scholarly journals GGBN Data Portal, GGBN Data Standard and GGBN Document Library

2018 ◽  
Vol 2 ◽  
pp. e25282
Author(s):  
Gabriele Droege

The GGBN Data Standard (https://terms.tdwg.org/wiki/GGBN_Data_Standard) provides a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. It builds upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA samples as well as sequences. The standard has been recently extended to support environmental DNA and High Throughput Sequencing (HTS) library samples. Both, eDNA and HTS library sample use cases have been published in the GGBN Sandbox (http://sandbox.ggbn.org) and will be presented here. The use case collection is documented in the GGBN wiki (http://wiki.ggbn.org/ggbn/Use_Case_Collection). In addition a general overview of the GGBN Data Portal (http://www.ggbn.org) will be given. Based on ABCD, DwC and the GGBN Data Standard the GGBN Data Portal is the gateway to standardized access of DNA, tissue and environmental samples and their associated specimens. The third core piece of GGBN is the GGBN Document Library (https://library.ggbn.org), today containing more than 300 documents about research, management and legal aspects of biodiversity biobanks. We will provide an overview of covered topics and gaps that the community can help to fill. Finally an outlook of goals and priority tasks for the next two years will be given.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.


2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.


PEDIATRICS ◽  
1959 ◽  
Vol 24 (1) ◽  
pp. 160-163

Children's Bureau Publication The Attorney's Part in Adoption, Children's Bureau Folder No. 47, is the third in the series of folders on adoption recently issued by the Children's Bureau. It deals with the part the attorney plays in the adoptive process. Fourteen attorneys, some engaged in the private practice of law, others faculty members in law schools and still others representatives of public or voluntary social agencies, met in Washington in May, 1958 to discuss the role of the attorney in adoption. Particular consideration was given to the legal aspects of adoption in relation to the natural parents, the child and to the adoptive parents. This leaflet is based on the principles discussed in this meeting. Copies are available from the Superintendent of Documents for 10 cents each with the usual discount of 25% on lots of 100 or more sent to one address.


2018 ◽  
Vol 51 (3) ◽  
pp. 427-468

Professor Yaël Ronen introduced the workshop as the fourth in a series of events on legal aspects of the Middle East conflict. The first two events concerned the Palestine Mandate of 1922. The third focused on the 1948 refugee issue. All these events have and are being held with the generous support of the Knapp Family Foundation and under the auspices of the International Law Forum of the Faculty of Law. Also, as part of the Shabtai Rosenne International Law Center Initiative, the first session was dedicated to the commemoration of the work of the late Shabtai Rosenne, whose scholarship spanned a host of international law issues but who is most renowned for his work on the International Court of Justice (ICJ).


2021 ◽  
Author(s):  
Sofia Rigou ◽  
Eugene Christo-Foroux ◽  
Sebastien Santini ◽  
Artemiy Goncharov ◽  
Jens Strauss ◽  
...  

Background: Antimicrobial resistance is one of the major challenges affecting public health. It is mostly due to the continuous emergence of extended-spectrum beta-lactamase from various environments followed by their rapid dissemination and selection in clinical settings. The warming of Earth' s climate is the other global threat facing human society, in particular with the Arctic regions experiencing a twice faster warming than the global average and permafrost affected by widespread thawing. A potentially dreadful combination of these two threats would be the release and dispersion of harmful microbes that have remained confined to largely uninhabited Arctic regions, or are stored dormant in permafrost. Methods: Environmental DNA was isolated from 12 soil samples from various Arctic and subarctic pristine regions in Siberia (Yakutia and Kamchatka), including 9 permafrost samples collected at various depths. The large datasets obtained from high throughput sequencing was assembled in contigs and their protein-gene contents predicted. We used exhaustive similarity searches to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. In addition, we specifically identified beta-lactamase genes and their prevalence per bacterial genome estimated through the detection of two universal single copy genes. Findings: A total of 9.217 1011 bp were exploited, leading to a total of 525,313 contigs at least 5kb in size. The DNA content of the various samples was found to be highly variable, not strictly correlated with the depth or radio-carbon-based deposit age, and most likely linked to the global density of microbes trapped in the corresponding permafrost layers. Bacteria account for more than 90% of the contigs in most samples, followed by Eukaryotes and Archaea (always lower than 10%). Viruses represented less than 2% of all contigs in all samples. The taxonomic profiles of surface cryosoils and deep permafrost samples exhibited a high diversity, including between permafrost samples originating from various depths in the same borehole. In all samples, bacterial contigs carrying different beta-lactamases from class A to D were identified. Interpretation: No clear common taxonomic feature could be found shared by surface cryosoils or ancient permafrost layers. However, most samples (9/12) exhibited a high frequency of beta-lactamase genes, with an estimated average close to 1 copy/bacterial genome. In addition to the well-documented reactivation of infectious ancient pathogens (bacteria, viruses, protozoa), we show now that global warming could contribute to the emergence of new antibiotic resistances through the mobilization by contemporary bacteria of ancient DNA released from thawing permafrost.


Author(s):  
Matt Woodburn ◽  
Gabriele Droege ◽  
Sharon Grant ◽  
Quentin Groom ◽  
Janeen Jones ◽  
...  

The utopian vision is of a future where a digital representation of each object in our collections is accessible through the internet and sustainably linked to other digital resources. This is a long term goal however, and in the meantime there is an urgent need to share data about our collections at a higher level with a range of stakeholders (Woodburn et al. 2020). To sustainably achieve this, and to aggregate this information across all natural science collections, the data need to be standardised (Johnston and Robinson 2002). To this end, the Biodiversity Information Standards (TDWG) Collection Descriptions (CD) Interest Group has developed a data standard for describing collections, which is approaching formal review for ratification as a new TDWG standard. It proposes 20 classes (Suppl. material 1) and over 100 properties that can be used to describe, categorise, quantify, link and track digital representations of natural science collections, from high-level approximations to detailed breakdowns depending on the purpose of a particular implementation. The wide range of use cases identified for representing collection description data means that a flexible approach to the standard and the underlying modelling concepts is essential. These are centered around the ‘ObjectGroup’ (Fig. 1), a class that may represent any group (of any size) of physical collection objects, which have one or more common characteristics. This generic definition of the ‘collection’ in ‘collection descriptions’ is an important factor in making the standard flexible enough to support the breadth of use cases. For any use case or implementation, only a subset of classes and properties within the standard are likely to be relevant. In some cases, this subset may have little overlap with those selected for other use cases. This additional need for flexibility means that very few classes and properties, representing the core concepts, are proposed to be mandatory. Metrics, facts and narratives are represented in a normalised structure using an extended MeasurementOrFact class, so that these can be user-defined rather than constrained to a set identified by the standard. Finally, rather than a rigid underlying data model as part of the normative standard, documentation will be developed to provide guidance on how the classes in the standard may be related and quantified according to relational, dimensional and graph-like models. So, in summary, the standard has, by design, been made flexible enough to be used in a number of different ways. The corresponding risk is that it could be used in ways that may not deliver what is needed in terms of outputs, manageability and interoperability with other resources of collection-level or object-level data. To mitigate this, it is key for any new implementer of the standard to establish how it should be used in that particular instance, and define any necessary constraints within the wider scope of the standard and model. This is the concept of the ‘collection description scheme,’ a profile that defines elements such as: which classes and properties should be included, which should be mandatory, and which should be repeatable; which controlled vocabularies and hierarchies should be used to make the data interoperable; how the collections should be broken down into individual ObjectGroups and interlinked, and how the various classes should be related to each other. which classes and properties should be included, which should be mandatory, and which should be repeatable; which controlled vocabularies and hierarchies should be used to make the data interoperable; how the collections should be broken down into individual ObjectGroups and interlinked, and how the various classes should be related to each other. Various factors might influence these decisions, including the types of information that are relevant to the use case, whether quantitative metrics need to be captured and aggregated across collection descriptions, and how many resources can be dedicated to amassing and maintaining the data. This process has particular relevance to the Distributed System of Scientific Collections (DiSSCo) consortium, the design of which incorporates use cases for storing, interlinking and reporting on the collections of its member institutions. These include helping users of the European Loans and Visits System (ELViS) (Islam 2020) to discover specimens for physical and digital loans by providing descriptions and breakdowns of the collections of holding institutions, and monitoring digitisation progress across European collections through a dynamic Collections Digitisation Dashboard. In addition, DiSSCo will be part of a global collections data ecosystem requiring interoperation with other infrastructures such as the GBIF (Global Biodiversity Information Facility) Registry of Scientific Collections, the CETAF (Consortium of European Taxonomic Facilities) Registry of Collections and Index Herbariorum. In this presentation, we will introduce the draft standard and discuss the process of defining new collection description schemes using the standard and data model, and focus on DiSSCo requirements as examples of real-world collection descriptions use cases.


2019 ◽  
Vol 4 ◽  
pp. 97-114
Author(s):  
Michał Biela

Celem niniejszego artykułu jest prezentacja założeń teoretycznych oraz praktycznej implementacji koncepcji alternatywnych źródeł finansowania społecznościowego w Polsce i Unii Europejskiej ze szczególnym uwzględnieniem aspektów formalno-prawnych crowdfundingu. Artykuł składa się z trzech części: w pierwszej opisano założenia definicyjne i koncepcyjne crowdfundingu, w drugiej przedstawiono propozycję zmiany ram regulacyjnych finansowania społecznościowego, przygotowanych przez instytucje Unii Europejskiej, natomiast trzecia zawiera uregulowania prawne finansowania społecznościowego w Polsce. W artykule jako metodę badawczą zastosowano desk research, której implementacja umożliwiła analizę istniejącej literatury przedmiotu. Theoretical assumptions of crowdfunding and its legal regulations in the European Union and in PolandThe aim of this article is to present the theoretical assumptions and practical implementation of the concept of alternative sources of funding in Poland and in the European Union, with emphasis on the formal and legal aspects of crowdfunding. The article consists of three parts. The first part describes the definition and conceptual assumptions of crowdfunding. The second part presents a proposal to change the crowdfunding regulatory framework at the European Union level. The third part includes legal regulations for crowdfunding in Poland. In the article, desk research was used as a research method, the implementation of which enabled the analysis of the existing literature on the subject.


Author(s):  
Yongguang Jiang ◽  
Peng Xiao ◽  
Gongliang Yu ◽  
Gaofei Song ◽  
Renhui Li

Harmful cyanobacterial blooms pose a risk to human health worldwide. To enhance understanding on the bloom-forming mechanism, the spatiotemporal changes in cyanobacterial diversity and composition in two eutrophic lakes (Erhai Lake and Lushui Reservoir) of China were investigated from 2010 to 2011 by high-throughput sequencing of environmental DNA. For each sample, 118 to 260 cpcBA-IGS operational taxonomic units (OTUs) were obtained. Fifty-two abundant OTUs were identified, which made up 95.2% of the total sequences and were clustered into nine cyanobacterial groups. Although the cyanobacterial communities of both lakes were mainly dominated by Microcystis, Erhai Lake had a higher cyanobacterial diversity. The abundance of mixed Nostocales species was lower than that of Microcystis, whereas Phormidium and Synechococcus were opportunistically dominant. The correlation between the occurrence frequency and relative abundance of OTUs was poorly fitted by the Sloan neutral model. Deterministic processes such as phosphorus availability were shown to have significant effects on the cyanobacterial community structure in Erhai Lake. In summary, the Microcystis-dominated cyanobacterial community was mainly affected by the deterministic process. Opportunistically dominant species have the potential to replace Microcystis and form blooms in eutrophic lakes, indicating the necessity to monitor these species for drinking water safety.


10.2196/17176 ◽  
2020 ◽  
Vol 8 (7) ◽  
pp. e17176
Author(s):  
Felipe Carvalho Pellison ◽  
Rui Pedro Charters Lopes Rijo ◽  
Vinicius Costa Lima ◽  
Nathalia Yukie Crepaldi ◽  
Filipe Andrade Bernardi ◽  
...  

Background Interoperability of health information systems is a challenge due to the heterogeneity of existing systems at both the technological and semantic levels of their data. The lack of existing data about interoperability disrupts intra-unit and inter-unit medical operations as well as creates challenges in conducting studies on existing data. The goal is to exchange data while providing the same meaning for data from different sources. Objective To find ways to solve this challenge, this research paper proposes an interoperability solution for the tuberculosis treatment and follow-up scenario in Brazil using Semantic Web technology supported by an ontology. Methods The entities of the ontology were allocated under the definitions of Basic Formal Ontology. Brazilian tuberculosis applications were tagged with entities from the resulting ontology. Results An interoperability layer was developed to retrieve data with the same meaning and in a structured way enabling semantic and functional interoperability. Conclusions Health professionals could use the data gathered from several data sources to enhance the effectiveness of their actions and decisions, as shown in a practical use case to integrate tuberculosis data in the State of São Paulo.


Author(s):  
Carla Bridget Milazzo ◽  
Katherine Grace Zulak ◽  
Mariano Jordi Muria-Gonzalez ◽  
Darcy Jones ◽  
Matthew Power ◽  
...  

Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies especially in agricultural contexts. Here we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, a HTS tool that constructs community profiles from environmental DNA (eDNA). We studied the fungal nuclear ribosomal large subunit (LSU) D2 and ITS2 DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis (PCoA) and PERMANOVA, ASV diversity did not change in response to barley cultivar or fungicide treatment, however the community structure of unsprayed plants did change between two collection times eight days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.


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