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

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. © 2021. Parker-Allie F et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedPeer reviewe

Towards a Curriculum for Biodiversity Informatics

Biodiversity informatics has been characterized as a rapidly growing interdisciplinary field, which aims to bring together the areas of biodiversity and informatics. A study was conducted looking at the current level of activity within the GBIF Participant countries and its associated network in relation to work-based training and/or academic teaching at universities, in the field of biodiversity informatics. It was intended to get an overview of GBIF Node Managers, (hence, member countries), already engaged in developing course curricula, or in providing training, and whether they would be willing to share resources or enter into collaborations, to further elaborate this field of science.This investigation followed a survey approach, conducted globally across the GBIF community to identify the existing capacities and resources within the network. The results indicated that the vast majority of GBIF Nodes survey respondents, are engaged in onsite training activities in biodiversity informatics areas, with a focus on professionals, mostly researchers, policy makers and students. Training includes data digitization, management, publishing, analysis and use, to enable the accessibility of analogue and digital biological data which currently resides as scattered databases/datasets.A list containing the associated URL's for training and dissemination activities in GBIF Nodes has been developed, based on survey results, and will be presented. An initial assessment of the academic teaching activities indicated that many countries across most regions were already engaged in the conceptualisation, development and/or implementation of formal academic programs in biodiversity informatics including Benin, Colombia, Costa Rica, Finland, France, India, Norway, South Africa, Sweden, Taiwan and Togo. This study also identified that digital e-learning platforms were a very important tool to help build capacity in a number of countries.To assess the level of potential in the network to support academic teaching and work-based training, sixty percent indicated that they would be willing to be recruited or commissioned to support teaching activities, demonstrating the value of the Nodes network to support the development of biodiversity informatics globally. The contributions and activities of various nodes across the network will be highlighted and a working high-level curriculum framework will be discussed

Cold-Temperature Adaptation in Nematodes from the Victoria Land Coast, Antarctica

The invertebrates that inhabit Antarctica’s terrestrial ice-free areas are a unique resource for the study of adaptations to extreme conditions and illustrate the limits to which physiology can be stretched by evolution to allow life to continue. Perhaps the most exciting result of past studies of these adaptations in the Antarctic’s terrestrial fauna was the discovery by Wharton and Ferns in 1995 of the survival of extensive intracellular freezing in the nematode Panagrolaimus davidi. Intracellular ice formation is generally considered fatal, and as the first and, so far, unique example of this adaptation in a multicellular organism, it has remained contentious. Understanding this adaptation could have important applications for cryopreservation, but research has currently been limited to this one species and based on a laboratory culture that have been isolated from its environment for over 20 years. There has been little research into the thermal tolerances of other Antarctic nematode species. This thesis explores three broad research themes in order to contribute to the understanding of adaptation in Antarctic nematodes generally, and the survival of intracellular freezing specifically. Firstly, to place their adaptations in an environmental context, the distribution of the nematode species found in two ice-free areas, around Cape Hallett in Northern Victoria Land and Gondwana station in Terra Nova Bay, is described and factors underlying their distribution patterns are investigated using regression models. Four nematode species were found: Panagrolaimus davidi, Scottnema lindsayae, Plectus murrayi and Eudorylaimus antarcticus. Their distribution patterns are correlated to both broad-scale habitat descriptors and to soil geochemistry, revealing species-specific differences in distribution patterns that are broadly consistent with other studies of these species in soils from the Dry Valleys and penguin rookeries on Ross Island. The importance of soil conductivity (as a measure of salinity) in predicting the distribution patterns of all four species supports the hypothesis that salinity plays a primary role in determining invertebrate distribution in the terrestrial Antarctic. The current environmental challenges faced by these Antarctic nematodes in their habitats are then described, providing context for laboratory investigations of their adaptations. Secondly, the survival strategies employed by these nematodes are investigated. For P. davidi the survival of intracellular freezing was found to be strongly correlated with its nutritional status, explaining some of the variation in survival rates reported in previous studies. Plectus murrayi was also found to survive intracellular ice formation, providing a second example of an organism able to employ this survival strategy. The appearance of internal ice differed markedly between these two nematode species and that in a temperate species, Panagrellus redivivus, suggesting that adaptations enabling the survival of intracellular freezing involve the control of internal ice. Further evidence was also provided for the use of a cryoprotective dehydration survival strategy in response to slow freezing rates in these Antarctic nematodes. Thirdly, to provide a historical context for their adaptations, and in order to distinguish between the Antarctic species and show their relation to nematode species worldwide, genetic techniques and phylogenetic analyses were employed. Genetic sequencing of the 18S and D3 expansion ribosomal RNA regions and comparisons with published phylogenies for the phylum Nematoda revealed that the Antarctic species do not form a discrete Antarctic clade, but rather are spread over the phylum. This supports current hypotheses of endemism and a long Antarctic history for these species. However, the laboratory culture of P. davidi (referred to now as P. sp. nov.) was found to be a distinct species from the wild populations of P. davidi that were sequenced in this study. The surprising lack of sequence divergence between P. sp. nov. and some Californian Panagrolaimus species brings its origin into question, and suggests that it may represent a relatively recent invasive species to the Ross Sea Region. This finding calls for further research to address the possibility that it is the first example of a successful animal invasion of Continental Antarctica and to investigate the origins of its remarkable adaptations to freezing

Diversifying the GBIF Data Model

The Global Biodiversity Information Facility (GBIF) has been immensely successful in mobilizing a large number of records documenting species occurrence through a global network of data publishers. Today over 2 billion records are available for search and download through the GBIF.org infrastructure, with over 200 million originating in natural science collections or gleaned from citations of specimens in literature. These data are most commonly made available through the TDWG standards Darwin Core and Access to Biological Collections Data (ABCD) with their various extensions. The growth of the GBIF network has generated new challenges and a desire for GBIF to accommodate more varied types of data (e.g., ecological, eDNA, biological interactions, material samples with subsamples and associated media, taxonomic treatments), acknowledging that biodiversity data are more complex than ‘just’ the occurrence of species in time and space. GBIF has initiated work to explore the diversification of the data model that underpins the datasets connected to GBIF, and the services provided by its infrastructure. During 2021, several case studies were drafted and analyzed to establish a draft common domain model that could satisfy the key aspects of the studies. The cases cover a range of concerns, including automated monitoring, identification through sequencing techniques, biotic interactions, environmental measurements, and improvements to the handling of data representing preserved material. The draft model has been presented publicly several times and is being tested and matured to accommodate real datasets during 2022. This presentation will summarise the process followed, provide an overview of the cases that have been explored, and show the resulting model. We will describe the ongoing opportunities for community engagement as this work continues. We will provide insight into some of the lessons we have learned and how this research has the potential to help integrate many efforts relating to the use of the Darwin Core-related standards today

Biodiversity Information for Development: Building a global community of practice to mobilize and use biodiversity data

Biodiversity Information for Development, or BID, is a programme funded by the European Union and led by the Global Biodiversity Information Facility (GBIF), aiming to increase the amount of biodiversity information available for use in scientific research and policymaking. In its first phase, BID provided funding to 61 projects in the nations of sub-Saharan Africa, the Caribbean and the Pacific between 2015-2019, with a strong focus on developing capacity to mobilize, manage and use biodiversity data within the project teams and their institutions, and through the establishment and strengthening of national nodes. The capacity development approach centred on establishing a community of practice to bring in the expertise in the broader GBIF network to support the project teams in meeting their goals. This involved designing curricula for two workshops in the areas of data mobilization and data use for decision making; developing activities and materials to strengthen a base of mentors and trainers; establishing technical helpdesk support; and matchmaking to provide mentoring support to the funded projects. The community of practice, through mentoring and reuse of the workshop materials, has been expanded to support the capacity development needs in other programmes, reaching other regions, including Asia, South-East Europe and Eurasia. During this presentation, we will review the main findings of the BID impact study and guiding examples from within the BID programme to identify the key successes and lessons learned relating to capacity development. As this approach has wider application to the biodiversity community, we invite discussion how we can build on the experience through the BID programme to further develop our community of practice, narrowing knowledge gaps between various groups of biodiversity professionals

Facilitating the Mobilization and Sharing of Biodiversity Data using a Standard, Open, and Replicable Course Curriculum

The Global Biodiversity Information Facility (GBIF) empowers its global network through capacity-building activities that promote and enable the efficient mobilization and use of information about biodiversity. These activities work across capacity development levels, targeting individuals, institutions, nations, and global regions. This work expands the communities of practice engaged with the collection and curation of biodiversity. GBIF efforts build partnerships that institutionalize new capacity within a growing network of data publishing institutions. Coordination and dissemination is supported through the development of Participant nodes and regional collaborations.The Biodiversity Information for Development (BID) and the Biodiversity Information Fund for Asia (BIFA) programmes illustrate how a standardized, open, and replicable training curriculum underpins the success of funding programmes. These programmes support the biodiversity community and increase the amount of data mobilized and shared openly for use in science and research.During this presentation, we will describe the role that the Biodiversity Data Mobilization course plays in GBIF’s approach to capacity enhancement. We will review successes and challenges and discuss the processes used to continually improve our approach to training and capacity development

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

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