What Kind of Ontologies Do We Need in the Biomedical Domain?

We tackle the question as to what sort of ontologies we primarily need in the biomedical domain. For this purpose, we will first provide a simple categorization of ontologies and describe an important use case related to modeling and documenting events. Then, the impact of using upper-level ontologies as a basis to address our use case will be shown in order to derive an answer to our research question. Although formal ontologies can serve as a starting point to understand conceptualization in a domain and facilitate interesting inferences, it is even more important to account for the dynamic and changing nature of knowledge. Being unconstrained by pre-defined categories and relationships can facilitate timely enrichment of a conceptual scheme and provide links and dependency structures in an informal manner. Semantic enrichment can be achieved by other mechanisms such as tagging or the creation of synsets as, for example, provided in WordNet.

Pattern-Based Logical Definitions of Prenatal Disorders Grounded on Dispositions

Biomedical ontologies define concepts having biomedical significance and the semantic relations among them. Developing high-quality and reusable ontologies in the biomedical domain is a challenging task. Pattern-based ontology design is considered a promising approach to overcome the challenges. Ontology Design Patterns (ODPs) are reusable modeling solutions to facilitate ontology development. This study relies on ODPs to semantically enrich biomedical ontologies by assigning logical definitions to ontological entities. Specifically, pattern-based logical definitions grounded on dispositions are given to prenatal disorders. The proposed approach is performed under the supervision of fetal domain experts.

Developing an Ontology for Documenting Adverse Events While Avoiding Pitfalls

Ontologies promise more benefits than terminologies in terms of data annotation and computer-assisted reasoning, by defining a hierarchy of terms and their relations within a domain. Here, we present central insights related to the development of an ontology for documenting events during interoperative neuromonitoring (IOM), for which we used the Basic Formal Ontology (BFO) as an upper-level ontology. This work has the following two goals: to describe the development of the IOM ontology and to guide the practice with respect to documenting of biomedical events, as available ontologies pose difficulties on certain issues. We address the following issues: (i) differentiate between the sets documentation, identification, continuant and explanation, understanding, occurrent as we had problems in applying the available ontology of adverse events, (ii) covering diseases and injuries in a consistent way, and (iii) deciding on which level to define relations.

Exotic Quad-Domain Textures and Transport Characteristics of Self-Assembled BiFeO3 Nanoislands on Nb-Doped SrTiO3

Topological quad-domain textures with interesting cross-shaped buffer domains (walls) have been recently observed in BiFeO₃ (BFO) nanoislands, indicating a new platform for exploring topological defects and multilevel memories. Such domain textures have nevertheless only been limited in BFO nanoislands grown on LaAlO₃ substrates with a large lattice mismatch of ∼-4.4%. Here, we report that such exotic domain textures could also form in BFO nanoislands directly grown on a conductive substrate with a much smaller lattice mismatch and the local transport characteristics of the BFO nanoislands are distinct from the previously reported ones. The angle-resolved piezoresponse force images verify that the domain textures consist of center-divergent quad-domains with upward polarizations and cross-shaped buffer domains with downward polarizations. Interestingly, textures with multiple crosses are also observed in nanoislands of larger sizes, besides the previously reported ones with a single cross. The nanoislands exhibit strong diodelike rectifying characteristics and the quad-domains show a higher average conductance than the cross-shaped buffer domains, indicating that there is a certain correlation between the local conductance of the nanoislands and the domain textures. This transport behavior is attributed to the effect of the depolarization field on the Schottky barriers at both the substrate/BFO interface and the tip/BFO junction. Our findings extend the current understanding of the exotic quad-domain textures of ferroelectric nanoislands and shed light on their potential applications for configurable electronic devices.

CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple clinical trials investigating Gleevec's related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed.

PID, BFO-optimized PID, and PD-FLC control of a two-wheeled machine with two-direction handling mechanism: a comparative study

In this paper; three control approaches are utilized in order to control the stability of a novel five-degrees-of-freedom two-wheeled robotic machine designed for industrial applications that demand a limited-space working environment. Proportional–integral–derivative (PID) control scheme, bacterial foraging optimization of PID control method, and fuzzy logic control method are applied to the wheeled machine to obtain the optimum control strategy that provides the best system stabilization performance. According to simulation results, considering multiple motion scenarios, the PID controller optimized by bacterial foraging optimization method outperformed the other two control methods in terms of minimum overshoot, rise time, and applied input forces.

Dielectric, Ferroelectric, and Magnetic Properties of Sm-Doped BiFeO₃ Ceramics Prepared by a Modified Solid-State-Reaction Method

Sm-doped BiFeO₃ (BFO) material was prepared using a modified solid-state-reaction method, which used fast heating and cooling during the sintering process. The Sm doping level varied between 1 mol % to 8 mol %. Processing parameters, such as sintering temperature and annealing temperature, were optimized to obtain high-quality samples. Based on their dielectric properties, the optimum sintering and annealing temperatures were found to be 300 °C and 825 °C, respectively. Leakage-free square-shaped ferroelectric hysteresis loops were observed in all samples. The remnant polarization was maximized in the 5 mol %-doped sample (~35 μC/cm²⁾. Furthermore, remnant magnetization was increased after the Sm doping and the 8 mol%-doped sample possessed the largest remnant magnetization of 0.007 emu/g. Our results demonstrated how the modified solid-state-reaction method proved to be an effective method for preparing high-quality BiFeO₃ ceramics, as well as how the Sm dopant can efficiently improve ferroelectric and magnetic properties.

The Knowledge Object Reference Ontology (KORO): A formalism to support management and sharing of computable biomedical knowledge for learning health systems

INTRODUCTION

Health systems are challenged by care underutilization, overutilization, disparities, and related harms. One problem is a multiyear latency between discovery of new best practice knowledge and its widespread adoption. Decreasing this latency requires new capabilities to better manage and more rapidly share biomedical knowledge in computable forms. Knowledge objects package machine-executable knowledge resources in a way that easily enables knowledge as a service. To help improve knowledge management and accelerate knowledge sharing, the Knowledge Object Reference Ontology (KORO) defines what knowledge objects are in a formal way.

METHODS

Development of KORO began with identification of terms for classes of entities and for properties. Next, we established a taxonomical hierarchy of classes for knowledge objects and their parts. Development continued by relating these parts via formally defined properties. We evaluated the logical consistency of KORO and used it to answer several competency questions about parthood. We also applied it to guide knowledge object implementation.

RESULTS

As a realist ontology, KORO defines what knowledge objects are and provides details about the parts they have and the roles they play. KORO provides sufficient logic to answer several basic but important questions about knowledge objects competently. KORO directly supports creators of knowledge objects by providing a formal model for these objects.

CONCLUSION

KORO provides a formal, logically consistent ontology about knowledge objects and their parts. It exists to help make computable biomedical knowledge findable, accessible, interoperable, and reusable. KORO is currently being used to further develop and improve computable knowledge infrastructure for learning health systems.

Bacterial foraging-optimized PID control of a two-wheeled machine with a two-directional handling mechanism

This paper presents the performance of utilizing a bacterial foraging optimization algorithm on a PID control scheme for controlling a five DOF two-wheeled robotic machine with two-directional handling mechanism. The system under investigation provides solutions for industrial robotic applications that require a limited-space working environment. The system nonlinear mathematical model, derived using Lagrangian modeling approach, is simulated in MATLAB/Simulink^® environment. Bacterial foraging-optimized PID control with decoupled nature is designed and implemented. Various working scenarios with multiple initial conditions are used to test the robustness and the system performance. Simulation results revealed the effectiveness of the bacterial foraging-optimized PID control method in improving the system performance compared to the PID control scheme.

Ferroelectric Domain Structure and Local Piezoelectric Properties of Lead-Free (Ka0.5Na0.5)NbO₃ and BiFeO₃-Based Piezoelectric Ceramics

Recent advances in the development of novel methods for the local characterization of ferroelectric domains open up new opportunities not only to image, but also to control and to create desired domain configurations (domain engineering). The morphotropic and polymorphic phase boundaries that are frequently used to increase the electromechanical and dielectric performance of ferroelectric ceramics have a tremendous effect on the domain structure, which can serve as a signature of complex polarization states and link local and macroscopic piezoelectric and dielectric responses. This is especially important for the study of lead-free ferroelectric ceramics, which is currently replacing traditional lead-containing materials, and great efforts are devoted to increasing their performance to match that of lead zirconate titanate (PZT). In this work, we provide a short overview of the recent progress in the imaging of domain structure in two major families of ceramic lead-free systems based on BiFeO₃ (BFO) and (Ka0.5Na0.5)NbO₃ (KNN). This can be used as a guideline for the understanding of domain processes in lead-free piezoelectric ceramics and provide further insight into the mechanisms of structure-property relationship in these technologically important material families.

Hybrid Bacterial Foraging and Particle Swarm Optimization for detecting Bundle Branch Block

Abnormal cardiac beat identification is a key process in the detection of heart diseases. Our present study describes a procedure for the detection of left and right bundle branch block (LBBB and RBBB) Electrocardiogram (ECG) patterns. The electrical impulses that control the cardiac beat face difficulty in moving inside the heart. This problem is termed as bundle branch block (BBB). BBB makes it harder for the heart to pump blood effectively through the heart circulatory system. ECG feature extraction is a key process in detecting heart ailments. Our present study comes up with a hybrid method combining two heuristic optimization methods: Bacterial Forging Optimization (BFO) and Particle Swarm Optimization (PSO) for the feature selection of ECG signals. One of the major controlling forces of BFO algorithm is the chemotactic movement of a bacterium that models a test solution. The chemotaxis process of the BFO depends on random search directions which may lead to a delay in achieving the global optimum solution. The hybrid technique: Bacterial Forging-Particle Swarm Optimization (BFPSO) incorporates the concepts from BFO and PSO and it creates individuals in a new generation. This BFPSO method performs local search through the chemotactic movement of BFO and the global search over the entire search domain is accomplished by a PSO operator. The BFPSO feature values are given as the input for the Levenberg-Marquardt Neural Network classifier.

Chemical protection of ZnO nanorods at ultralow pH To form a hierarchical BiFeO3/ZnO core-shell structure

ZnO is an interesting material for photoactive and optoelectronic devices because of the wide range of available nanostructures and advantageous semiconducting properties. However, a significant drawback of ZnO is the low stability in high or low pH solutions. This has limited the development of ZnO core-shell materials for use in Z-scheme systems or photovoltaics, where any secondary phase is produced using chemical solution processing at low or high pH. Here, we show a simple process to produce an organic capping layer of 3-aminopropyltriethoxysilane that can successfully stabilize nanostructured ZnO for processing below pH 1. We demonstrate that this process can be used to produce a ZnO-BiFeO3 (BFO) core-shell structure by a sol-gel process. Using a range of physical and analytical techniques, we show that BFO is highly crystalline and produces a conformal coating with a thickness of 2.5 nm. X-ray photoelectron spectroscopy and X-ray diffraction confirm the phase and expected chemical composition of BFO. Finally we are able to demonstrate that diodes produced using the ZnO-BFO core-shell structure have improved performance with a rectification ratio at ±3 V of 2800 because of the reduction in reverse current typically associated with surface recombination on ZnO. Our process opens a route to producing a range of hitherto prohibited ZnO core-shell structures that may have applications ranging from photovoltaic devices to core-shell photocatalysts.

Why functions are not special dispositions: an improved classification of realizables for top-level ontologies

Background

The concept of function is central to both biology and technology, but neither in philosophy nor in formal ontology is there a generally accepted theory of functions. In particular, there is no consensus how to include functions into a top-level ontology or whether to include them at all.

Methods

We first review current conceptions of functions in philosophy and formal ontology and evaluate them against a set of criteria. These evaluation criteria are derived from a synopsis of theoretical and practical requirements that have been suggested for formal accounts of functions. In a second step, we elucidate in particular the relation between functions and dispositions.

Results

We argue that functions should not be taken as a subtype of dispositions. The strongest reason for this is that any view that identifies functions with certain dispositions cannot account for malfunctioning, which is having a function but lacking the matching disposition. As a result, we suggest a cross-classification of realizables with dispositions supervening on the physical structure of their bearer, whereas both functions and roles also have some external grounding. While bearers can survive the gain, loss and change of roles, functions are rigid properties that are essentially connected to their particular bearers. Therefore, Function should not be regarded as a subtype of Disposition; rather, the classes of functions and dispositions are disjoint siblings of Realizable.