20,006 research outputs found
Knowledge Driven Phenotyping
Extracting patient phenotypes from routinely collected health data (such as Electronic Health Records) requires translating clinically-sound phenotype definitions into queries/computations executable on the underlying data sources by clinical researchers. This requires significant knowledge and skills to deal with heterogeneous and often imperfect data. Translations are time-consuming, error-prone and, most importantly, hard to share and reproduce across different settings. This paper proposes a knowledge driven framework that (1) decouples the specification of phenotype semantics from underlying data sources; (2) can automatically populate and conduct phenotype computations on heterogeneous data spaces. We report preliminary results of deploying this framework on five Scottish health datasets
Evaluating openEHR for storing computable representations of electronic health record phenotyping algorithms
Electronic Health Records (EHR) are data generated during routine clinical
care. EHR offer researchers unprecedented phenotypic breadth and depth and have
the potential to accelerate the pace of precision medicine at scale. A main EHR
use-case is creating phenotyping algorithms to define disease status, onset and
severity. Currently, no common machine-readable standard exists for defining
phenotyping algorithms which often are stored in human-readable formats. As a
result, the translation of algorithms to implementation code is challenging and
sharing across the scientific community is problematic. In this paper, we
evaluate openEHR, a formal EHR data specification, for computable
representations of EHR phenotyping algorithms.Comment: 30th IEEE International Symposium on Computer-Based Medical Systems -
IEEE CBMS 201
Opportunities and limitations of crop phenotyping in southern european countries
ReviewThe Mediterranean climate is characterized by hot dry summers and frequent droughts.
Mediterranean crops are frequently subjected to high evapotranspiration demands,
soil water deficits, high temperatures, and photo-oxidative stress. These conditions
will become more severe due to global warming which poses major challenges to the
sustainability of the agricultural sector in Mediterranean countries. Selection of crop
varieties adapted to future climatic conditions and more tolerant to extreme climatic events
is urgently required. Plant phenotyping is a crucial approach to address these challenges.
High-throughput plant phenotyping (HTPP) helps to monitor the performance of improved
genotypes and is one of the most effective strategies to improve the sustainability of
agricultural production. In spite of the remarkable progress in basic knowledge and
technology of plant phenotyping, there are still several practical, financial, and political
constraints to implement HTPP approaches in field and controlled conditions across the
Mediterranean. The European panorama of phenotyping is heterogeneous and integration
of phenotyping data across different scales and translation of “phytotron research” to the
field, and from model species to crops, remain major challenges. Moreover, solutions
specifically tailored to Mediterranean agriculture (e.g., crops and environmental stresses)
are in high demand, as the region is vulnerable to climate change and to desertification
processes. The specific phenotyping requirements of Mediterranean crops have not
yet been fully identified. The high cost of HTPP infrastructures is a major limiting factor,
though the limited availability of skilled personnel may also impair its implementation in
Mediterranean countries. We propose that the lack of suitable phenotyping infrastructures
is hindering the development of new Mediterranean agricultural varieties and will negatively
affect future competitiveness of the agricultural sector. We provide an overview of the
heterogeneous panorama of phenotyping within Mediterranean countries, describing the
state of the art of agricultural production, breeding initiatives, and phenotyping capabilities
in five countries: Italy, Greece, Portugal, Spain, and Turkey. We characterize some of the main impediments for development of plant phenotyping in those countries and identify
strategies to overcome barriers and maximize the benefits of phenotyping and modeling
approaches to Mediterranean agriculture and related sustainabilityinfo:eu-repo/semantics/publishedVersio
Measurement of plant growth in view of an integrative analysis of regulatory networks
As the regulatory networks of growth at the cellular level are elucidated at a fast pace, their complexity is not reduced; on the contrary, the tissue, organ and even whole-plant level affect cell proliferation and expansion by means of development-induced and environment-induced signaling events in growth regulatory processes. Measurement of growth across different levels aids in gaining a mechanistic understanding of growth, and in defining the spatial and temporal resolution of sampling strategies for molecular analyses in the model Arabidopsis thaliana and increasingly also in crop species. The latter claim their place at the forefront of plant research, since global issues and future needs drive the translation from laboratory model-acquired knowledge of growth processes to improvements in crop productivity in field conditions
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