A set of ontologies to drive tools for the control of vector-borne diseases

We are developing a set of ontologies that deal with vector-borne diseases and the arthropod vectors that transmit them. For practical reasons (application priorities), we initiated this project with an ontology of insecticide resistance followed by a series of ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease transmission. These will be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide the community with a set of ontological tools that can be used both in the development of specific databases and, most importantly, in the construction of decision support systems to control these diseases

Urban energy exchanges monitoring from space

One important challenge facing the urbanization and global environmental change community is to understand the relation between urban form, energy use and carbon emissions. Missing from the current literature are scientific assessments that evaluate the impacts of different urban spatial units on energy fluxes; yet, this type of analysis is needed by urban planners, who recognize that local scale zoning affects energy consumption and local climate. However, satellite-based estimation of urban energy fluxes at neighbourhood scale is still a challenge. Here we show the potential of the current satellite missions to retrieve urban energy budget, supported by meteorological observations and evaluated by direct flux measurements. We found an agreement within 5% between satellite and in-situ derived net all-wave radiation; and identified that wall facet fraction and urban materials type are the most important parameters for estimating heat storage of the urban canopy. The satellite approaches were found to underestimate measured turbulent heat fluxes, with sensible heat flux being most sensitive to surface temperature variation (-64.1, +69.3 W m-2 for ±2 K perturbation); and also underestimate anthropogenic heat flux. However, reasonable spatial patterns are obtained for the latter allowing hot-spots to be identified, therefore supporting both urban planning and urban climate modelling

Urban surface temperature time series estimation at the local scale by spatial-spectral unmixing of satellite observations

The study of urban climate requires frequent and accurate monitoring of land surface temperature (LST), at the local scale. Since currently, no space-borne sensor provides frequent thermal infrared imagery at high spatial resolution, the scientific community has focused on synergistic methods for retrieving LST that can be suitable for urban studies. Synergistic methods that combine the spatial structure of visible and near-infrared observations with the more frequent, but low-resolution surface temperature patterns derived by thermal infrared imagery provide excellent means for obtaining frequent LST estimates at the local scale in cities. In this study, a new approach based on spatial-spectral unmixing techniques was developed for improving the spatial resolution of thermal infrared observations and the subsequent LST estimation. The method was applied to an urban area in Crete, Greece, for the time period of one year. The results were evaluated against independent high-resolution LST datasets and found to be very promising, with RMSE less than 2 K in all cases. The developed approach has therefore a high potential to be operationally used in the near future, exploiting the Copernicus Sentinel (2 and 3) observations, to provide high spatio-temporal resolution LST estimates in cities

Incorporating bio-physical sciences into a decision support tool for sustainable urban planning

Deciding upon optimum planning actions in terms of sustainable urban planning involves the consideration of multiple environmental and socio-economic criteria. The transformation of natural landscapes to urban areas affects energy and material fluxes. An important aspect of the urban environment is the urban metabolism, and changes in such metabolism need to be considered for sustainable planning decisions. A spatial Decision Support System (DSS) prototyped within the European FP7-funded project BRIDGE (sustainaBle uRban plannIng Decision support accountinG for urban mEtabolism), enables accounting for the urban metabolism of planning actions, by exploiting the current knowledge and technology of biophysical sciences. The main aim of the BRIDGE project was to bridge the knowledge and communication gap between urban planners and environmental scientists and to illustrate the advantages of considering detailed environmental information in urban planning processes. The developed DSS prototype integrates biophysical observations and simulation techniques with socio-economic aspects in fiveEuropean cities, selected as case studies for the pilot application of the tool. This paper describes the design and implementation of the BRIDGE DSS prototype, illustrates some examples of use, and highlights the need for further research and development in the field

Chapter Earth Observation for Urban Climate Monitoring: Surface Cover and Land Surface Temperature

The rate at which global climate change is happening is arguably the most pressing environmental challenge of the century, and it affects our cities. Climate change exerts added stress on urban areas through increased numbers of heat waves threatening people’s well-being and, in many cases, human lives. Earth observation (EO) systems and the advances in remote sensing technology increase the opportunities for monitoring the thermal behavior of cities. The Sentinels constitute the first series of operational satellites for Copernicus, a program launched to provide data, information, services, and knowledge in support of Europe’s goals regarding sustainable development and global governance of the environment. This chapter examines the exploitation of EO data for monitoring the urban climate, with particular focus on the urban surface cover and temperature. Two example applications are analyzed: the mapping of the urban surface and its characteristics, using EO data and the estimation of urban temperatures. Approaches, like the ones described in this chapter, can become operational once adapted to Sentinels, since their long-term operation plan guarantees the future supply of satellite observations. Thus, the described methods may support planning activities related to climate change mitigation and adaptation in cities, as well as routine urban planning activities

Remote Sensing Studies of Urban Canopies: 3D Radiative Transfer Modeling

Need for better understanding and more accurate estimation of radiative fluxes in urban environments, specifically urban surface albedo and exitance, motivates development of new remote sensing and three‐dimensional (3D) radiative transfer (RT) modeling methods. The discrete anisotropic radiative transfer (DART) model, one of the most comprehensive physically based 3D models simulating Earth/atmosphere radiation interactions, was used in combination with satellite data (e.g., Landsat‐8 observations) to better parameterize the radiative budget components of cities, such as Basel in Switzerland. After presenting DART and its recent RT modeling functions, we present a methodological concept for estimating urban fluxes using any satellite image data

Anthropogenic Heat Flux Estimation from Space: Results of the first phase of the URBANFLUXES Project

H2020-Space project URBANFLUXES (URBan ANthrpogenic heat FLUX from Earth observation Satellites) investigates the potential of Copernicus Sentinels to retrieve anthropogenic heat flux, as a key component of the Urban Energy Budget (UEB). URBANFLUXES advances the current knowledge of the impacts of UEB fluxes on urban heat island and consequently on energy consumption in cities. This will lead to the development of tools and strategies to mitigate these effects, improving thermal comfort and energy efficiency. In URBANFLUXES, the anthropogenic heat flux is estimated as a residual of UEB. Therefore, the rest UEB components, namely, the net all-wave radiation, the net change in heat storage and the turbulent sensible and latent heat fluxes are independently estimated from Earth Observation (EO), whereas the advection term is included in the error of the anthropogenic heat flux estimation from the UEB closure. The project exploits Sentinels observations, which provide improved data quality, coverage and revisit times and increase the value of EO data for scientific work and future emerging applications. These observations can reveal novel scientific insights for the detection and monitoring of the spatial distribution of the urban energy budget fluxes in cities, thereby generating new EO opportunities. URBANFLUXES thus exploits the European capacity for space-borne observations to enable the development of operational services in the field of urban environmental monitoring and energy efficiency in cities. H2020-Space project URBANFLUXES (URBan ANthrpogenic heat FLUX from Earth observation Satellites)investigates the potential of Copernicus Sentinels to retrieve anthropogenic heat flux, as a key component of the UrbanEnergy Budget (UEB). URBANFLUXES advances the current knowledge of the impacts of UEB fluxes on urban heatisland and consequently on energy consumption in cities. This will lead to the development of tools and strategies tomitigate these effects, improving thermal comfort and energy efficiency. In URBANFLUXES, the anthropogenic heatflux is estimated as a residual of UEB. Therefore, the rest UEB components, namely, the net all-wave radiation, the netchange in heat storage and the turbulent sensible and latent heat fluxes are independently estimated from EarthObservation (EO), whereas the advection term is included in the error of the anthropogenic heat flux estimation from theUEB closure. The project exploits Sentinels observations, which provide improved data quality, coverage and revisittimes and increase the value of EO data for scientific work and future emerging applications. These observations canreveal novel scientific insights for the detection and monitoring of the spatial distribution of the urban energy budgetfluxes in cities, thereby generating new EO opportunities. URBANFLUXES thus exploits the European capacity forspace-borne observations to enable the development of operational services in the field of urban environmentalmonitoring and energy efficiency in cities

Variability of urban surface temperatures and implications for aerodynamic energy exchange in unstable conditions

Sensible heat flux (QH) is a critical driver of surface and boundary layer meteorological processes, especially in urban areas. Aerodynamic resistance methods (ARM) to model QH are promising because, in principle, all that is needed is surface temperature (T0), air temperature (TA) and an aerodynamic resistance term (rH). There are significant challenges in urban areas however, due to uncertainties in satellite-derived land surface temperatures (LST), logistical challenges to obtain high-resolution air temperatures, and limited understanding of spatial and temporal variability of rH and associated variables (e.g. thermal roughness length). This work uses an extensive LST dataset covering six years (2011-2016) in central London and a long-term in situ observation network to analyse variability of LST and rH variables. Results show that LST is spatially correlated with building and vegetation land cover with coherent thermal structures at length scales less than 500-1000 m. Additionally, satellite-observed LST varies with average building height (up to 10% cooler in areas with tall buildings). The rH term and associated variables are observed to vary on daily and seasonal cycles and findings are used to model QH using five variations of an ARM-based approach on a 100 m pixel basis. Modelled QH is compared to observations from three scintillometer paths and an eddy covariance flux tower. We find generally good agreement between observations and models, though there is uncertainty in all methods (mean absolute error ranges from 58.1-129.3 W m-2) due to challenges in determining high-resolution meteorological and surface inputs, particularly LST and friction velocity (u*). Additional complexity in evaluating modelled QH arises from anthropogenic heat sources: long-term tower-based observations show that TA and radiometer-derived T0 are warmer during working weekdays than non-working days (up to 0.7C) and that there is an observed lag (2-3 hours) between energy consumption and observed warming and QH

IDOMAL: an ontology for malaria

<p>Abstract</p> <p>Background</p> <p>Ontologies are rapidly becoming a necessity for the design of efficient information technology tools, especially databases, because they permit the organization of stored data using logical rules and defined terms that are understood by both humans and machines. This has as consequence both an enhanced usage and interoperability of databases and related resources. It is hoped that IDOMAL, the ontology of malaria will prove a valuable instrument when implemented in both malaria research and control measures.</p> <p>Methods</p> <p>The OBOEdit2 software was used for the construction of the ontology. IDOMAL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.</p> <p>Results</p> <p>The first version of the malaria ontology covers both clinical and epidemiological aspects of the disease, as well as disease and vector biology. IDOMAL is meant to later become the nucleation site for a much larger ontology of vector borne diseases, which will itself be an extension of a large ontology of infectious diseases (IDO). The latter is currently being developed in the frame of a large international collaborative effort.</p> <p>Conclusions</p> <p>IDOMAL, already freely available in its first version, will form part of a suite of ontologies that will be used to drive IT tools and databases specifically constructed to help control malaria and, later, other vector-borne diseases. This suite already consists of the ontology described here as well as the one on insecticide resistance that has been available for some time. Additional components are being developed and introduced into IDOMAL.</p

IDOMAL: the malaria ontology revisited

Abstract Background With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated. Findings In addition to the improvement of IDOMAL’s structure and the correction of some inaccuracies, there were some major subdomain additions such as a section on natural products and remedies, and the import, from other, higher order ontologies, of several terms, which were merged with IDOMAL terms. Effort was put on rendering IDOMAL fully compatible as an extension of IDO, the Infectious Disease Ontology. The reason for the difficulties in fully reaching that target were the inherent differences between vector-borne diseases and “classical” infectious diseases, which make it necessary to specifically adjust the ontology’s architecture in order to comprise vectors and their populations. Conclusions In addition to a higher coverage of domain-specific terms and optimizing its usage by databases and decision-support systems, the new version of IDOMAL described here allows for more cross-talk between it and other ontologies, and in particular IDO. The malaria ontology is available for downloading at the OBO Foundry (http://www.obofoundry.org/cgi-bin/detail.cgi?id=malaria_ontology) and the NCBO BioPortal (http://bioportal.bioontology.org/ontologies/1311). </jats:sec