2,533 research outputs found
Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository
A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology
Clonal Complexes in Biomedical Ontologies
An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies
Towards an Ontological Representation of Resistance: The Case of MRSa
This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. Resistance terms from various existing ontologies are examined and found to be either overly narrow, inconsistent, or
otherwise problematic. We propose a more coherent ontological representation using the antibiotic resistance in Methicillin-Resistant _Staphylococcus aureus_ (MRSa) as a case study
Ontological representation of CDC Active Bacterial Core Surveillance Case Reports
The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes
Decision making with decision event graphs
We introduce a new modelling representation, the Decision Event Graph (DEG), for asymmetric
multistage decision problems. The DEG explicitly encodes conditional independences
and has additional significant advantages over other representations of asymmetric decision
problems. The colouring of edges makes it possible to identify conditional independences on
decision trees, and these coloured trees serve as a basis for the construction of the DEG.
We provide an efficient backward-induction algorithm for finding optimal decision rules on
DEGs, and work through an example showing the efficacy of these graphs. Simplifications of
the topology of a DEG admit analogues to the sufficiency principle and barren node deletion
steps used with influence diagrams
The Infectious Disease Ontology in the Age of COVID-19
The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research
Estimation of Parameters in DNA Mixture Analysis
In Cowell et al. (2007), a Bayesian network for analysis of mixed traces of
DNA was presented using gamma distributions for modelling peak sizes in the
electropherogram. It was demonstrated that the analysis was sensitive to the
choice of a variance factor and hence this should be adapted to any new trace
analysed. In the present paper we discuss how the variance parameter can be
estimated by maximum likelihood to achieve this. The unknown proportions of DNA
from each contributor can similarly be estimated by maximum likelihood jointly
with the variance parameter. Furthermore we discuss how to incorporate prior
knowledge about the parameters in a Bayesian analysis. The proposed estimation
methods are illustrated through a few examples of applications for calculating
evidential value in casework and for mixture deconvolution
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Validation of an STR peak area model
In analyzing a DNA mixture sample, the measured peak areas of alleles of STR markers amplified using the polymerase chain-reaction (PCR) technique provide valuable information concerning the relative amounts of DNA originating from each contributor to the mixture. This information can be exploited for the purpose of trying to predict the genetic profiles of those contributors whose genetic profiles are not known. The task is non-trivial, in part due to the need to take into account the stochastic nature of peak area values. Various methods have been proposed suggesting ways in which this may be done. One recent suggestion is a probabilistic expert system model that uses gamma distributions to model the size and stochastic variation in peak area values. In this paper we carry out a statistical analysis of the gamma distribution assumption, testing the assumption against synthetic peak area values computer generated using an independent model that simulates the PCR amplification process. Our analysis shows the gamma assumption works very well when allelic dropout is not present, but performs less and less well as dropout becomes more and more of an issue, such as occurs, for example, in Low Copy Template amplifications
Reliability analysis of a rodding anode plant in aluminum industry with multiple units failure and single repairman
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