The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)
A deterministic weakening \ of the Belnap–Dunn four-valued logic \ is introduced to formalize the acceptance and rejection of a proposition at a state in a linearly ordered informational frame with persistent valuations. The logic \ is formalized as a sequent calculus. The completeness and decidability of \ with respect to relational semantics are shown in terms of normal forms. From an algebraic perspective, the class of all algebras for \ is described, and found to be a subvariety of Berman’s (...) variety \. Every linearly ordered frame is logically equivalent to its dual algebra. It is proved that \ is the logic of a nine-element distributive lattice with a negation. Moreover, \ is embedded into \ by Glivenko’s double-negation translation. (shrink)
Every Berman’s variety \ which is the subvariety of Ockham algebras defined by the equation \ and \) determines a finitary substitution invariant consequence relation \. A sequent system \ is introduced as an axiomatization of the consequence relation \. The system \ is characterized by a single finite frame \ under the frame semantics given for the formal language. By the duality between frames and algebras, \ can be viewed as a \-valued logic as it is characterized by a (...) distributive lattice of \ elements with a unary operator. Moreover, a structural-rule-free, cut-free and terminating sequent system \ is established for \. The Craig interpolation property of \ is shown proof-theoretically utilizing \. (shrink)
Globalization is a part of modern life. Sharing a common set of professional nursing values is critical in this global environment. The purpose of this research was to examine the professional values of nursing students from two distinct cultural perspectives. Nurse educators in Taiwan partnered with nurse educators in the United States to compare professional values of their respective graduating nursing students. The American Nurses Association Code of Ethics served as the philosophical framework for this examination. The convenience sample comprised (...) 94 Taiwanese students and 168 US students. Both groups reported high scores on an overall measure of values. They did differ substantially on the relative importance of individual items related to advocacy, competence, education, self-evaluation, professional advancement, and professional associations. Global implications for the collaborative practice of nurses from different cultures working together can be improved by first recognizing and then attending to these differences in value priorities. (shrink)
A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)
Professional values are standards for action and provide a framework for evaluating behavior. This study examined changes in the professional values of nursing students between their entrance to and graduation from an undergraduate nursing program. A pre- and post-test design was employed. A convenience sample of 94 students from a university in Taiwan was surveyed. Data were collected from students during the sophomore and senior years. Total scores obtained for the revised Nurses Professional Values Scale during the senior year of (...) the nursing program were significantly higher than upon program entry. The ‘caring’ subscale was scored highest at both program entry and graduation, but the pre- and post-test scores were not significantly different from each other. The students scored significantly higher on the ‘professionalism’ and ‘activism’ subscales at post-test than they did at pre-test. Professional values changed in a positive direction between the beginning of the student nurses’ educational experience and their graduation. The results supported the premise that education had a positive effect on these students’ professional values but causality could not be assumed. (shrink)
The minimal weakening \ of Belnap-Dunn logic under the polarity semantics for negation as a modal operator is formulated as a sequent system which is characterized by the class of all birelational frames. Some extensions of \ with additional sequents as axioms are introduced. In particular, all three modal negation logics characterized by a frame with a single state are formalized as extensions of \. These logics have the finite model property and they are decidable.
Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)
Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)
Packed with ideas designed to help children learn to sing, this booklet offers criteria for selecting songs, strategies to bring out the best in children's voices, and suggestions for games, ideas, and resources.
In this paper, we discuss the development and piloting of a new methodology for illuminating the socio-material constitution of data objects and flows as data move between different sites of practice. The data journeys approach contributes to the development of critical, qualitative methodologies that can address the geographic and temporal scale of emerging knowledge infrastructures, and capture the ‘life of data’ from their initial generation through to re-use in different contexts. We discuss the theoretical development of the data journeys methodology (...) and the application of the approach on a project examining meteorological data on their journey from initial production through to being re-used in climate science and financial markets. We then discuss three key conceptual findings from this project about: the socio-material constitution of digital data objects, ‘friction’ in the movement of data through space and time and the mutability of digital data as a material property that contributes to driving the movement of data between different sites of practice. (shrink)
Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)
The importance of data literacy and the need of raising and improving it through formal educational channel or public engagement has repeatedly been flagged up in each of the past Economic and Social Research Council-funded Data-Psst! Seminar I attended in 2014–2016. There is a real demand for action taking. I took advantage of the knowledge I learned from the Data-Psst seminars and devised a module teaching Level 5 undergraduate media students about critical issues in today’s data-centric digital society, including privacy (...) and surveillance. In this article, I share how the class activities were devised and carried out, and how guided engagement with the current debate in privacy and surveillance were realised. I also draw on relevant pedagogical theories to discuss my educational approaches, student performance, the challenges of the project, and evaluate and reflect upon the outcomes. This report from the field provides fresh first-hand information about the data ethics of the younger public who are practising media arts and their behaviours and attitudes towards privacy and surveillance. This article shall open up the discussion about the role educators play in enriching public engagement with critical thinking about Big Data. The lessons learned can also contextualise the pedagogical implication of the recent scholarly research on Big Data and privacy, and provide a framework for constructing future collaborative or creative projects. (shrink)
The language of Belnap–Dunn modal logic \ expands the language of Belnap–Dunn four-valued logic with the modal operator \. We introduce the polarity semantics for \ and its two expansions \ and \ with value operators. The local finitary consequence relation \ in the language \ with respect to the class of all frames is axiomatized by a sequent system \ where \. We prove by using translations between sequents and formulas that these languages under the polarity semantics have the (...) same expressive power on the level of frames with the language \ under the relational semantics for classical modal logic. (shrink)
In corporate social responsibility reporting, companies are expected to fully disclose the negative social and environmental impacts of their activities. This study investigates how Chinese companies respond to this challenge by analyzing the representations of occupational fatalities and injuries in 92 CSR reports from 37 Chinese Fortune 500 companies. A move-step analysis was performed on one part of the CSR report, which is the section providing information on occupational incidents. It was found that the negative information was typically disclosed via (...) four rhetorical moves, which are ‘preparing the reader’, ‘delivering the bad news’, ‘mitigating the bad news’ and ‘reassuring the reader’. Communicating bad news through the four moves helps manage the reader’s perception of the reporting company and its CSR performance. The study calls for greater attention to the impression-managing aspects of companies’ self-disclosure of organizational bad news. (shrink)
Drawing textual evidences from the Analects and other Confucian classics, this article attempts to clarify the contents, methods, and ultimately the nature of learning in the eyes of Confucius. The paper set out to argue that a better understanding of the concept of learning by Confucius must be angled on: Confucius’s political aspiration and life pursuit rather than his teaching; The personal preference of Confucius along with his zhi that has motivated his study and practice of the finer aspects of (...) the Zhou legacies. And on the above basis, the paper suggests that: TO BE one’s mandate self is at the core of Confucius’s concept of learning and that naturally determines the methods and characteristics of learning; the three opening lines of Lunyu in fact made a statement on the way Confucius learns. (shrink)
We define DNA sequence by a bottom-up approach, starting with a real sequence from an actual biological sample. By providing axioms for notions of string, substring and strand, we formally define a DNA sequence, and a DNA molecule as composed of two antiparallel strands. We note that a sequence is a kind of group in which each member stands a certain relation to every other. The spatial aspects of a DNA sequence are also described.
Given the widespread acceptance of computational thinking in educational systems around the world, primary and higher education has begun thinking about how to cultivate students' CT competences. The artificial intelligence of things combines artificial intelligence and the Internet of things and involves integrating sensing technologies at the lowest level with relevant algorithms in order to solve real-world problems. Thus, it has now become a popular technological application for CT training. In this study, a novel AIoT learning with Augmented Reality technology (...) was proposed and explored the effect of CT skills. The students used AR applications to understand AIoT applications in practice, attempted the placement of different AR sensors in actual scenarios, and further generalized and designed algorithms. Based on the results of the experimental course, we explored the influence of prior knowledge and usage intention on students' CT competence training. The results show that proposed AIoT learning can increase students' learning intention and that they had a positive impact on problem solving and comprehension with AR technology, as well as application planning and design. (shrink)
A treatise on living a rich life from a Chinese point of view advocates a pursuit of self enjoyment through humor, joy, creativity, conversation, reading, nature appreciation, balanced inaction, and other non-material activities.