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)

This paper is an attempt to present a Kripkean (Causal) picture of Reference where the cognitive content in fixing reference plays a vital role. It also points out that Kripke is not a pure causal theorist. By introducing Thomas Kuhn and his theory on vulnerability of the rigid designation, I have shown that there is a danger for causal theory of reference. However Kuhn’s argument fails to have an impact if a Knowledge aspect is augmented to Kripkean theory of reference. (...) This new causal theory of reference preserves the truth of the referential term in spite of the vulnerability of the rigid designation and problem of reference change. It can also adequately answer the question of theoretical terms reference failure. (shrink)

The Road less travelled often leads nowhere. But seldom, the uncharted path is the most sensible journey. Writing on this topic is an attempt to wade against the current discourse, not because it is a perspective from minority but it is a topic knowingly neglected by the majority. Tribal philosophy in India stands in contrast to majoritarian philosophy and hence, either looked down as insignificant or even considered the impossible. But its metaphysics illustrates the very heart of a worldview which (...) offers an alternative to the chaotic human experiences and institutions. This worldview is the oldest yet the newest. Tribal societies have lived the worldview without ever requiring the need of articulation. This paper, in that sense, is an attempt to capture and articulate first, the Philosophy inherent in a tribal lifestyle, second, pointing out the fusion of modernity in the life of a tribe. Articulating Philosophy of a tribal being is not a construction of metaphysics; rather it is a representation of thoughts of an indigenous being arising from her/his association with world, nature and life. Philosophy of the tribal world is the inner voice of the community diffusing through every member of the community. That inner voice of the community brings forth the indigeneity or ‘Adivasiyat’ – a strong sense of connection to land, nature, spirits and community. With modernity unsettling the life of a tribal person, a fusion in life must be sought to preserve the tradition and culture. Hence this paper will point out the outlook of tribals and shall try to bridge the gap between present and the past. (shrink)

Public trust in research and its output is essential for a healthy modern society. Although the research enterprise is self- correcting, this self-regulation occasionally needs help. Over the years, research institutions, professional societies, and governments have established several protocols, codes of conduct, norms, and principles to enhance that trust in research institutions, funders, producers, publishers, and products.

The modern abundance and prominence of data has led to the development of “data science” as a new field of enquiry, along with a body of epistemological reflections upon its foundations, methods, and consequences. This article provides a systematic analysis and critical review of significant open problems and debates in the epistemology of data science. We propose a partition of the epistemology of data science into the following five domains: (i) the constitution of data science; (ii) the kind of enquiry (...) that it identifies; (iii) the kinds of knowledge that data science generates; (iv) the nature and epistemological significance of “black box” problems; and (v) the relationship between data science and the philosophy of science more generally. (shrink)

Persian translation by Ashkan M. Roshan of _God, Soul and the Meaning of Life_.