Towards an open, zoomable atlas for invasion science and beyond

Jeschke, Jonathan M.; Heger, Tina; Kraker, Peter; Schramm, Maxi; Kittel, Christopher; Mietchen, Daniel

doi:10.3897/neobiota.68.66685

Cited by 15 publications

(10 citation statements)

References 36 publications

(46 reference statements)

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“…One way to achieve this could be to incentivize the publication of fine-grained description of hypotheses and summaries of respective results of empirical tests as nanopublications (Kuhn et al 2018). Another possibility would be to build an encompassing interactive online tool that maps existing hypotheses, for example based on the hi-knowledge tool introduced above (for a suggestion, see Jeschke et al 2021), enriched with causal network diagrams providing fine-grained descriptions of hypothesized mechanisms. In the future, such a tool could allow for (pre-) registration of empirical tests and summary reports of respective results (Heger and Jeschke 2018a).…”

Section: Challenges For Assessing the Empirical Relevance Of Hypothes...mentioning

confidence: 99%

What are ecological mechanisms? Suggestions for a fine-grained description of causal mechanisms in invasion ecology

Heger

2022

Biol Philos

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Invasion ecology addresses the spread of species outside of their native ranges. A central aim of this field is to find mechanistic explanations for why species are able to establish and spread in an area in which they did not evolve. Usually it remains unclear, however, what exactly is meant by ‘mechanistic explanation’ or ‘mechanism’. The paper argues that the field can benefit from the philosophical discussion of what a mechanism is. Based on conceptions of mechanisms as processes in concrete systems, causal mechanisms can be defined as one type of mechanism, representing recurring networks of causal relationships. With the example of a well-known hypothesized mechanism in invasion ecology, namely enemy release, the paper demonstrates how such causal mechanisms can be depicted as causal network diagrams. This approach could facilitate the development of step-by-step explanations, enhance clear argumentation and allow for more precise linkage of empirical tests to theory. Challenges to assessing the empirical relevance of hypothesized mechanisms are discussed, and suggestions are made concerning how the proposed approach could help in overcoming some of them.

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Section: Challenges For Assessing the Empirical Relevance Of Hypothes...mentioning

confidence: 99%

What are ecological mechanisms? Suggestions for a fine-grained description of causal mechanisms in invasion ecology

Heger

2022

Biol Philos

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“…Efficient restoration of ecosystems, as a second example, requires knowledge about methods for facilitating the recovery of soils, re-establishment of species and triggering of ecosystem functions. In the respective research areas, specifically invasion biology and restoration ecology, publication workflows are impeding progress, since much of the locally produced scholarly knowledge remains hidden in PDFs that are hard to discover, not machine readable, and often hidden behind paywalls (Jeschke et al 2021). Databases exist for providing some of the much needed information, but these focus on particular groups of organisms (e.g.…”

Section: T51 -Addressing the Biodiversity And Ecosystem Crisis With F...mentioning

confidence: 99%

SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC

Stocker¹,

Heger²,

Schweidtmann³

et al. 2022

RIO

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In the age of advanced information systems powering fast-paced knowledge economies that face global societal challenges, it is no longer adequate to express scholarly information - an essential resource for modern economies - primarily as article narratives in document form. Despite being a well-established tradition in scholarly communication, PDF-based text publishing is hindering scientific progress as it buries scholarly information into non-machine-readable formats. The key objective of SKG4EOSC is to improve science productivity through development and implementation of services for text and data conversion, and production, curation, and re-use of FAIR scholarly information. This will be achieved by (1) establishing the Open Research Knowledge Graph (ORKG, orkg.org), a service operated by the SKG4EOSC coordinator, as a Hub for access to FAIR scholarly information in the EOSC; (2) lifting to EOSC of numerous and heterogeneous domain-specific research infrastructures through the ORKG Hub’s harmonized access facilities; and (3) leverage the Hub to support cross-disciplinary research and policy decisions addressing societal challenges. SKG4EOSC will pilot the devised approaches and technologies in four research domains: biodiversity crisis, precision oncology, circular processes, and human cooperation. With the aim to improve machine-based scholarly information use, SKG4EOSC addresses an important current and future need of researchers. It extends the application of the FAIR data principles to scholarly communication practices, hence a more comprehensive coverage of the entire research lifecycle. Through explicit, machine actionable provenance links between FAIR scholarly information, primary data and contextual entities, it will substantially contribute to reproducibility, validation and trust in science. The resulting advanced machine support will catalyse new discoveries in basic research and solutions in key application areas.

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“…An openly-accessible, searchable knowledge base for invasion biology that provides search outputs in an intuitively structured way would, therefore, be a major achievement (Jeschke et al 2021). Ideally, this tool would allow customised searches and interactive displays of search results, with direct links to the respective publications and underlying data.…”

Section: Enhanced Knowledge Management and Presentationmentioning

confidence: 99%

“…A tool that could deliver such kind of information is not necessarily an idealistic vision that will never be realised. First suggestions, making use of advances in data visualisation, machine learning and semantic modelling, are already being developed (Jeschke et al 2021).…”

Section: Enhanced Knowledge Management and Presentationmentioning

confidence: 99%

Some reflections on current invasion science and perspectives for an exciting future

Heger¹,

Jeschke²,

Kollmann³

2021

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Species spreading beyond their native ranges are important study objects in ecology and environmental sciences and research on biological invasions is thriving. Along with an increase in the number of publications, the research field is experiencing an increase in the diversity of methods applied and questions asked. This development has facilitated an upsurge in information on invasions, but it also creates conceptual and practical challenges. To provide more transparency on which kind of research is actually done in the field, the distinction between invasion science, encompassing the full spectrum of studies on biological invasions and the sub-field of invasion biology, studying patterns and mechanisms of species invasions with a focus on biological research questions, can be useful. Although covering a smaller range of topics, invasion biology today still is the driving force in invasion science and we discuss challenges stemming from its embeddedness in the social context. Invasion biology consists of the building blocks ‘theory’, ‘case studies’ and ‘application’, where theory takes the form of conceptual frameworks, major hypotheses and statistical generalisations. Referencing recent work in philosophy of science, we argue that invasion biology, like other biological or ecological disciplines, does not rely on the development of an all-encompassing theory in order to be efficient. We suggest, however, that theory development is nonetheless necessary and propose improvements. Recent advances in data visualisation, machine learning and semantic modelling are providing opportunities for enhancing knowledge management and presentation and we suggest that invasion science should use these to transform its ways of publishing, archiving and visualising research. Along with a stronger focus on studies going beyond purely biological questions, this would facilitate the efficient prevention and management of biological invasions.

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Towards an open, zoomable atlas for invasion science and beyond

Cited by 15 publications

References 36 publications

What are ecological mechanisms? Suggestions for a fine-grained description of causal mechanisms in invasion ecology

What are ecological mechanisms? Suggestions for a fine-grained description of causal mechanisms in invasion ecology

SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of knowledge graphs for FAIR Scholarly Information in EOSC

Some reflections on current invasion science and perspectives for an exciting future

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