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)
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)
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)
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)
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)
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)
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.
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)
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)
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)
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.
Kripke’s Fregean quantification logic FQ fails to formalize the usual first-order logic with identity due to the interpretation of the conditional operator. Motivated by Kripke’s syntax and semantics, the three-valued Fregean quantification logic FQ3 is proposed. This three valued logic differs from Kleene and Łukasiewicz’s three-valued logics. The logic FQ3 is decidable. A sound and complete Hilbert-style axiomatic system for the logic FQ3 is presented.
This is Palmer 2004 years come to Taiwan, Lo Fu Jen Catholic University in light of the second lecture series lecture, described as vulgar different flow history of Western hermeneutics. This means a comprehensive history of hermeneutics unifying different from the contemporary general domain of hermeneutics for individual study. This ancient Egypt, Rome hope臘nervous, then interpretation of the Bible, the Protestant development, the liberation of neural science, until the liberation of Latin America contemporary neural science, etc., all kinds of important (...) interpretation of the provision of interpretation of the form of sperm Jie. Tirelessly road ahead, not only the context of the history of hermeneutics with management and to clarify the effect of comb, more understanding of how hermeneutics itself with the meaning of integration, resulting in program like dragon eye-dotting enlightening. This article is the second lecture made by Richard Palmer in Taiwan in 2004, entitled as "An Unconventional History of Hermeneutics in the West," indicating that such a general history of hermeneutics is different from the various hermeneutic studies on individual fields. This paper makes outstanding explications on those important hermeneutic forms of ancient Egypt mythology, Greek and Roman mythology, Biblical interpretation, the development of the Protestant, liberation theology and even the contemporary liberation theology of Latin America, not only sorting out and clarifying the historical contexts of hermeneutics but also inspiring us on how to understand and unify the meanings of hermeneutics itself. (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.
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)
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.