scholarly journals Connecting data and expertise: a new alliance for biodiversity knowledge

2019 ◽  
Vol 7 ◽  
Author(s):  
Donald Hobern ◽  
Brigitte Baptiste ◽  
Kyle Copas ◽  
Robert Guralnick ◽  
Andrea Hahn ◽  
...  
Keyword(s):  
Research Policy ◽  
Coordination Mechanism ◽  
Environmental Research ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
Global Alliance ◽  
Global Biodiversity Information Facility ◽  
Sustainable Solutions ◽  
Biodiversity Knowledge ◽  
Global Biodiversity

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. This paper summarises the GBIC2 discussions and presents a set of 23 complementary ambitions to be addressed by the global community in the context of the proposed alliance. The authors call on all who are responsible for describing and monitoring natural systems, all who depend on biodiversity data for research, policy or sustainable environmental management and all who are involved in developing biodiversity informatics solutions to register interest at https://biodiversityinformatics.org/ and to participate in the next steps to establishing a collaborative alliance. The supplementary materials include brochures in a number of languages (English, Arabic, Spanish, Basque, French, Japanese, Dutch, Portuguese, Russian, Traditional Chinese and Simplified Chinese). These summarise the need for an alliance for biodiversity knowledge and call for collaboration in its establishment.

scholarly journals An alliance for biodiversity knowledge: Rethinking international collaboration in biodiversity informatics

2019 ◽  
Vol 3 ◽  
Author(s):  
Donald Hobern ◽  
Joseph Miller
Keyword(s):  
Building Blocks ◽  
Coordination Mechanism ◽  
Environmental Research ◽  
Biodiversity Informatics ◽  
Global Alliance ◽  
Global Biodiversity Information Facility ◽  
Sustainable Solutions ◽  
Biodiversity Knowledge ◽  
Global Biodiversity ◽  
Biodiversity Information

There has been major progress over the last two decades in digitising historical knowledge of biodiversity and in making biodiversity data freely and openly accessible. Interlocking efforts bring together international partnerships and networks, national, regional and institutional projects and investments and countless individual contributors, spanning diverse biological and environmental research domains, government agencies and non-governmental organisations, citizen science and commercial enterprise. However, current efforts remain inefficient and inadequate to address the global need for accurate data on the world's species and on changing patterns and trends in biodiversity. Significant challenges include imbalances in regional engagement in biodiversity informatics activity, uneven progress in data mobilisation and sharing, the lack of stable persistent identifiers for data records, redundant and incompatible processes for cleaning and interpreting data and the absence of functional mechanisms for knowledgeable experts to curate and improve data. The first Global Biodiversity Informatics Conference (GBIC) in 2012 delivered the Global Biodiversity Informatics Outlook (GBIO, Hobern et al. 2012), an architectural vision for the major components of a distributed global infrastructure for biodiiversity information, but realigning the work of existing organisations and projects to achieve this vision remains challenging. Recognising the need for greater alignment between efforts at all scales, the Global Biodiversity Information Facility (GBIF) convened the second Global Biodiversity Informatics Conference (GBIC2) in July 2018 to propose a coordination mechanism for developing shared roadmaps for biodiversity informatics. GBIC2 attendees reached consensus on the need for a global alliance for biodiversity knowledge, learning from examples such as the Global Alliance for Genomics and Health (GA4GH) and the open software communities under the Apache Software Foundation. These initiatives provide models for multiple stakeholders with decentralised funding and independent governance to combine resources and develop sustainable solutions that address common needs. GBIF was asked to coordinate next steps following GBIC2, including publication of a paper, Connecting data and expertise: a new alliance for biodiversity knowledge (Hobern et al. 2019). The supplementary materials for the paper include PDF brochures explaining the concept in eleven languages. During 2019, GBIF is coordinating further consultations to establish an optimal model for the governance and operations of the alliance and to advance collaboration around some of the major building blocks of the GBIO. Collaboration at this scale, and across all aspects of biodiversity information, is essential for effective delivery of important information products such as the Essential Biodiversity Variables and the planned pan-European natural history collections infrastructure, DiSSCo. This presentation explains the goals for this alliance and updates on progress during 2019 in operationalising the concept.

scholarly journals Considerable Progress in Russian GBIF Community

2019 ◽  
Vol 3 ◽  
Author(s):  
Maxim Shashkov ◽  
Natalya Ivanova
Keyword(s):  
Komi Republic ◽  
Russian Language ◽  
Data Sources ◽  
Data Publishing ◽  
Software Project ◽  
Biodiversity Informatics ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Science System ◽  
Global Biodiversity

Russia is a huge gap on the open access global biodiversity map of the Global Biodiversity Information Facility (GBIF). National biodiversity data are stored in various sources including museums, herbaria, scientific literature and reports as well as in the private collections and local databases. The best known and largest of the Russian herbarium collections are the collections stored in Komarov Botanical Institute of the Russian Academy of Science (>6 M sheets) and Moscow University (>1 M sheets). The largest zoological collection is located in Zoological institute of the Russian Academy of Science, with >60 M specimens. But most of the national biodiversity data is not yet digitized. The national biodiversity portal as well as the list of Russian biodiversity data sources are still absent. Despite this, projects and other activities are implemented to mobilize a national data using international biodiversity data standards. Currently Russia is not a GBIF member, but in the last 5 years, more than 1.6 M occurrences were published by Russian publishers through GBIF.org (69 datasets at the end of March 2019). The largest GBIF data provider in Russia is the Lomonosov Moscow State University. The Digital Moscow University Herbarium includes 971,732 specimens collected from Russia and many other countries. The Russian GBIF community is steadily expanding (Fig. 1); this is reflected in an increase in the number of publishers and published datasets. The current GBIF network infrastructure in Russia includes 5 IPT (Integrated Publishing Toolkit) installations in Saint Petersburg (two), Pushchino (Moscow region), Moscow, and Syktyvkar (Komi Republic). Russian-language biodiversity informatics materials are collected and presented from an informal web site http://gbif.ru/ with three main sections: data publishing through GBIF, Russian GBIF activities, and Russian biodiversity data sources. data publishing through GBIF, Russian GBIF activities, and Russian biodiversity data sources. Additional sections are dedicated to iNaturalist citizen science system and Russian Specify Software Project community. We provide technical helpdesk support not only for Russian publishers, but also for Russian speakers from the former USSR. The national mailing-list (via google groups) aims to provide a platform for news sharing. Now it includes >240 subscribers. Since the end of 2014, regular biodiversity informatics events are being held in Russia. Last year, two data training courses, funded by GBIF (project ID Russia-02 - "GBIF.ru data mobilization activities") and ForBIO (Research school in biosystematics), were organized in Moscow and Irkutsk region with the participation of 29 Russian researchers. National biodiversity informatics conferences were held in Apatity (2017) and Irkutsk (2018). We believe Russia already has a well established community that can become the basis for further development when Russia becomes a GBIF member.

scholarly journals Storing, Maintaining and Mobilizing Botswana National Museum’s Entomology Digital Collections: The GBIF/BID Approach

2018 ◽  
Vol 2 ◽  
pp. e26328
Author(s):  
Boikhutso Lerato Rapalai
Keyword(s):  
National Museum ◽  
Global Biodiversity Information Facility ◽  
Digital Collections ◽  
Natural Heritage ◽  
Heritage Sites ◽  
Biodiversity Knowledge ◽  
Insect Biodiversity ◽  
Decision Making Processes ◽  
Global Biodiversity ◽  
Biodiversity Information

The Botswana National Museum is mandated to protect, preserve and promote Botswana’s cultural and natural heritage for sustainable utilization thereof by collecting, researching, conserving and exhibiting for public education and appreciation. The Entomology Section of the museum is aiming towards becoming the national center for entomology collections as well as contributing to the monitoring and enhancement of natural heritage sites in Botswana. The Botswana National Museum entomology collection was assembled over more than three decades by a succession of collectors, curators and technical officers. Specimens are carefully prepared and preserved, labelled with field data, sorted and safely stored. The collection is preserved as wet (ethanol preserved) or as dry pinned specimens in drawers. This collection is invaluable for reference, research, baseline data and educational purposes. As a way of mobilizing insect biodiversity data and making it available online for conservation efforts and decision making processes, in 2016 the Botswana National Museum collaborated with five other African states to implement the Biodiversity Information for Development (BID) and Global Biodiversity Information Facility (GBIF) funded African Insect Atlas’ Project (https://www.gbif.org/project/82632/african-insect-atlas). This collaborative project was initiated to move biodiversity knowledge out of select insect collections into the hands of a new generation of global biodiversity researchers interested in direct outcomes. To date, the Botswana National Museum has been instrumental through the efforts of this project in storing, maintaining and mobilizing insect digital collections and making the data available online through the GBIF Platform.

scholarly journals Completeness of Digital Accessible Knowledge of the Plants of Ghana

2016 ◽  
Vol 11 ◽  
Author(s):  
Alex Asase ◽  
A. Townsend Peterson
Keyword(s):  
Geographic Distance ◽  
Northern Ghana ◽  
Biodiversity Informatics ◽  
Primary Research ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Herbarium Data ◽  
Research Grade ◽  
Biodiversity Information

Providing comprehensive, informative, primary, research-grade biodiversity information represents an important focus of biodiversity informatics initiatives. Recent efforts within Ghana have digitized >90% of primary biodiversity data records associated with specimen sheets in Ghanaian herbaria; additional herbarium data are available from other institutions via biodiversity informatics initiatives such as the Global Biodiversity Information Facility. However, data on the plants of Ghana have not as yet been integrated and assessed to establish how complete site inventories are, so that appropriate levels of confidence can be applied. In this study, we assessed inventory completeness and identified gaps in current Digital Accessible Knowledge (DAK) of the plants of Ghana, to prioritize areas for future surveys and inventories. We evaluated the completeness of inventories at ½° spatial resolution using statistics that summarize inventory completeness, and characterized gaps in coverage in terms of geographic distance and climatic difference from well-documented sites across the country. The southwestern and southeastern parts of the country held many well-known grid cells; the largest spatial gaps were found in central and northern parts of the country. Climatic difference showed contrasting patterns, with a dramatic gap in coverage in central-northern Ghana. This study provides a detailed case study of how to prioritize for new botanical surveys and inventories based on existing DAK.

scholarly journals Mapping and Publishing Sequence-Derived Data through Biodiversity Data Platforms

2020 ◽  
Vol 4 ◽  
Author(s):  
Dmitry Schigel ◽  
Anders Andersson ◽  
Andrew Bissett ◽  
Anders Finstad ◽  
Frode Fossøy ◽  
...  
Keyword(s):  
Policy Design ◽  
Molecular Ecology ◽  
Added Value ◽  
Data Publishing ◽  
Ecological Knowledge ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Wide Range ◽  
Global Biodiversity ◽  
Derived Data

Most users will foresee the use of genetic sequences in the context of molecular ecology or phylogenetic research, however, a sequence with coordinates and a timestamp is a valuable biodiversity occurrence that is useful in a much broader context than its original purpose. To uncover this potential, sequence-derived data need to become findable, accessible, interoperable, and reusable through generalist biodiversity data platforms. Stimulated by the Biodiversity_Next discussions in 2019, we have worked for about 10 months to put together practical data mapping and data publishing experiences in Norway, Australia, Sweden, and Denmark, as well as in the UNITE and the GBIF (Global Biodiversity Information Facility) networks. The resulting guide was put together to provide practical instruction for mapping sequence-derived data. Biodiversity data communities remain dominated by the macroscopic, easily detectable, morphologically identifiable species. This is not only true for citizen science and other forms of biodiversity popularization, but is also visible in the university and museum department structures, financial resource allocations, biodiversity legislation, and policy design. Recent decades of molecular advances have increased the power of genetic methods for detecting, describing, and documenting global biodiversity. We have yet to see the wide shift of data generating efforts from the traditional taxonomic foci of biodiversity assesments to the more balanced and inclusive systems focusing on all functionally important taxa and environments. These include soil, limnic and marine environments, decomposing plants and deadwood, and all life therein. Environmental DNA data enable recording of present and past presence of micro- and macroscopic organisms with minimal effort and by non-invasive methods. The apparent ease of these methods requires a cautious approach to the resulting data and their interpretation. It remains important to define and agree on the organism recording and reporting routines for genetic data. DNA data represent a major addition to the many ways in which GBIF and other biodiversity data platforms index the living world. Our guide is resting on the shoulders of those who have been developing and improving MIxS (Minimum Information about any (x) Sequence), GGBN (Global Genome Biodiversity Network) and other data standards. The added value of publishing sequence-derived data through non-genetic biodiversity discovery platforms relates to spatio-temporal occurrences and sequence-based names. Reporting sequence-derived occurrences in an open and reproducible way has a wide range of benefits: notably, it increases citability, highlights the taxa concerned in the context of biological conservation, and contributes to taxonomic and ecological knowledge.

scholarly journals Towards a Post-Graduate Level Curriculum for Biodiversity Informatics. Perspectives from the Global Biodiversity Information Facility (GBIF) Community

2021 ◽  
Vol 9 ◽  
Author(s):  
Fatima Parker-Allie ◽  
Francisco Pando ◽  
Anders Telenius ◽  
Jean Ganglo ◽  
Danny Vélez ◽  
...  
Keyword(s):  
Biological Data ◽  
Initial Assessment ◽  
Biodiversity Informatics ◽  
Global Biodiversity Information Facility ◽  
Policy Makers ◽  
Academic Teaching ◽  
E Learning ◽  
Learning Platforms ◽  
Global Biodiversity ◽  
Biodiversity Information

Biodiversity informatics is a new and evolving field, requiring efforts to develop capacity and a curriculum for this field of science. The main objective was to summarise the level of activity and the efforts towards developing biodiversity informatics curricula, for work-based training and/or academic teaching at universities, taking place within the Global Biodiversity Information Facility (GBIF) countries and its associated network. A survey approach was used to identify existing capacities and resources within the network. Most of GBIF Nodes survey respondents (80%) are engaged in onsite training activities, with a focus on work-based professionals, mostly researchers, policy-makers and students. Training topics include data mobilisation, digitisation, management, publishing, analysis and use, to enable the accessibility of analogue and digital biological data that currently reside as scattered datasets. An initial assessment of academic teaching activities highlighted that countries in most regions, to varying degrees, were already engaged in the conceptualisation, development and/or implementation of formal academic programmes in biodiversity informatics, including programmes in Benin, Colombia, Costa Rica, Finland, France, India, Norway, South Africa, Sweden, Taiwan and Togo. Digital e-learning platforms were an important tool to help build capacity in many countries. In terms of the potential in the Nodes network, 60% expressed willingness to be recruited or commissioned for capacity enhancement purposes. Contributions and activities of various country nodes across the network have been highlighted and a working curriculum framework has been defined.

scholarly journals Data integration enables global biodiversity synthesis

2021 ◽  
Vol 118 (6) ◽  
pp. e2018093118
Author(s):  
J. Mason Heberling ◽  
Joseph T. Miller ◽  
Daniel Noesgaard ◽  
Scott B. Weingart ◽  
Dmitry Schigel
Keyword(s):  
Data Integration ◽  
Species Interactions ◽  
Large Scale ◽  
Data Use ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Research Areas ◽  
Global Biodiversity ◽  
Biodiversity Information ◽  
Global Data

The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world’s largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.

scholarly journals Unlocking the Entomological Collection of the Natural History Museum of Maputo, Mozambique

2021 ◽  
Vol 9 ◽  
Author(s):  
Domingos Sandramo ◽  
Enrico Nicosia ◽  
Silvio Cianciullo ◽  
Bernardo Muatinte ◽  
Almeida Guissamulo
Keyword(s):  
Natural History ◽  
Crucial Role ◽  
Development Programme ◽  
Natural History Museum ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
History Museum ◽  
Data Portal ◽  
Global Biodiversity ◽  
Biodiversity Information

The collections of the Natural History Museum of Maputo have a crucial role in the safeguarding of Mozambique's biodiversity, representing an important repository of data and materials regarding the natural heritage of the country. In this paper, a dataset is described, based on the Museum’s Entomological Collection recording 409 species belonging to seven orders and 48 families. Each specimen’s available data, such as geographical coordinates and taxonomic information, have been digitised to build the dataset. The specimens included in the dataset were obtained between 1914–2018 by collectors and researchers from the Natural History Museum of Maputo (once known as “Museu Alváro de Castro”) in all the country’s provinces, with the exception of Cabo Delgado Province. This paper adds data to the Biodiversity Network of Mozambique and the Global Biodiversity Information Facility, within the objectives of the SECOSUD II Project and the Biodiversity Information for Development Programme. The aforementioned insect dataset is available on the GBIF Engine data portal (https://doi.org/10.15468/j8ikhb). Data were also shared on the Mozambican national portal of biodiversity data BioNoMo (https://bionomo.openscidata.org), developed by SECOSUD II Project.

scholarly journals Harvestmen occurrence database (Arachnida, Opiliones) of the Museu Paraense Emílio Goeldi, Brazil

2019 ◽  
Vol 7 ◽  
Author(s):  
Valéria da Silva ◽  
Manoel Aguiar-Neto ◽  
Dan Teixeira ◽  
Cleverson Santos ◽  
Marcos de Sousa ◽  
...  
Keyword(s):  
Public Consultation ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
The Third ◽  
The World ◽  
Northern Brazil ◽  
Global Biodiversity ◽  
The Government ◽  
Biodiversity Information ◽  
Brazilian Biodiversity

We present a dataset with information from the Opiliones collection of the Museu Paraense Emílio Goeldi, Northern Brazil. This collection currently has 6,400 specimens distributed in 13 families, 30 genera and 32 species and holotypes of four species: Imeri ajuba Coronato-Ribeiro, Pinto-da-Rocha & Rheims, 2013, Phareicranaus patauateua Pinto-da-Rocha & Bonaldo, 2011, Protimesius trocaraincola Pinto-da-Rocha, 1997 and Sickesia tremembe Pinto-da-Rocha & Carvalho, 2009. The material of the collection is exclusive from Brazil, mostly from the Amazon Region. The dataset is now available for public consultation on the Sistema de Informação sobre a Biodiversidade Brasileira (SiBBr) (https://ipt.sibbr.gov.br/goeldi/resource?r=museuparaenseemiliogoeldi-collection-aracnologiaopiliones). SiBBr is the Brazilian Biodiversity Information System, an initiative of the government and the Brazilian node of the Global Biodiversity Information Facility (GBIF), which aims to consolidate and make primary biodiversity data available on a platform (Dias et al. 2017). Harvestmen or Opiliones constitute the third largest arachnid order, with approximately 6,500 described species. Brazil is the holder of the greatest diversity in the world, with more than 1,000 described species, 95% (960 species) of which are endemic to the country. Of these, 32 species were identified and deposited in the collection of the Museu Paraense Emílio Goeldi.

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