scholarly journals CETAF Collection Dashboard: Mapping natural history collections diversity

2019 ◽  
Vol 3 ◽  
Author(s):  
Patrick Semal ◽  
Marielle Adam ◽  
Didier Van den Spiegel ◽  
Franck Theeten ◽  
Henry Engledow ◽  
...  
Keyword(s):  
Natural History ◽  
Geographic Distribution ◽  
Large Scale ◽  
Central Africa ◽  
Global Biodiversity Information Facility ◽  
Faceted Search ◽  
Natural Heritage ◽  
General Data Protection Regulation ◽  
The Creation ◽  
Global Registry

Several initiatives aim to map the diversity of Natural History (NH) collections and standardise their descriptions. The Global Registry of Biodiversity Repositories (GRBio) is the most recent global registry. Unfortunately the server has been down since mid-2018 but the Global Biodiversity Information Facility (GBIF) recently "rescued" this data. In addition to this, the One World Collection exercise is a set of high-level collection descriptors (size, group coverage and geographic distribution) supporting a common strategy between the largest world institutions. Despite these efforts, a large part of the NH collections remains digitally unavailable and digitisation at the specimen level will take several decades. A new NH collections dashboard is needed in order to harmonise the efforts of the institutions. The Consortium of European Taxonomic Facilities (CETAF) is a good place to introduce this excercise. CETAF’s members hold over half of the world’s NH collections, representing 80% of the world's bio- and geo-diversity. Most of these collections are now engaged in the preparation for the common process of the Distributed System of Scientific Collections (DiSSCo, European Strategy Forum on Research Infrastructure). Additionally in Belgium, the Royal Belgian Institute of Natural Sciences (RBINS), Royal Museum of Central Africa (RMCA), Meise Botanic Garden (MBG) and CETAF have joined efforts to set up a common research portal (Natural Heritage, BRAIN-be project). The goal is to link together several collection management systems (CMS) and to (re)create links between isolated collection items. The CETAF collections dashboard splits the information into small metadata units related to topics relevant to the collections (taxonomy, geographic distribution, digitisation strategy and coverage, stratigraphy, etc.). The model allows for the creation of new units without a complete modification of the database structure. All units are defined by the Dublin Core and by fields derived from the Innovation and consolidation for large scale digitisation of natural heritage (ICEDIG) d2.3 deliverable (van Egmond et al. 2019). The object hierarchy allows for the creation of sub-collections and preserves the unity of the information. The CMS has an internal object database with a full index and a faceted search interface. It also has web services and XLS (Microsoft® Excel®) import/export functionalities. The collection dashboard also includes a complete workflow and access rights management at the object level. This is important for the information that is protected by the EU General Data Protection Regulation (GDPR). The dashboard is now being evaluated with the collections hosted by the partners of Natural Heritage. The system will be proposed to CETAF members and connections will be established with the international portals such as the GBIF or the future DiSSCo portal.

scholarly journals State of Digitisation and Gap Analysis Surveys

2018 ◽  
Vol 2 ◽  
pp. e25969
Author(s):  
Sarah Phillips ◽  
Elspeth Haston ◽  
Laura Green ◽  
Marie-Helene Weech ◽  
Robert Cubey ◽  
...  
Keyword(s):  
Natural History ◽  
Working Group ◽  
Large Scale ◽  
Gap Analysis ◽  
Vast Number ◽  
Natural Heritage ◽  
Future Programme ◽  
Natural History Collection ◽  
Recent Developments ◽  
Successes And Challenges

Recent developments in digitisation technologies and equipment have enabled advances in the rate of natural history specimen digitisation. However Europe’s Natural History Collection Institutions are home to over one billion specimens and currently only a small fraction of these have been digitally catalogued with fewer imaged. It is clear that institutions still face huge challenges when digitising the vast number of specimens in their collections. I will present the results of two surveys that aimed to discover the main successes and challenges facing institutions in their digitisation programmes. The first survey was undertaken in 2014 within the SYNTHESYS 3 project and gathered information from project partners on their current digitisation facilities, equipment and workflows providing some key recommendations based on these findings. The second survey was completed more recently in 2017, through the Consortium of European Taxonomic Facilities (CETAF) Digitisation Working Group. This survey aimed to discover the successful protocols and implementation of digitisation, and to identify the shortfalls in resources and protocols. Results from both surveys will be fed into the future programme of the CETAF Digitisation Working Group as well as forthcoming and proposed EU projects, including Innovation and Consolidation for large-scale Digitisation of natural heritage (ICEDIG).

scholarly journals Data Attribution from Download to Publication

2018 ◽  
Vol 2 ◽  
pp. e26060
Author(s):  
Pamela Soltis
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Sequence Data ◽  
Research Process ◽  
Global Biodiversity Information Facility ◽  
Data Set ◽  
Dna Sequence Data ◽  
Large Scale Data ◽  
Data Tracking ◽  
Biodiversity Information

Digitized natural history data are enabling a broad range of innovative studies of biodiversity. Large-scale data aggregators such as Global Biodiversity Information facility (GBIF) and Integrated Digitized Biocollections (iDigBio) provide easy, global access to millions of specimen records contributed by thousands of collections. A developing community of eager users of specimen data – whether locality, image, trait, etc. – is perhaps unaware of the effort and resources required to curate specimens, digitize information, capture images, mobilize records, serve the data, and maintain the infrastructure (human and cyber) to support all of these activities. Tracking of specimen information throughout the research process is needed to provide appropriate attribution to the institutions and staff that have supplied and served the records. Such tracking may also allow for annotation and comment on particular records or collections by the global community. Detailed data tracking is also required for open, reproducible science. Despite growing recognition of the value and need for thorough data tracking, both technical and sociological challenges continue to impede progress. In this talk, I will present a brief vision of how application of a DOI to each iteration of a data set in a typical research project could provide attribution to the provider, opportunity for comment and annotation of records, and the foundation for reproducible science based on natural history specimen records. Sociological change – such as journal requirements for data deposition of all iterations of a data set – can be accomplished using community meetings and workshops, along with editorial efforts, as were applied to DNA sequence data two decades ago.

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'.

Regeneration of Floodplain Biotopes on the Upper Rhine – The “Polder Altenheim” Case

1994 ◽  
Vol 29 (3) ◽  
pp. 281-288 ◽  
Author(s):  
A. Siepe
Keyword(s):  
Large Scale ◽  
Freshwater Snail ◽  
Red Alga ◽  
Flood Protection ◽  
Flooding Regime ◽  
Theodoxus Fluviatilis ◽  
The Creation ◽  
Early Succession ◽  
Upper Rhine

The floodplain of the Upper Rhine and its biocoenoses have, through different river-regulatory activities over the last 175 years, undergone large scale degradation. At the same time flood protection for the downstream inhabitants has been greatly reduced. For reasons of flood protection, the “Polder Altenheim” in Baden-Württemberg, Germany southwest of Strasbourg, France, with so called retention flooding, was put into operation in 1987. The original floodplain had been diked for the previous 17 years, during which no flooding occurred. Since 1989 “ecological flooding” also is carried out. This has assisted in the regeneration of floodplain biotopes and promoted the floodplain biotic communities and the readaption of the bioceonosis to a regular flooding regime. The creation of new floodplain biotopes of early succession stages, particularly through geomorphodynamic processes, has followed the more than ten flood ocassions and typical biotic communities have colonised these sites. This will be presented together with selected examples of terrestrial and limnical species and communities. The following species and communities will be discussed: kingfisher Alcedo atthis, carabid communities (Coleoptera), the red alga Hildenbrandia rivularis (Rhodophyceae), the freshwater snail Theodoxus fluviatilis (Neritacea) and the freshwater bug Aphelocheirus aestivalis (Hydrocorisae).

The creation and application of a large-scale corpus-based academic multi-word unit list

2021 ◽  
Vol 62 ◽  
pp. 142-157
Author(s):  
James Rogers ◽  
Amanda Müller ◽  
Frank E. Daulton ◽  
Paul Dickinson ◽  
Cosmin Florescu ◽  
...  
Keyword(s):  
Large Scale ◽  
The Creation

scholarly journals Within-Season Changes in Land-Use Impact Pest Abundance in Smallholder African Cassava Production Systems

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 269 ◽  
Author(s):  
Andrew Kalyebi ◽  
Sarina Macfadyen ◽  
Andrew Hulthen ◽  
Patrick Ocitti ◽  
Frances Jacomb ◽  
...  
Keyword(s):  
Land Use ◽  
Bemisia Tabaci ◽  
Large Scale ◽  
Production Systems ◽  
Smallholder Farmers ◽  
Negative Relationship ◽  
Central Africa ◽  
Sub Saharan Africa ◽  
Smallholder Farming ◽  
Manihot Esculenta Crantz

Cassava (Manihot esculenta Crantz), an important commercial and food security crop in East and Central Africa, continues to be adversely affected by the whitefly Bemisia tabaci. In Uganda, changes in smallholder farming landscapes due to crop rotations can impact pest populations but how these changes affect pest outbreak risk is unknown. We investigated how seasonal changes in land-use have affected B. tabaci population dynamics and its parasitoids. We used a large-scale field experiment to standardize the focal field in terms of cassava age and cultivar, then measured how Bemisia populations responded to surrounding land-use change. Bemisia tabaci Sub-Saharan Africa 1 (SSA1) was identified using molecular diagnostics as the most prevalent species and the same species was also found on surrounding soybean, groundnut, and sesame crops. We found that an increase in the area of cassava in the 3–7-month age range in the landscape resulted in an increase in the abundance of the B. tabaci SSA1 on cassava. There was a negative relationship between the extent of non-crop vegetation in the landscape and parasitism of nymphs suggesting that these parasitoids do not rely on resources in the non-crop patches. The highest abundance of B. tabaci SSA1 nymphs in cassava fields occurred at times when landscapes had large areas of weeds, low to moderate areas of maize, and low areas of banana. Our results can guide the development of land-use strategies that smallholder farmers can employ to manage these pests.

scholarly journals Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

2019 ◽  
Vol 7 ◽  
Author(s):  
Brian Stucky ◽  
James Balhoff ◽  
Narayani Barve ◽  
Vijay Barve ◽  
Laura Brenskelle ◽  
...  
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Use Cases ◽  
Data Systems ◽  
Multiple Sources ◽  
History Data ◽  
Insect Ecology ◽  
Many Sources ◽  
Multicellular Organisms ◽  
Initial Results

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.

Multinational Enterprises and the Globalization of Medicine: Siemens and the Business of X-ray Equipment in Non-Western Markets, 1900–1939

2014 ◽  
Vol 15 (4) ◽  
pp. 820-848
Author(s):  
Pierre-Yves Donzé
Keyword(s):  
International Organizations ◽  
Multinational Enterprises ◽  
Large Scale ◽  
Multinational Enterprise ◽  
Central Africa ◽  
Great Difficulty ◽  
X Ray ◽  
Hospital Development ◽  
Slight Growth ◽  
The 19Th Century

Whereas the globalization of medicine since the middle of the 19th century has primarily been approached as the sociopolitical and cultural outcome of imperialism, this article argues that Western big business also played a major role through the worldwide export of standardized medical technologies. It focuses on the expansion of Siemens on the X-ray equipment market in non-Western countries during the first half of the twentieth century. This German multinational enterprise experienced slight growth from the mid-1920s onwards but relied mainly on two markets (Argentina and Brazil). It specialized in providing large-scale equipment to a few urban hospitals and engaged during the 1930s in large-scale hospital development together with local authorities and international organizations in various countries (China, Peru, and Central Africa). However, Siemens had great difficulty in expanding its business to include private doctors and inland outlets, where it faced intense competition from other Western X-ray producers. This paper emphasizes that this shortcoming stemmed from a direct application of the European strategy (high-quality, expensive equipment for hospitals) to non-Western markets, where health systems differed.

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