakeholders in the biodiversity-related field and beyond, including industry and the private sector, but also policy-driving entities. Hence, it is opportune to reach out to relevant stakeholders in the European environmental policy domain represented by the European Environment Agency (EEA). The EEA aims to support sustainable development by helping to achieve significant and measurable improvement in Europe's environment, through the provision of timely, targeted, relevant and reliable information to policy-making agents and the public. The EEA provides information through the European Environment Information and Observation System (Eionet). The aim of this white paper is to open the discussion between DiSSCo and the EEA and identify the common service interests that are relevant for the European environmental policy domain. The first section describes the significance of (digital) Natural Science Collections (NHCs). Section two describes the DiSSCo programme with all DiSSCo aligned projects. Section three provides background information on the EEA and the biodiversity infrastructures that are developed and maintained by the EEA. The fourth section illustrates a number of use cases where the DiSSCo consortium sees opportunities for interaction between the DiSSCo RI and the Eionet portal of the EEA. Opening the discussion with the EEA in this phase of maturity of DiSSCo will ensure that the infrastructural design of DiSSCo and the development of e-Services accommodate the present and future needs of the EEA and assure data interoperability between the two infrastructures.The aim of this white paper is to present benefits from identifying the common service interests of DiSSCo and the EEA. A brief introduction to natural science collections as well as the two actors is given to facilitate the understanding of the needs and possibilities in the alignment of DiSSCo with the EEA.

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Project Report Wed, 30 Dec 2020 12:45:00 +0200
Research and development in robotics with potential to automate handling of biological collections https://riojournal.com/article/61366/ Research Ideas and Outcomes 6: e61366

DOI: 10.3897/rio.6.e61366

Authors: Helen Hardy, Myriam van Walsum, Laurence Livermore, Stephanie Walton

Abstract: This report investigates the current state of physical (mechanical) robotics, automated warehousing approaches and assistive technologies in relation to the storage, handling and processing (particularly digitisation) of natural history collections.Robotics can sound futuristic, however we provide case studies that show many and growing examples of physical automation in the natural history and cultural heritage sectors, including barcodes and conveyor belts for digitisation; robots that handle multiple vials for molecular and genetic work; robots for use in in display or exhibition contexts; and automated warehousing of library collections. We provide a non-exhaustive example of an end to end workflow of storage, retrieval and processing and discuss aspects of the tools and challenges relevant to these stages. The Distributed System of Scientific Collections (DiSSCo), a new Research Infrastructure for natural science collections, should build on this, leading a future programme of pilots that develop understanding of independent stages, and can be connected to make progress towards end-to-end solutions.Robots, or automated systems, excel at repetitive tasks, and are developing rapidly to be able to handle more complex object types, at lower cost. High volume, high variety of objects, and considerations such as fragility are not unique to the natural history sector - they apply for example to major retail operations - however natural history collections do offer some of the more extreme examples of these challenges, and in particular are not replaceable. Increased consistency of storage units is likely to be a critical factor in enabling automated handling in future, as well as looking at automation possibilities when new collections storage spaces are developed and built. Engagement with industry and subject matter experts has been patchy and again we recommend that DiSSCo help to ensure a joined up engagement with the right incentives in place, and with clear communication of requirements and challenges for shared R&D.When examining return on investment for particular automation, collections-holding institutions need to consider not only time and cost of automation compared to human labour, but wider factors including: health and safety such as physical environment and repetitve strain injury; security; quality and consistency of outputs; degree of criticality in response times (e.g. if digitising on demand); effective use of spaces; and freeing up staff to conduct other tasks.Purely software-based automation is outside the scope of this report, but is also in increasing use and has enormous potential, for example to transform the extraction of label and specimen data at scale from images. The challenges of managing and digitising collections at scale under DiSSCo are likely to require a combination of hardware and software automation approaches.

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Research Article Fri, 27 Nov 2020 11:30:00 +0200
Digitisation of private collections https://riojournal.com/article/57767/ Research Ideas and Outcomes 6: e57767

DOI: 10.3897/rio.6.e57767

Authors: Luc Willemse, Veljo Runnel, Hannu Saarenmaa, Ana Casino, Karsten Gödderz

Abstract: Results are presented of a study investigating solutions and procedures to incorporate private natural history collections into the international collections data infrastructure. Results are based on pilot projects carried out in three European countries aimed at approaches on how to best motivate and equip citizen collectors for digitisation:1) In Estonia, the approach was to outline tools for registering, digitising and publishing private collection data in the biodiversity data management system PlutoF.2) In Finland, the functionality of FinBIF, a portal offering a popular Notebook Service for citizens to store observations has been expanded to include collection specimens related to a field gathering event.3) In the Netherlands private collection owners were approached directly and asked to start digitising their collection using dedicated software, either by themselves or with the help of volunteers who were recruited specifically for this task.In addition to management tools, pilots also looked at motivation, persons undertaking the work, scope, planning, specific knowledge or skills required and the platform for online publication. Future ownership, legality of specimens residing in private collections and the use of unique identifiers are underexposed aspects effecting digitisation. Besides streamlining the overall process of digitising private collections and dealing with local, national or international challenges, developing a communication strategy is crucial in order to effectively distribute information and keep private collection owners aware of ongoing developments.Besides collection owners other stakeholders were identified and for each of them a roadmap is outlined aimed at further streamlining the data from private collections into the international infrastructure.In conclusion recommendations are presented based on challenges encountered during this task that are considered important to really make significant progress towards the overall accessibility of data stored in privately held natural history collections.

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Project Report Thu, 20 Aug 2020 17:30:00 +0300
Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton https://riojournal.com/article/54284/ Research Ideas and Outcomes 6: e54284

DOI: 10.3897/rio.6.e54284

Authors: Marina Cunha, Luciana Génio, Florence Pradillon, Morane Clavel Henry, Stace Beaulieu, James Birch, Francisco Campuzano, Marta Carretón, Fabio De Leo, Jonathan Gula, Sven Laming, Dhugal Lindsay, Fábio Matos, Anna Metaxas, Kirstin Meyer-Kaiser, Susan Mills, Henrique Queiroga, Clara Rodrigues, Jozée Sarrazin, Hiromi Watanabe, Robert Young, Craig Young

Abstract: Recent advances in technology have enabled an unprecedented development of underwater research, extending from near shore to the deepest regions of the globe. However, monitoring of biodiversity is not fully implemented in political agendas and biological observations in the deep ocean have been even more limited in space and time.The Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton was convened to to foster advances in the knowledge on deep-ocean invertebrate larval distributions and improve our understanding of fundamental deep-ocean ecological processes such as connectivity and resilience of benthic communities to natural and human-induced disturbance. This Meroplankton Observations Workshop had two specific goals: 1) review the state-of-the-art instrumentation available for meroplankton observations; 2) develop a strategy to implement technological innovations for in-situ meroplankton observation. Presentations and discussions are summarised in this report covering: i) key challenges and priorities for advancing the knowledge of deep-sea larval diversity and distribution: ii) recent developments in technology and future needs for plankton observation, iii) data integration and oceanographic modelling; iv) synergies and added value of a sustained observation system for meroplankton; v) steps for developing a sustained observation system for deep-ocean meroplankton and plans to maximise collaborative opportunities.

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Workshop Report Mon, 18 May 2020 17:00:00 +0300
Conceptual design blueprint for the DiSSCo digitization infrastructure - DELIVERABLE D8.1 https://riojournal.com/article/54280/ Research Ideas and Outcomes 6: e54280

DOI: 10.3897/rio.6.e54280

Authors: Alex Hardisty, Hannu Saarenmaa, Ana Casino, Mathias Dillen, Karsten Gödderz, Quentin Groom, Helen Hardy, Dimitris Koureas, Abraham Nieva de la Hidalga, Deborah Paul, Veljo Runnel, Xavier Vermeersch, Myriam van Walsum, Luc Willemse

Abstract: DiSSCo, the Distributed System of Scientific Collections, is a pan-European Research Infrastructure (RI) mobilising, unifying bio- and geo-diversity information connected to the specimens held in natural science collections and delivering it to scientific communities and beyond. Bringing together 120 institutions across 21 countries and combining earlier investments in data interoperability practices with technological advancements in digitisation, cloud services and semantic linking, DiSSCo makes the data from natural science collections available as one virtual data cloud, connected with data emerging from new techniques and not already linked to specimens. These new data include DNA barcodes, whole genome sequences, proteomics and metabolomics data, chemical data, trait data, and imaging data (Computer-assisted Tomography (CT), Synchrotron, etc.), to name but a few; and will lead to a wide range of end-user services that begins with finding, accessing, using and improving data. DiSSCo will deliver the diagnostic information required for novel approaches and new services that will transform the landscape of what is possible in ways that are hard to imagine today.With approximately 1.5 billion objects to be digitised, bringing natural science collections to the information age is expected to result in many tens of petabytes of new data over the next decades, used on average by 5,000 – 15,000 unique users every day. This requires new skills, clear policies and robust procedures and new technologies to create, work with and manage large digital datasets over their entire research data lifecycle, including their long-term storage and preservation and open access. Such processes and procedures must match and be derived from the latest thinking in open science and data management, realising the core principles of 'findable, accessible, interoperable and reusable' (FAIR).Synthesised from results of the ICEDIG project ("Innovation and Consolidation for Large Scale Digitisation of Natural Heritage", EU Horizon 2020 grant agreement No. 777483) the DiSSCo Conceptual Design Blueprint covers the organisational arrangements, processes and practices, the architecture, tools and technologies, culture, skills and capacity building and governance and business model proposals for constructing the digitisation infrastructure of DiSSCo. In this context, the digitisation infrastructure of DiSSCo must be interpreted as that infrastructure (machinery, processing, procedures, personnel, organisation) offering Europe-wide capabilities for mass digitisation and digitisation-on-demand, and for the subsequent management (i.e., curation, publication, processing) and use of the resulting data. The blueprint constitutes the essential background needed to continue work to raise the overall maturity of the DiSSCo Programme across multiple dimensions (organisational, technical, scientific, data, financial) to achieve readiness to begin construction.Today, collection digitisation efforts have reached most collection-holding institutions across Europe. Much of the leadership and many of the people involved in digitisation and working with digital collections wish to take steps forward and expand the efforts to benefit further from the already noticeable positive effects. The collective results of examining technical, financial, policy and governance aspects show the way forward to operating a large distributed initiative i.e., the Distributed System of Scientific Collections (DiSSCo) for natural science collections across Europe. Ample examples, opportunities and need for innovation and consolidation for large scale digitisation of natural heritage have been described. The blueprint makes one hundred and four (104) recommendations to be considered by other elements of the DiSSCo Programme of linked projects (i.e., SYNTHESYS+, COST MOBILISE, DiSSCo Prepare, and others to follow) and the DiSSCo Programme leadership as the journey towards organisational, technical, scientific, data and financial readiness continues.Nevertheless, significant obstacles must be overcome as a matter of priority if DiSSCo is to move beyond its Design and Preparatory Phases during 2024. Specifically, these include:Organisational:Strengthen common purpose by adopting a common framework for policy harmonisation and capacity enhancement across broad areas, especially in respect of digitisation strategy and prioritisation, digitisation processes and techniques, data and digital media publication and open access, protection of and access to sensitive data, and administration of access and benefit sharing.Pursue the joint ventures and other relationships necessary to the successful delivery of the DiSSCo mission, especially ventures with GBIF and other international and regional digitisation and data aggregation organisations, in the context of infrastructure policy frameworks, such as EOSC. Proceed with the explicit aim of avoiding divergences of approach in global natural science collections data management and research.Technical:Adopt and enhance the DiSSCo Digital Specimen Architecture and, specifically as a matter of urgency, establish the persistent identifier scheme to be used by DiSSCo and (ideally) other comparable regional initiatives.Establish (software) engineering development and (infrastructure) operations team and direction essential to the delivery of services and functionalities expected from DiSSCo such that earnest engineering can lead to an early start of DiSSCo operations.Scientific:Establish a common digital research agenda leveraging Digital (extended) Specimens as anchoring points for all specimen-associated and -derived information, demonstrating to research institutions and policy/decision-makers the new possibilities, opportunities and value of participating in the DiSSCo research infrastructure.Data:Adopt the FAIR Digital Object Framework and the International Image Interoperability Framework as the low entropy means to achieving uniform access to rich data (image and non-image) that is findable, accessible, interoperable and reusable (FAIR).Develop and promote best practice approaches towards achieving the best digitisation results in terms of quality (best, according to agreed minimum information and other specifications), time (highest throughput, fast), and cost (lowest, minimal per specimen).FinancialBroaden attractiveness (i.e., improve bankability) of DiSSCo as an infrastructure to invest in.Plan for finding ways to bridge the funding gap to avoid disruptions in the critical funding path that risks interrupting core operations; especially when the gap opens between the end of preparations and beginning of implementation due to unsolved political difficulties.Strategically, it is vital to balance the multiple factors addressed by the blueprint against one another to achieve the desired goals of the DiSSCo programme. Decisions cannot be taken on one aspect alone without considering other aspects, and here the various governance structures of DiSSCo (General Assembly, advisory boards, and stakeholder forums) play a critical role over the coming years.

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Research Article Mon, 18 May 2020 13:00:00 +0300
Deep reef ecosystems of the Western Indian Ocean: addressing the great unknown https://riojournal.com/article/53913/ Research Ideas and Outcomes 6: e53913

DOI: 10.3897/rio.6.e53913

Authors: Paris Stefanoudis, Sheena Talma, Kaveh Samimi-Namin, Lucy Woodall

Abstract: Indian Ocean coral reef ecosystems are some of the least explored, least funded and least protected worldwide. "First Descent: Indian Ocean" represents a series of research expeditions undertaken by Nekton between 2018-2022 in partnership with Governments in the Indian Ocean region to contribute to establishing a baseline of marine life and catalyse 30% protection by 2030. Two recent expeditions, the 2018 WILDOCEANS/ACEP Comoros Mesophotic Biodiversity Expedition (led by WILDTRUST), and the 2019 First Descent: Seychelles (led by Nekton Foundation) systematically surveyed deeper reef ecosystems in those areas, resulting in collections of biological meterial and underwater footage.In August 2019, taxonomic experts from across the globe, attended a workshop in order to identify the collected material and provide a first snapshot of the diversity of the surveyed habitats. Part of the workshop also focused on providing taxonomic training to host nation scientists and early career researchers.This document is a report on the proceedings and some of the first outcomes of this workshop.

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Workshop Report Wed, 6 May 2020 11:00:00 +0300
Deep-sea Coral Taxonomy Workshop, Colombia 2019 https://riojournal.com/article/53181/ Research Ideas and Outcomes 6: e53181

DOI: 10.3897/rio.6.e53181

Authors: Luisa Dueñas, Cristina Cedeño-Posso, Juan Sanchez, Santiago Herrera

Abstract: Corals are some of the conspicuous taxa in deep-sea ecosystems. Yet, characterizing coral diversity is difficult and requires a combination of both morphological and genetic data. Many leading coral taxonomy experts are close-to retirement or have already retired. It is now imperative that the hands-on expertise that these taxonomists have – much of which is not captured in manuscripts or books – is transferred to the next generation. The Deep-Sea Coral Taxonomy Workshop, funded by a Lounsbery award from the Deep-Sea Biology Society, aimed to provide a training opportunities and build taxonomic capacity in Colombia and Latin America. Workshop participants examined the deep-sea coral diversity of the southern western Caribbean, a poorly explored region. The three-day workshop was based mainly on hands-on activities focused on octocorals and black corals, and included introductory talks to the taxonomy of these groups and identification activities using specimens. Thanks to the workshop, it was possible to review and update the classification database of the Makuriwa Marine Natural History Museum collection. Additionally, four new species from the families Clavulariidae, Plexauridae and Gorgoniidae were identified and will be described in the near future.

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Workshop Report Thu, 16 Apr 2020 15:00:00 +0300
A complete digitization of German herbaria is possible, sensible and should be started now https://riojournal.com/article/50675/ Research Ideas and Outcomes 6: e50675

DOI: 10.3897/rio.6.e50675

Authors: Thomas Borsch, Albert-Dieter Stevens, Eva Häffner, Anton Güntsch, Walter G. Berendsohn, Marc Appelhans, Christina Barilaro, Bánk Beszteri, Frank Blattner, Oliver Bossdorf, Helmut Dalitz, Stefan Dressler, Rhinaixa Duque-Thüs, Hans-Joachim Esser, Andreas Franzke, Dethardt Goetze, Michaela Grein, Uta Grünert, Frank Hellwig, Jörn Hentschel, Elvira Hörandl, Thomas Janßen, Norbert Jürgens, Gudrun Kadereit, Timm Karisch, Marcus Koch, Frank Müller, Jochen Müller, Dietrich Ober, Stefan Porembski, Peter Poschlod, Christian Printzen, Martin Röser, Peter Sack, Philipp Schlüter, Marco Schmidt, Martin Schnittler, Markus Scholler, Matthias Schultz, Elke Seeber, Josef Simmel, Michael Stiller, Mike Thiv, Holger Thüs, Natalia Tkach, Dagmar Triebel, Ursula Warnke, Tanja Weibulat, Karsten Wesche, Andrey Yurkov, Georg Zizka

Abstract: Plants, fungi and algae are important components of global biodiversity and are fundamental to all ecosystems. They are the basis for human well-being, providing food, materials and medicines. Specimens of all three groups of organisms are accommodated in herbaria, where they are commonly referred to as botanical specimens.The large number of specimens in herbaria provides an ample, permanent and continuously improving knowledge base on these organisms and an indispensable source for the analysis of the distribution of species in space and time critical for current and future research relating to global biodiversity. In order to make full use of this resource, a research infrastructure has to be built that grants comprehensive and free access to the information in herbaria and botanical collections in general. This can be achieved through digitization of the botanical objects and associated data.The botanical research community can count on a long-standing tradition of collaboration among institutions and individuals. It agreed on data standards and standard services even before the advent of computerization and information networking, an example being the Index Herbariorum as a global registry of herbaria helping towards the unique identification of specimens cited in the literature.In the spirit of this collaborative history, 51 representatives from 30 institutions advocate to start the digitization of botanical collections with the overall wall-to-wall digitization of the flat objects stored in German herbaria. Germany has 70 herbaria holding almost 23 million specimens according to a national survey carried out in 2019. 87% of these specimens are not yet digitized. Experiences from other countries like France, the Netherlands, Finland, the US and Australia show that herbaria can be comprehensively and cost-efficiently digitized in a relatively short time due to established workflows and protocols for the high-throughput digitization of flat objects.Most of the herbaria are part of a university (34), fewer belong to municipal museums (10) or state museums (8), six herbaria belong to institutions also supported by federal funds such as Leibniz institutes, and four belong to non-governmental organizations. A common data infrastructure must therefore integrate different kinds of institutions.Making full use of the data gained by digitization requires the set-up of a digital infrastructure for storage, archiving, content indexing and networking as well as standardized access for the scientific use of digital objects. A standards-based portfolio of technical components has already been developed and successfully tested by the Biodiversity Informatics Community over the last two decades, comprising among others access protocols, collection databases, portals, tools for semantic enrichment and annotation, international networking, storage and archiving in accordance with international standards. This was achieved through the funding by national and international programs and initiatives, which also paved the road for the German contribution to the Global Biodiversity Information Facility (GBIF).Herbaria constitute a large part of the German botanical collections that also comprise living collections in botanical gardens and seed banks, DNA- and tissue samples, specimens preserved in fluids or on microscope slides and more. Once the herbaria are digitized, these resources can be integrated, adding to the value of the overall research infrastructure. The community has agreed on tasks that are shared between the herbaria, as the German GBIF model already successfully demonstrates.We have compiled nine scientific use cases of immediate societal relevance for an integrated infrastructure of botanical collections. They address accelerated biodiversity discovery and research, biomonitoring and conservation planning, biodiversity modelling, the generation of trait information, automated image recognition by artificial intelligence, automated pathogen detection, contextualization by interlinking objects, enabling provenance research, as well as education, outreach and citizen science.We propose to start this initiative now in order to valorize German botanical collections as a vital part of a worldwide biodiversity data pool.

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Policy Brief Mon, 3 Feb 2020 14:15:00 +0200
Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers https://riojournal.com/article/32449/ Research Ideas and Outcomes 4: e32449

DOI: 10.3897/rio.4.e32449

Authors: Katja Seltmann, Sara Lafia, Deborah Paul, Shelley James, David Bloom, Nelson Rios, Shari Ellis, Una Farrell, Jessica Utrup, Michael Yost, Edward Davis, Rob Emery, Gary Motz, Julien Kimmig, Vaughn Shirey, Emily Sandall, Daniel Park, Christopher Tyrrell, R. Sean Thackurdeen, Matthew Collins, Vincent O'Leary, Heather Prestridge, Christopher Evelyn, Ben Nyberg

Abstract: Georeferencing is the process of aligning a text description of a geographic location with a spatial location based on a geographic coordinate system. Training aids are commonly created around the georeferencing process to disseminate community standards and ideas, guide accurate georeferencing, inform users about new tools, and help users evaluate existing geospatial data. The Georeferencing for Research Use (GRU) workshop was implemented as a training aid that focused on the creation and research use of geospatial coordinates, and included both data researchers and data providers, to facilitate communication between the groups. The workshop included 23 participants with a wide background of expertise ranging from students (undergraduate and graduate), professors, researchers and educators, scientific data managers, natural history collections personnel, and spatial analyst specialists. The conversations and survey results from this workshop demonstrate that it is important to provide opportunities for biocollections data providers to interact directly with the researchers using the data they produce and vice versa.

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Workshop Report Mon, 17 Dec 2018 09:24:57 +0200
Increasing understanding of alien species through citizen science (Alien-CSI) https://riojournal.com/article/31412/ Research Ideas and Outcomes 4: e31412

DOI: 10.3897/rio.4.e31412

Authors: Helen Roy, Quentin Groom, Tim Adriaens, Gaia Agnello, Marina Antic, Anne-Sophie Archambeau, Sven Bacher, Aletta Bonn, Peter Brown, Giuseppe Brundu, Bernat López, Michelle Cleary, Dan Cogălniceanu, Maarten de Groot, Tiago De Sousa, Alan Deidun, Franz Essl, Živa Fišer Pečnikar, Anna Gazda, Eugenio Gervasini, Milka Glavendekic, Guillaume Gigot, Sven Jelaska, Jonathan Jeschke, Dariusz Kaminski, Paraskevi Karachle, Tamas Komives, Katharina Lapin, Frances Lucy, Elizabete Marchante, Dragana Marisavljevic, Riho Marja, Laura Martín Torrijos, Angeliki Martinou, Dinka Matosevic, Clare Mifsud, Jurga Motiejūnaitė, Henn Ojaveer, Nataša Pasalic, Ladislav Pekárik, Esra Per, Jan Pergl, Vladimir Pesic, Michael Pocock, Luís Reino, Christian Ries, Laurentiu Rozylowicz, Sven Schade, Snorri Sigurdsson, Ofer Steinitz, Nir Stern, Aco Teofilovski, Johann Thorsson, Rumen Tomov, Elena Tricarico, Teodora Trichkova, Konstantinos Tsiamis, Johan van Valkenburg, Noel Vella, Laura Verbrugge, Gábor Vétek, Cristina Villaverde, Johanna Witzell, Argyro Zenetos, Ana Cristina Cardoso

Abstract: There is no sign of saturation in accumulation of alien species (AS) introductions worldwide, additionally the rate of spread for some species has also been shown to be increasing. However, the challenges of gathering information on AS are recognized. Recent developments in citizen science (CS) provide an opportunity to improve data flow and knowledge on AS while ensuring effective and high quality societal engagement with the issue of IAS (Invasive Alien Species). Advances in technology, particularly on-line recording and smartphone apps, along with the development of social media, have revolutionized CS and increased connectivity while new and innovative analysis techniques are emerging to ensure appropriate management, visualization, interpretation and use and sharing of the data. In early July 2018 we launched a European CO-operation in Science and Technology (COST) Action to address multidisciplinary research questions in relation to developing and implementing CS, advancing scientific understanding of AS dynamics while informing decision-making specifically implementation of technical requirements of relevant legislation such as the EU Regulation 1143/2014 on IAS. It will also support the EU biodiversity goals and embedding science within society. The Action will explore and document approaches to establishing a European-wide CS AS network. It will embrace relevant innovations for data gathering and reporting to support the implementation of monitoring and surveillance measures, while ensuring benefits for society and citizens, through an AS CS European network. The Action will, therefore, increase levels of participation and quality of engagement with current CS initiatives, ensuring and evaluating educational value, and improve the value outcomes for potential users including citizens, scientists, alien species managers, policy-makers, local authorities, industry and other stakeholders.

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Grant Proposal Wed, 7 Nov 2018 11:23:06 +0200
Jellyfish Identification Software for Underwater Laser Cameras (JTRACK) https://riojournal.com/article/24716/ Research Ideas and Outcomes 4: e24716

DOI: 10.3897/rio.4.e24716

Authors: Patrizio Mariani

Abstract: Jellyfish can form erratic blooms in response to seasonal and irregular changes in environmental conditions with often large, transient effects on local ecosystem structure as well as effects on several sectors of the marine and maritime economy. Early warning systems able to detect conditions for jelly fish proliferation can enable management responses to mitigate such effects providing benefit to local ecosystems and economies. We propose here the creation of a research team in response to the EU call for proposal under the European Maritime and Fisheries Fund called “Blue Labs: innovative solutions for maritime challenges”. The project will establish a BLUELAB team with a strong cross-sectorial component that will benefit of the expertise of researchers in IT and Marine Biology, Computer Vision and embedded systems, which will work in collaboration with Industry and Policy maker to develop an early warning system using a new underwater imaging system based on Time of Flight Laser cameras. The camera will be combined to machine learning algorithm allowing autonomous early detection of jellyfish species (e.g. polyp, ephyra and planula stages). The team will develop the system and the companion software and will demonstrate its applications in real case conditions.

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Grant Proposal Wed, 28 Feb 2018 16:40:04 +0200
The project EcoNAOS: vision and practice towards an open approach in the Northern Adriatic Sea ecological observatory https://riojournal.com/article/24224/ Research Ideas and Outcomes 4: e24224

DOI: 10.3897/rio.4.e24224

Authors: Annalisa Minelli, Alessandro Oggioni, Alessandra Pugnetti, Alessandro Sarretta, Mauro Bastianini, Caterina Bergami, Fabrizio Bernardi Aubry, Elisa Camatti, Tiziano Scovacricchi, Giorgio Socal

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Research Idea Tue, 6 Feb 2018 09:27:40 +0200
The Biodiversity Informatics Landscape: Elements, Connections and Opportunities https://riojournal.com/article/14059/ Research Ideas and Outcomes 3: e14059

DOI: 10.3897/rio.3.e14059

Authors: Heather Bingham, Michel Doudin, Lauren Weatherdon, Katherine Despot-Belmonte, Florian Wetzel, Quentin Groom, Edward Lewis, Eugenie Regan, Ward Appeltans, Anton Güntsch, Patricia Mergen, Donat Agosti, Lyubomir Penev, Anke Hoffmann, Hannu Saarenmaa, Gary Geller, Kidong Kim, HyeJin Kim, Anne-Sophie Archambeau, Christoph Häuser, Dirk Schmeller, Ilse Geijzendorffer, Antonio García Camacho, Carlos Guerra, Tim Robertson, Veljo Runnel, Nils Valland, Corinne Martin

Abstract: There are a multitude of biodiversity informatics projects, datasets, databases and initiatives at the global level, and many more at regional, national, and sometimes local levels. In such a complex landscape, it can be unclear how different elements relate to each other. Based on a high-level review of global and European-level elements, we present a map of the biodiversity informatics landscape. This is a first attempt at identifying key datasets/databases and data services, and mapping them in a way that can be used to identify the links, gaps and redundancies in the landscape. While the map is predominantly focused on elements with a global scope, the sub-global focus at the European-level was incorporated in the map in order to demonstrate how a regional network such as the European Biodiversity Observation Network (EU BON) can usefully contribute to connecting some of the nodes within the landscape. We identify 74 elements, and find that the informatics landscape is complex in terms of the characteristics and diversity of these elements, and that there is high variability in their level of connectedness. Overall, the landscape is highly connected, with one element boasting 28 connections. The average "degrees of separation" between elements is low, and the landscape is deemed relatively robust to failures since there is no single point that information flows through. Examples of possible effort duplication are presented, and the inclusion of five policy-level elements in the map helps illustrate how informatics products can contribute to global processes that define and direct political targets. Beyond simply describing the existing landscape, this map will support a better understanding of the landscape’s current structure and functioning, enabling responsible institutions to establish or strengthen collaborations, work towards avoiding effort duplication, and facilitate access to the biodiversity data, information and knowledge required to support effective decision-making, in the context of comparatively limited funding for biodiversity knowledge and conservation. To support this, we provide the input matrix and code that created this map as supplementary materials, so that readers can more closely examine the links in the landscape, and edit the map to suit their own purposes.

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Research Article Fri, 9 Jun 2017 15:33:27 +0300
Towards a biodiversity knowledge graph https://riojournal.com/article/8767/ Research Ideas and Outcomes 2: e8767

DOI: 10.3897/rio.2.e8767

Authors: Roderic Page

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Research Idea Thu, 7 Apr 2016 11:07:34 +0300
Unifying European Biodiversity Informatics (BioUnify) https://riojournal.com/article/7787/ Research Ideas and Outcomes 2: e7787

DOI: 10.3897/rio.2.e7787

Authors: Dimitrios Koureas, Alex Hardisty, Rutger Vos, Donat Agosti, Christos Arvanitidis, Peter Bogatencov, Pier Luigi Buttigieg, Yde de Jong, Ferenc Horvath, Georgios Gkoutos, Quentin Groom, Tomas Kliment, Urmas Kõljalg, Ioannis Manakos, Arnald Marcer, Karol Marhold, David Morse, Patricia Mergen, Lyubomir Penev, Lars Pettersson, Jens-Christian Svenning, Anton van de Putte, Vincent Smith

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COST Grant Proposal Tue, 19 Jan 2016 09:30:43 +0200