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)

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Philosophy 41.3 (2003) 417-418 [Access article in PDF] Heidi M. Ravven and Lenn E. Goodman, editors. Jewish Themes in Spinoza's Philosophy. Albany: The State University of New York Press, 2002. Pp. ix + 290. Cloth, $78.50. Paper, $26.95.The current anthology presents an important contribution to the study of Spinoza's relation to Jewish philosophy as well as to contemporary scholarship of Spinoza's metaphysics and political (...) theory.In the opening essay, Lenn Goodman takes upon himself the ambitious task of evaluating Spinoza's positions as to several central disputes throughout the history of philosophy. In this rich and extensive essay Goodman argues that Spinoza's radical rationalism makes him pursue syntheses between traditionally opposed poles. Lee Rice's article, "Love of God in Spinoza," carefully analyzes Spinoza's concept of love and suggests the existence of three kinds of love parallel to the three kinds of knowledge. Warren Montag addresses the unresolved issue of Spinoza's relation to the Kabbalah. Montag sides with Deleuze against the association of Spinozism with the Neo-Platonic theory of emanation, arguing that unlike the Neo-Platonists and Kabbalists, Spinoza's view of God rules out any hierarchy, and does not assume a descent from primal simplicity into complexity. Edwin Curley contributes a beautiful reading of the story of Job and of Maimonides' interpretation of the story. Curley follows Maimonides' discussion of the various positions regarding the question of divine providence and his attempt to identify the speeches of the characters of the book of Job with each of these positions. Following a sensitive consideration of various attempts to [End Page 417] recover Maimonides' own rather concealed view about providence, Curley concludes that "[W]hatever you think Maimonides' final word on Job is, our examination of him certainly supports [Spinoza's] claim that [Maimonides] reads Scripture in terms of Platonic or Aristotelian speculations" (170).Warren Zev Harvey's essay addresses Spinoza's most neglected work, the Compendium of the Grammar of the Hebrew Language. Apart from providing an outline of Spinoza's work as a Hebrew grammarian ("a noun-intoxicated grammarian") and pointing out some of Spinoza's more eccentric views about the nature of the Hebrew language, Harvey makes a compelling case for the importance of the book for the study of Spinoza's metaphysics. He points out a fascinating analogy which Spinoza draws between the parts of speech: (proper) noun, adjectives, and participles, and Spinoza's key metaphysical terms: substance, attributes, and modes. (Think about the weighty implications of this analogy for Curley's interpretation of the substance-mode relation.) According to Harvey, Spinoza's claim that all Hebrew words are derived from nouns is a linguistic parallel to Spinoza's pivotal metaphysical doctrine which makes all things be in the substance (or God). Kenneth Seeskin's article discusses the views of Maimonides and Spinoza on the question of creation and God's relation to the world. Seeskin reconstructs an interesting critical dialogue between these two philosophers. According to Seeskin, both philosophers held that an effect must be similar to its cause. Maimonides' commitment to Negative Theology and to the denial of any common measure between God and finite things forced him to deny causal or explanatory relation between God and the world. What Maimonides can suggest instead is rather to prove that the emergence of the world ex nihilo and according to the divine will, is possible, and even likely given certain astronomical facts of medieval science. Thus, Maimonides would hold that "although we have grounds for believing that creation occurred, we will never be in a position to say how" (120). For Spinoza, such a view constitutes nothing but a "sanctuary of ignorance." Thus, according to Seeskin, Spinoza affirms a clear causal relation between God and the world of finite things insofar as God is said to explain the world. While I tend to agree with most aspects of this analysis, it is important to note that Spinoza also claims that "between the finite and infinite there is no relation" (Letter 54). This... (shrink)

The years following Israel’s founding were formative ones for the development of philosophy as an academic discipline in this country. During this period, the distinction between philosophy seen as contiguous with the humanities and social sciences, and philosophy seen as adjacent to the natural and exact sciences began to make its presence felt in the Hebrew University of Jerusalem. This distinction, which was manifest in the curriculum, was by no means unique to the Hebrew University, but reflected the broader bifurcation (...) between two schools of Western philosophy in the twentieth century. In English-speaking countries, it is generally referred to as the divide between analytic and continental philosophy. What was special about the situation at the Hebrew University, however, was that the split manifested itself in a rather small department, being embodied, basically, in one prominent representative of each school – Nathan Rotenstreich and Yehoshua Bar-Hillel. This article will focus on some key aspects of the lives and thought of Rotenstreich and Bar-Hillel. It will address their philosophical maturation as S.H. Bergmann’s students, their views on the goals of twentieth-century philosophy, on the philosopher’s role in public life, and the circumstances under which they started teaching in Jerusalem right after the founding of the State of Israel. (shrink)