scholarly journals SYNTHESYS+ Abridged Grant Proposal

2019 ◽  
Vol 5 ◽  
Author(s):  
Vincent Smith ◽  
Kristina Gorman ◽  
Wouter Addink ◽  
Christos Arvanitidis ◽  
Ana Casino ◽  
...  
Keyword(s):  
Natural History ◽  
Natural Science ◽  
Critical Infrastructure ◽  
Natural Systems ◽  
Geological Processes ◽  
Natural History Collections ◽  
Access Programme ◽  
Important Challenge ◽  
Scientific Collections ◽  
First Time

European natural history collections are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – creating a sustainable future for ourselves and the natural systems on which we depend – and for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Since 2004 SYNTHESYS has been an essential instrument supporting this community, underpinning new ways to access and exploit collections, harmonising policy and providing significant new insights for thousands of researchers, while fostering the development of new approaches to face urgent societal challenges. SYNTHESYS+ is a fourth iteration of this programme, and represents a step change in the evolution of this community. For the first time SYNTHESYS+ brings together the European branches of the global natural science organisations (GBIF https://www.gbif.org/, TDWG https://www.tdwg.org/, GGBN http://www.ggbn.org/ggbn_portal/ and CETAF https://cetaf.org/) with an unprecedented number of collections, to integrate, innovate and internationalise our efforts within the global scientific collections community. Major new developments addressed by SYNTHESYS+ include the delivery of a new virtual access programme, providing digitisation on demand services to a significantly expanded user community; the construction of a European Loans and Visits System (ELViS) providing, for the first time, a unified gateway to accessing digital, physical and molecular collections; and a new data processing platform (the Specimen Data Refinery), applying cutting edge artificial intelligence to dramatically speed up the digital mobilisation of natural history collections. The activities of SYNTHESYS+ form a critical dependency for DiSSCo - the Distributed System of Scientific Collections (https://dissco.eu/), which is the European Research Infrastructure for natural science collections, under the ESFRI umbrella. DiSSCo will undertake the maintenance and sustainability of SYNTHESYS+ products at the end of the programme.

scholarly journals ALICE: Angled Label Image Capture and Extraction for high throughput insect specimen digitisation

2018 ◽  
Author(s):  
Benjamin Wills Price ◽  
Steen Dupont ◽  
Elizabeth Louise Allan ◽  
Vladimir Blagoderov ◽  
Alice Jenny Butcher ◽  
...  
Keyword(s):  
Natural History ◽  
Primary Data ◽  
Image Capture ◽  
Specimen Handling ◽  
History Museum ◽  
Natural Systems ◽  
Geological Processes ◽  
Natural History Collections ◽  
Single User ◽  
Data Source

The world’s natural history collections contain at least 2 billion specimens, representing a unique data source for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Unlocking this treasure trove of data, stored in thousands of museum drawers and cabinets, is crucial to help map a sustainable future for ourselves and the natural systems on which we depend. The rate-limiting steps in the digitisation of natural history collections often involve specimen handling due to their fragile nature. Insects comprise the single largest collection type in the Natural History Museum, London (NHM), reflecting their global diversity. The NHM pinned insect collection, estimated at 25 million specimens, will take over 700 person years to digitise at current rates. In order to ramp up digitisation we have developed ALICE for Angled Label Image Capture and Extraction. This multi-camera setup and associated software processing pipeline enables primary data capture from angled images, without removal of the labels from the specimen pin. As a result ALICE enables a single user to sustainably image over 1,000 specimens per day, allowing us to digitally unlock the insect collections at an unprecedented rate.

scholarly journals SYNTHESYS+ Virtual Access - Report on the Ideas Call (October to November 2019)

2020 ◽  
Vol 6 ◽  
Author(s):  
Helen Hardy ◽  
Sandra Knapp ◽  
E. Louise Allan ◽  
Frederik Berger ◽  
Katherine Dixey ◽  
...  
Keyword(s):  
Natural History ◽  
Natural History Collections ◽  
Access Programme ◽  
Physical Access ◽  
First Time

The SYNTHESYS consortium has been operational since 2004, and has facilitated physical access by individual researchers to European natural history collections through its Transnational Access programme (TA). For the first time, SYNTHESYS+ will be offering virtual access to collections through digitisation, with two calls for the programme, the first in 2020 and the second in 2021. The Virtual Access (VA) programme is not a direct digital parallel of Transnational Access - proposals for collections digitisation will be prioritised and carried out based on community demand, and data must be made openly available immediately. A key feature of Virtual Access is that, unlike TA, it does not select the researchers to whom access is provided. Because Virtual Access in this way is new to the community and to the collections-holding institutions, the SYNTHESYS+ consortium invited ideas through an Ideas Call, that opened on 7th October 2019 and closed on 22nd November 2019, in order to assess interest and to trial procedures. This report is intended to provide feedback to those who participated in the Ideas Call and to help all applicants to the first SYNTHESYS+Virtual Access Call that will be launched on 20th of February 2020.

scholarly journals Taxonomic changes resulting from a review of the types of Australian Anoplognathini (Coleoptera: Scarabaeidae: Rutelinae) housed in Swedish natural history collections

Zootaxa ◽  
2021 ◽  
Vol 4908 (2) ◽  
pp. 225-238
Author(s):  
MATTHIAS SEIDEL ◽  
CHRIS A.M. REID
Keyword(s):  
Natural History ◽  
The Other ◽  
Type Material ◽  
Type Specimens ◽  
Natural History Collections ◽  
New Synonym ◽  
Senior Synonym ◽  
Taxonomic Changes ◽  
First Time ◽  
Total Type

The type material of Australian Anoplognathini (Coleoptera: Scarabaeidae: Rutelinae) housed in Swedish natural history collections is reviewed, concerning three genera: Anoplognathus Leach, 1815, Amblyterus MacLeay, 1819, and Repsimus MacLeay, 1819. The species were described by G.J. Billberg, J.W. Dalman, L. Gyllenhal, C.J. Schönherr, O. Swartz, and C.P. Thunberg. The contemporary type material of W.S. MacLeay in the Macleay Museum, Sydney, is also examined as it has been overlooked by previous researchers. In total, type specimens for 12 species described between 1817 and 1822 were found in the Naturhistoriska Riksmuseet in Stockholm the Evolutionsmuseet in Uppsala and the Macleay Museum. Five of these species are valid: Anoplognathus brunnipennis, (Gyllenhal, 1817); A. olivieri (Schönherr & Dalman, 1817); A. porosus (Dalman, 1817); Amblyterus cicatricosus (Gyllenhal, 1817); and Repsimus manicatus (Swartz, 1817). The other seven species are junior synonyms, as follows (senior synonym first): A. brunnipennis = Rutela chloropyga Thunberg, 1822 (new synonym); A. olivieri = Rutela lacunosa Thunberg, 1822 (new synonym); A. viridiaeneus (Donovan, 1805) = A. latreillei (Schönherr & Gyllenhal, 1817); A. viriditarsus Leach, 1815 = Rutela analis Dalman, 1817; and R. manicatus = Anoplognathus brownii W.J. MacLeay, 1819 = A. dytiscoides W. J. MacLeay, 1819 = Rutela ruficollis Thunberg, 1822 (new synonym). Authorship of A. latreillei and A. olivieri is corrected, as noted above. Anoplognathus brunnipennis has been misidentified for the last 60 years at least, leading to the synonymy noted above. Anoplognathus flavipennis Boisduval, 1835 (revised status), is reinstated as the oldest available name for the misidentified A. brunnipennis and the types of A. flavipennis in the Muséum National d’Histoire Naturelle, Paris, are illustrated. Lectotypes are designated for: Anoplognathus brownii, A. flavipennis, A. dytiscoides, Melolontha cicatricosa, Rutela analis, R. brunnipennis, R. lacunosa, R. latreillei, R. manicata, R. olivieri, R. porosa, R. ruficollis, and R. chloropyga. Photographs of all type specimens examined are presented for the first time. 

scholarly journals DiSSCo as a New Regional Model for Scientific Collections in Europe

2019 ◽  
Vol 3 ◽  
Author(s):  
Wouter Addink ◽  
Dimitrios Koureas ◽  
Ana Rubio
Keyword(s):  
Natural History ◽  
Natural Science ◽  
Large Scale ◽  
Advisory Board ◽  
Political Support ◽  
Research Infrastructure ◽  
Morphological Data ◽  
Natural History Museums ◽  
History Museums ◽  
Scientific Collections

European Natural Science Collections (NSC) are part of the global natural and cultural capital and represent 80% of the world bio-and geo-diversity. Data derived from these collections underpin thousands of scholarly publications and official reports (used to support legislative and regulatory processes relating to health, food, security, sustainability and environmental change) and let to inventions and products that today play an important role in our bio-economy. In the last decades, the research practice in natural sciences changed dramatically. Advances in digital, genomic and information technologies enable natural science collections to provide new insights but also ask for changing the current operational and business models of individual collections held at local natural history museums and universities. A new business model that provides unified access to collection objects and all scientific data derived from them. Although aggregating infrastructures like the Global Biodiversity Information Facility, GenBank and Catalogue of Life now successfully aggregate data on specific data classes, the landscape remains fragmented with limited capacity to bring together this information in a systematic and robust manner and with scattered access to the physical objects. The Distributed System of Scientific Collections (DiSSCo) represents a pan-European initiative, and the largest ever agreement of natural science museums, to jointly address the fragmentation of European collections. DiSSCo is unifying European natural science collections into a coherent new research infrastructure, able to provide bio- and geo-diversity data at the scale, form and precision required by a multi-disciplinary user base in science. DiSSCo is harmonising digitisation, curation and publication processes and workflows across the scientific collections in Europe and enables linking of occurrence, genomic, chemical and morphological data classes as well as publications and experts to the physical object. In this paper we will present the socio-cultural and governance aspects of this research infrastructure. DiSSCo is receiving political support from 11 countries in Europe and will gradually change its funding model from institutional to national funding, with temporary funding from the EC to support the preparation and development. Solutions to achieve large scale digitisation are currently designed in the EC funded ICEDIG project to underpin the future large scale digitisation carried out by the countries. Unified virtual (digitisation on demand) and transnational physical access to the collections is over the next four years being developed in the EC funded SYNTHESYS+ project. The governance of DiSSCo is designed to gradually change from a steering committee composed of a few large natural history museums contributing in cash to initiate the development into a legal entity in which national consortia are represented, with a central coordination office for daily management. Each country individually decides how its entities (scientific collection facilities, research councils, governmental bodies) are organised in their national consortium. A stakeholder and user forum, Scientific Advisory Board and International Advisory Board will ensure that DiSSCo will be functional in enabling science across disciplines and within the international landscape of infrastructures. Training and short scientific missions are being developed in the MOBILISE COST Action to build capacity in FAIR data production, publication and usage of scientific collection-derived data in Europe and to initiate the socio-cultural changes needed in the collection-holding institutes. A Helpdesk is being constructed in the SYNTHESYS+ and DiSSCo Prepare projects to further facilitate the use and scientific use cases have been collected in ICEDIG to develop and facilitate e-services tailored to scientific needs.

scholarly journals ALICE, MALICE and VILE: High throughput insect specimen digitisation using angled imaging techniques

2019 ◽  
Vol 3 ◽  
Author(s):  
Steen Dupont ◽  
Benjamin Price
Keyword(s):  
Natural History ◽  
Imaging Techniques ◽  
Natural History Museum ◽  
Primary Data ◽  
Image Capture ◽  
Specimen Handling ◽  
History Museum ◽  
Geological Processes ◽  
Natural History Collections ◽  
Insect Collection

The world’s natural history collections contain at least 2 billion specimens (Ariño 2010), representing a unique data source for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Unlocking this treasure trove of data, stored in thousands of museum drawers and cabinets, is crucial to help map a sustainable future for ourselves and the natural systems on which we depend. The rate-limiting steps in the digitisation of natural history collections often involve specimen handling, due to their fragile nature. Insects comprise the single largest collection type in the Natural History Museum, London (NHM) and in many other collections, reflecting their global diversity and multiplicity. The NHM pinned insect collection, estimated at 25 million specimens, will take over 700 person years to digitise at current rates (Price et al. 2018: estimated from Blagoderov et al. 2017). In order to ramp up digitisation, we have developed ALICE for Angled Label Image Capture and Extraction from pinned insects. This multi-camera setup (Fig. 1) and associated software processing pipeline, enables primary data capture from angled images, without removal of the labels from the specimen pin. As a result ALICE enables a single user to sustainably digitise (add a catalogue label, image and prepare images for database import) over 800 specimens per day (Price et al. 2018), allowing us to digitally unlock large parts of the insect collection (e.g., Hymenoptera, Diptera, Coleoptera) at up to seven times the previous rate. We are continuing to refine hardware approaches to reduce specimen handling and extract data, for both human and machine interpretation, from labels without removing them from the object. More recently we are also trialing multiple mirrors in our Mirror Angled Label Image Capture Equipment (MALICE) (Fig. 2) or a rotating stage for our Vial Image Label Extraction (VILE) (Fig. 3) aimed at spirit-preserved specimens housed in vials. In this talk, we will outline the current approaches in use at the Natural History Museum, next generation prototypes, and challenges that need to be addressed before these techniques can be fully optimized.

scholarly journals An Introduction to Ally Skills for Natural History Collections Professionals

2021 ◽  
Author(s):  
Molly A Phillips ◽  
Hao Ye ◽  
Ellen Bledsoe
Keyword(s):  
Natural History ◽  
Natural Science ◽  
Shared Values ◽  
Natural History Collections

Natural science collections are, by their nature, collaborative and cumulative and benefit from the inclusion of diverse people with varied experiences and backgrounds. Yet many of us recognize that our workplaces, and STEM at large, are not welcoming to all, even after decades of efforts. It is increasingly clear that one of the challenges is that we lack training in turning our shared values into action. In this paper, we introduce allyship skills as a path to change, discuss both preemptive and responsive allyship efforts, and share some simple daily actions you can take to get started.

scholarly journals Documenting Natural History Collections in GBIF

2019 ◽  
Vol 3 ◽  
Author(s):  
Tim Robertson ◽  
Marcos Gonzalez ◽  
Morten Høfft ◽  
Marie Grosjean
Keyword(s):  
Natural History ◽  
Data Publishing ◽  
Digital Object Identifier ◽  
Digital Object ◽  
Global Biodiversity Information Facility ◽  
Global Science ◽  
Natural History Collections ◽  
The People ◽  
Citation Practice ◽  
Scientific Collections

The Global Biodiversity Information Facility (GBIF) was established by governments in 2001, largely through the initiative and leadership of the natural history collections community, following the 1999 recommendation by a working group under the Megascience Forum (predecessor of the Global Science Forum) of the Organization for Economic Cooperation and Development (OECD). Over 20 years, GBIF has helped develop standards and convened a global community of data-publishing institutions, aggregating over one billion species occurrence records freely and openly available for use in research and policy making. Of these more than 150 million records originate from specimens preserved by the collections community. The recent adoption of the Global Registry of Scientific Collections by GBIF (https://www.gbif.org/news/5kyAslpqTVxYqZTwYn1cub) is the first step by GBIF to better enable a picture of the natural history collections of the world along with the associated science that they have and continue to enable. Recognising that other collection metadata initiatives exists, GBIF aims to discuss with the community and progress topics such as: Synchronising with existing metadata catalogues to ensure accurate, up-to-date information is available without unnecessary burden for authors Defining, testing and formalizing the Collection Descriptions standard (https://github.com/tdwg/cd) Providing clear guidelines of citation practice for collections, potentially building on the success of the Digital Object Identifier (DOI) approach used for datasets mediated through GBIF.org. Tracking citations of use through both data downloads and through references in literature, such as materials examined in a taxonomic publication Improving the linkages and discoverability of specimen records derived from the same collecting event but preserved in multiple institutions Improving the linkages between the people involved in collecting, preserving, and identifying specimen records through the use of Open Researcher and Contributor IDs (ORCID) Lowering the technical threshold to deploy tools such as “data dashboards” and specimen search/download on collection related websites Synchronising with existing metadata catalogues to ensure accurate, up-to-date information is available without unnecessary burden for authors Defining, testing and formalizing the Collection Descriptions standard (https://github.com/tdwg/cd) Providing clear guidelines of citation practice for collections, potentially building on the success of the Digital Object Identifier (DOI) approach used for datasets mediated through GBIF.org. Tracking citations of use through both data downloads and through references in literature, such as materials examined in a taxonomic publication Improving the linkages and discoverability of specimen records derived from the same collecting event but preserved in multiple institutions Improving the linkages between the people involved in collecting, preserving, and identifying specimen records through the use of Open Researcher and Contributor IDs (ORCID) Lowering the technical threshold to deploy tools such as “data dashboards” and specimen search/download on collection related websites The progress made to date will be summarised and a roadmap for the future will be introduced.

scholarly journals Towards a Global Collection Description Standard

2019 ◽  
Vol 3 ◽  
Author(s):  
Niels Raes ◽  
Emily van Egmond ◽  
Ana Casino ◽  
Matt Woodburn ◽  
Deborah L Paul
Keyword(s):  
Natural History ◽  
Large Scale ◽  
The United States ◽  
Fragmented Landscape ◽  
Global Biodiversity Information Facility ◽  
Classification Schemes ◽  
Natural History Collections ◽  
Natural History Collection ◽  
World Collection ◽  
Scientific Collections

With digitisation of natural history collections over the past decades, their traditional roles — for taxonomic studies and public education — have been greatly expanded into the fields of biodiversity assessments, climate change impact studies, trait analyses, sequencing, 3D object analyses etc. (Nelson and Ellis 2019; Watanabe 2019). Initial estimates of the global natural history collection range between 1.2 and 2.1 billion specimens (Ariño 2010), of which 169 million (8-14% - as of April 2019) are available at some level of digitisation through the Global Biodiversity Information Facility (GBIF). With iDigBio (Integrated Digitized Biocollections) established in the United States and with the European DiSSCo (Distributed Systems of Scientific Collections) accepted on the ESFRI roadmap, it has become a priority to digitize natural history collections at an industrialized scale. Both iDigBio and DiSSCo aim at mobilising, unifying and delivering bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. In order to prioritise digitisation based on scientific demand, and efficiency using industrial digitisation pipelines, it is required to arrive at a uniform and unambiguously accepted collection description standard that would allow comparing, grouping and analysing natural history collections at diverse levels. Several initiatives attempt to unambiguously describe natural history collections using taxonomic and storage classification schemes. These initiatives include One World Collection, Global Registry of Scientific Collections (GRSciColl), TDWG (Taxonomic Databases Working Group) Natural Collection Descriptions (NCD) and CETAF (Consortium of European Taxonomy Facilities) passports, among others. In a collaborative effort of DiSSCo, ICEDIG (Innovation and consolidation for large scale digitisation of natural heritage), iDigBio, TDWG and the Task Group Collection Digitisation Dashboards, the various schemes were compared in a cross-walk analysis to propose a preliminary natural collection description standard that is supported by the wider community. In the process, two main user groups of collection descriptions standards were identified; scientists and collection managers. The classification produced intends to meet requirements from them both, resulting in three classification schemes that exist in parallel to each other (van Egmond et al. 2019). For scientific purposes a ‘Taxonomic’ and ‘Stratigraphic’ classification were defined, and for management purposes a ‘Storage’ classification. The latter is derived from specimen preservation types (e.g. dried, liquid preserved) defining storage requirements and the physical location of specimens in collection holding facilities. The three parallel collection classifications can be cross-sectioned with a ‘Geographic’ classification to assign sub-collections to major terrestrial and marine regions, which allow scientists to identify particular taxonomic or stratigraphic (sub-)collections from major geographical or marine regions of interest. Finally, to measure the level of digitisation of institutional collections and progress of digitisation through time, the number of digitised specimens for each geographically cross-sectioned (sub-)collection can be derived from institutional collection management systems (CMS). As digitisation has different levels of completeness a ‘Digitisation’ scheme has been adopted to quantify the level of digitisation of a collection from Saarenmaa et al. 2019, ranging from ‘not digitised’ to extensively digitised, recorded in a progressive scale of MIDS (Minimal Information for Digital Specimen). The applicability of this preliminary classification will be discussed and visualized in a Collection Digitisation Dashboards (CDD) to demonstrate how the implementation of a collection description standard allows the identification of existing gaps in taxonomic and geographic coverage and levels of digitisation of natural history collections. This set of common classification schemes and dashboard design (van Egmond et al. 2019) will be contributed to the TDWG Collection Description interest group to ultimately arrive at the common goal of a 'World Collection Catalogue'.

scholarly journals Access to Natural History Collections – from SYNTHESYS to DiSSCo

2019 ◽  
Vol 3 ◽  
Author(s):  
Sandra Knapp ◽  
Sarah Vincent ◽  
Christos Arvanitidis ◽  
Katherine Dixey ◽  
Patricia Mergen
Keyword(s):  
Natural History ◽  
Community Change ◽  
Single Individual ◽  
Natural History Collections ◽  
Technological Advances ◽  
Access Programme ◽  
History Of ◽  
The Times ◽  
The Individual ◽  
Physical Access

Any one collection of objects never tells the whole story. Enabling access to natural history collections by users external to a given institution, has a long history–even that great stay-at-home, Linnaeus, relied on specimens in the hands of others. Neglecting collections outside one’s institution results in duplication and inefficiency, as can be seen in the history of synonymy. Physical access had always been the norm, but difficult for the single individual. A student in the late 20th century had to decide if money were better spent going to one collection or another, or if the sometimes rather fuzzy photographs really represented the taxon she was working with. Loans between institutions were a way to provide access, but came with their own risks. The very individualised–to users as well as institutions–system of access provisioning still operates today but has fundamentally changed in several respects. The SYNTHESYS (Synthesis of Systematic Resources) projects brought a set of European institutions into a consortium with one aim: to provide access to natural history collections in order to stimulate their use across communities. The SYNTHESYS Transnational Access (TA) programme provided access not only to the collections of participating institutions, but also to infrastructures such as laboratories and analytical facilities. The trajectory of TA has led to a change in thinking about natural history collections, along with access to them. Because access has been subsidised at both the individual and institutional levels, participating institutions began to function more as a collective; one infrastructure, albeit loosely dispersed. In the most recent iteration of the SYNTHESYS programme, SYNTHESYS+, access has changed yet again with the times. Technological advances in imaging permit high-quality surrogates of natural history specimens to be exchanged more freely, and Virtual Access (VA) forms an integral part of the SYNTHESYS+ access programme, alongside TA. Virtual access has been operating for some time in the natural history collections community, but like TA, with individual scientists requesting images/sequences/scans from individual institutions or curators. VA, as a centralised service, will be piloted in SYNTHESYS+ in order to establish the basis for community change in access provisioning. But what next? Will we continue to need physical access to specimens and facilities as VA becomes increasingly feasible? As European collections-based institutions coalesce into the DiSSCo (Distributed System of Systematics Collections) infrastructure, will the model established in SYNTHESYS+ continue to function in the absence of centralised funding? In this talk, we will explore the trajectory of access through SYNTHESYS and provide some scenarios for how access to natural history collections–both physical and virtual–may change as we transition to the broader infrastructure that DiSSCo represents.

Seized natural-history collections and the redefinition of scientific cosmopolitanism in the era of the French Revolution

2013 ◽  
Vol 47 (1) ◽  
pp. 15-41 ◽  
Author(s):  
ELISE S. LIPKOWITZ
Keyword(s):  
Natural History ◽  
Property Rights ◽  
French Revolution ◽  
Natural History Collections ◽  
Universal Approach ◽  
Scientific Collections ◽  
The Relationship ◽  
Science And State ◽  
The French Revolution

AbstractIn order to recast scholarly understanding of scientific cosmopolitanism during the French Revolution, this essay examines the stories of the natural-history collections of the Dutch Stadholder and the French naturalist Labillardière that were seized as war booty. The essay contextualizes French and British savants' responses to the seized collections within their respective understandings of the relationship between science and state and of the property rights associated with scientific collections, and definitions of war booty that antedated modern transnational legal conventions. The essay argues that the French and British savants' responses to seized natural-history collections demonstrate no universal approach to their treatment. Nonetheless, it contends that the French and British approaches to these collections reveal the emergence in the 1790s of new forms of scientific nationalism that purported to be cosmopolitan – French scientific universalism and British liberal scientific improvement.

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