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Measures for interoperability of phenotypic data: minimum information requirements and formatting
(2016)
Background: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. Results: In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a document called "Minimum Information About a Plant Phenotyping Experiment", which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA-Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA-Tab-formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Conclusions: Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.
Background:
Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked
to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research
comprising manifold, diverse and time
‑consuming experiments, the findings can be fostered by reusing and combin‑
ing existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible
provided that the collected observations are equipped with an adequate set of metadata. So far there have been no
common standards governing phenotypic data description, which hampered data exchange and reuse.
Results:
In this paper we propose the guidelines for proper handling of the information about plant phenotyping
experiments, in terms of both the recommended content of the description and its formatting. We provide a docu‑
ment called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about
each experiment should be given, and a Phenotyping Configuration for the ISA
‑Tab format, which allows to practically
organise this information within a dataset. We provide examples of ISA
‑Tab
‑formatted phenotypic data, and a general
description of a few systems where the recommendations have been implemented.
Conclusions:
Acceptance of the rules described in this paper by the plant phenotyping community will help to
achieve findable, accessible, interoperable and reusable data.
Anthropogenic pressures increasingly alter natural systems. Therefore, understanding the resilience of agent-based complex systems such as ecosystems, i.e. their ability to absorb these pressures and sustain their functioning and services, is a major challenge. However, the mechanisms underlying resilience are still poorly understood. A main reason for this is the multidimensionality of both resilience, embracing the three fundamental stability properties recovery, resistance and persistence, and of the specific situations for which stability properties can be assessed. Agent-based models (ABM) complement empirical research which is, for logistic reasons, limited in coping with these multiple dimensions. Besides their ability to integrate multidimensionality through extensive manipulation in a fully controlled system, ABMs can capture the emergence of system resilience from individual interactions and feedbacks across different levels of organization. To assess the extent to which this potential of ABMs has already been exploited, we reviewed the state of the art in exploring resilience and its multidimensionality in ecological and socio-ecological systems with ABMs. We found that the potential of ABMs is not utilized in most models, as they typically focus on a single dimension of resilience by using variability as a proxy for persistence, and are limited to one reference state, disturbance type and scale. Moreover, only few studies explicitly test the ability of different mechanisms to support resilience. To overcome these limitations, we recommend to simultaneously assess multiple stability properties for different situations and under consideration of the mechanisms that are hypothesised to render a system resilient. This will help us to better exploit the potential of ABMs to understand and quantify resilience mechanisms, and hence support solving real-world problems related to the resilience of agent-based complex systems.
Resilience trinity
(2020)
Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.
Resilience trinity
(2020)
Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.
1. Savanna systems exhibit a high plant functional diversity. While aridity and livestock grazing intensity have been widely discussed as drivers of savanna vegetation composition, physical soil properties have received less attention. Since savannas can show local differences in soil properties, these might act as environmental filters and affect plant diversity and ecosystem functioning at the patch scale. However, research on the link between savanna vegetation diversity and ecosystem function is widely missing. 2. In this study, we aim at understanding the impact of local heterogeneity in soil conditions on plant diversity and on ecosystem functions. For this, we used the ecohydrological savanna model EcoHyD. The model simulates the fate of multiple plant functional types and their interactions with local biotic and abiotic conditions. We applied the model to a set of different landscapes under a wide range of livestock grazing and precipitation scenarios to assess the impact of local heterogeneity in soil conditions on the composition and diversity of plant functional types and on ecosystem functions. 3. Comparisons between homogeneous and heterogeneous landscapes revealed that landscape soil heterogeneity allowed for a higher functional diversity of vegetation under conditions of high competition, i.e. scenarios of low grazing stress. However, landscape heterogeneity did not have this effect under low grazing stress in combination with high mean annual precipitation. Further, landscape heterogeneity led to a higher community biomass, especially for lower rainfall conditions, but also dependent on grazing stress. Total transpiration of the plant community decreased in heterogeneous landscapes under arid conditions. 4. This study highlights that local soil conditions interact with precipitation and grazing in driving savanna vegetation. It clearly shows that vegetation diversity and resulting ecosystem functioning can be driven by landscape heterogeneity. We therefore suggest that future research on ecosystem functioning of savanna systems should focus on the links between local environmental conditions via plant functional diversity to ecosystem functioning.