LOBD: Linked Data Dashboard for Marine Biodiversity

Zárate, Marcos Daniel; Buckle, Carlos

doi:10.1007/978-3-030-84825-5_11

Cited by 3 publications

(3 citation statements)

References 23 publications

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“…Data driven science is already generating massive datasets that help to inform the development of biodiversity and environmental indicators ( 108 , 109 ), and to steer policy and regulation ( 110 ). A number of important initiatives on biodiversity have taken root to develop and deploy tools and techniques to generate data and transform them into synthesized information for a range of purposes.…”

Section: Ecosystems and Biodiversitymentioning

confidence: 99%

Operationalizing “One Health” as “One Digital Health” Through a Global Framework That Emphasizes Fair and Equitable Sharing of Benefits From the Use of Artificial Intelligence and Related Digital Technologies

2022

Front. Public Health

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The operationalization of One Health (OH) through digitalization is a means to deploy digital technologies (including Artificial Intelligence (AI), big data and related digital technologies) to better capacitate us to deal with growing climate exigency and related threats to human, animal and plant health. With reference to the concept of One Digital Health (ODH), this paper considers how digital capabilities can help to overcome ‘operational brakes’ in OH through new and deeper insights, better predictions, and more targeted or precise preventive strategies and public health countermeasures. However, the data landscape is fragmented and access to certain types of data is increasingly restrictive as individuals, communities and countries seek to assert greater control over data taken from them. This paper proposes for a dedicated global ODH framework—centered on fairness and equity—to be established to promote data-sharing across all the key knowledge domains of OH and to devise data-driven solutions to challenges in the human-animal-ecosystems interface. It first considers the data landscape in relation to: (1) Human and population health; (2) Pathogens; (3) Animal and plant health; and (4) Ecosystems and biodiversity. The complexification from the application of advance genetic sequencing technology is then considered, with focus on current debates over whether certain types of data like digital (genetic) sequencing information (DSI) should remain openly and freely accessible. The proposed ODH framework must augment the existing access and benefit sharing (ABS) framework currently prescribed under the Nagoya Protocol to the Convention on Biological Diversity (CBD) in at least three different ways. First, the ODH framework should apply to all genetic resources and data, including DSI, whether from humans or non-humans. Second, the FAIRER principles should be implemented, with focus on fair and equitable benefit-sharing. Third, the ODH framework should adopt multilateral approaches to data sharing (such as through federated data systems) and to ABS. By operationalizing OH as ODH, we are more likely to be able to protect and restore natural habitats, secure the health and well-being of all living things, and thereby realize the goals set out in the post-2020 Global Biodiversity Framework under the CBD.

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Section: Ecosystems and Biodiversitymentioning

confidence: 99%

Operationalizing “One Health” as “One Digital Health” Through a Global Framework That Emphasizes Fair and Equitable Sharing of Benefits From the Use of Artificial Intelligence and Related Digital Technologies

2022

Front. Public Health

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“…Indispensable to the curation process of marine data have been the standards of the Biodiversity Information Standards 2 , more specifically Darwin Core (Wieczorek et al, 2012) and vocabularies such as those included in the International Commission on Zoological Nomenclature 3 , the World Register of Marine Species 4 (WoRMS) (WoRMS Editorial Board, 2022), the Environmental Ontology 5 (ENVO) (Buttigieg et al, 2016) and Marine Regions 6 (Claus et al, 2014). These standards and vocabularies and their adoption by biodiversity initiatives like GBIF and OBIS align with the goal of marine biodiversity Linked Open Data and support their interoperability and reusability (Page, 2016;Penev et al, 2019;Zárate and Buckle, 2021).…”

Section: Introductionmentioning

confidence: 99%

Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow

et al. 2022

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Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research.

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“…Nevertheless, they can still be met with a lot of resistance and suspicion in academic circles [3,4].Since its launch in 2012, Wikidata has rapidly grown into a cross-disciplinary open knowledgebase with items ranging from genes to cell types to researchers [2,[5][6][7]. It has wide-ranging applications, such as validating statistical information about disease outbreaks [8], aligning resources on human coronaviruses [9], or assessing biodiversity [10,11]. It can be thought of as a vast network graph (Fig 1A), wherein the items act as nodes (now over 100 million) linked to one another by over a billion statements, and further linked out to the wider web by many billions more.…”

mentioning

confidence: 99%