The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

The present article is a slightly revised version of my article in Journal of Chinese Philosophy 39, no. 2 (2012): 174–91. I appreciate the opportunity to republish with very minor corrections. This article highlights sympathies between Wang Yangming’s notion of zhenzhi (real knowing) and Stanley Cavell’s concept of acknowledgment. I begin by noting a problem in interpreting Wang on the unity of knowing and acting, which leads to considering how our suffering pain figures in our “real knowing” of (...) another’s pain. I then turn to Cavell’s description of a related problem in modern skepticism, where Cavell argues that knowing another’s pain requires acknowledging it. Cavell’s concept of acknowledgment answers to Wang’s insistence that knowing and acting are one, and corrects Antonio Cua’s very different appropriation of “acknowledgment” to explain Wang’s doctrine. (shrink)

This article highlights sympathies between Wang Yangming's notion of zhenzhi (real knowing) and Stanley Cavell's concept of acknowledgment. I begin by noting a problem in interpreting Wang on the unity of knowing and acting, which leads to considering how our suffering pain figures in our “real knowing” of another's pain. I then turn to Cavell's description of a related problem in modern skepticism, where Cavell argues that knowing another's pain requires acknowledging it. Cavell's concept of acknowledgment answers to (...) Wang's insistence that knowing and acting are one, and corrects Antonio Cua's very different appropriation of “acknowledgment” to explain Wang's doctrine. (shrink)

In this paper I contrast William Clifford’s and William James’ perspectives on faith and reason. I argue that James is right in his sympathetic approach towards the rationality of faith. I defend James' account of the permissibility of faith by highlighting that faithful intents are always good; the thoughtfulness within the value of faith’s rationality can justify our actionable beliefs, resulting in us becoming morally purposeful in our decisions.

ABSTRACT Approaching Cognitive-Behavioral and Existential Therapy Through Neo-Confucianism (December 1984). Joffre Denis Meyer, B. A. Texas A&M University Chairman of Graduate Committee: Dr. William R. Nash -/- The thesis is an effort to bring Neo-Confucian insights to modern cognitive- behavioral and existential therapy. The adaptability of Neo-Confucianism is illustrated through the growth-system inherent in its concepts. Frequently, Neo-Confucian sages and modern psychologists used virtually identical statements. Moreover, humanity faces the same basic issues while the particularizations vary. The importance of (...) reason, manners, appropriate behavior and self-actualization remains constant. However, the methods of their attainment change with time. The history of the Confucian/Neo-Confucian tradition is filled with such conceptual modifications. -/- Neo-Confucianism is a syncretic philosophy that utilized elements of Zen, Taoism, and Legalism within Confucian teachings. This adaptation increased the sages' ability to communicate with a wider range of people. In effect, the Neo-Confucian movement was perhaps the earliest practice of eclectic counseling. Neo-Confucianism itself has undergone development from its eleventh-century origins to the present-day scholarly journals. -/- The researcher does not believe the key issue in inter- disciplinary studies is whether psychology is being applied to philosophy or vice-versa. Neo-Confucianism pragmatically asserts that the true test of a philosophy rests in its ability to help the individual. Mere intellectual exercise contradicts the unity of knowledge and action. The thesis has five chapters. The existential therapy chapter uses a predominantly Western psychology format while the cognitive-behavioral therapy chapter uses Wang Yang-ming's Four Axiom Teaching as an outline. -/- The thesis also includes Neo-Confucian cognitive-moral development observations reminiscent of Lawrence Kohlberg's stage theories. Neo-Confucianism could be described as an education in evolving from preconventional to principled reasoning. Occasional parallels are drawn between process philosophy and Neo-Confucianism as well. -/- There is also a chapter in which Confucian commentaries are provided to actual case studies faced by Albert Ellis and Maxie Maultsby. A Chinese glossary is provided at the end of the introduction. There are five figures in the text, two of which are summarizing models in the conclusion. -/- . (shrink)