When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

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)

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)

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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

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)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (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)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Shang ce. Ru xue yu si xiang -- xia ce. Qing dai xue shu si chao.

Xuantong 玄同 (tentatively translated as dark oneness) is a unique Daoist idea that represents an ideally mental and physical state as a result of cultivation. However, owing to limited context in the Laozi, there is no consensus on the interpretation of xuantong. Contemporary studies have also neglected xuantong’s evolution in early texts and assumed a homogeneous understanding, and hence, failed to provide a nuanced account. In this article, I investigate how xuantong evolves from the Guodian Laozi to the Huainanzi and (...) Wenzi. I argue that although xuantong may originate from the Laozi, it is in the Wenzi that a coherent theory of xuantong is accomplished. This theory advocates an orderly process of cultivation that covers internal mental states, external acts, and integration with the whole universe. The cultivation would eventually lead people to adopt an undifferentiated perspective on, and reach oneness with, all things in the universe. (shrink)

Safeguarding public interest was vital to early modern state legitimacy in Western Europe and East Asia. Wenkai He identifies similar patterns in state-society interactions surrounding public goods provision and explores how conflicts over public interest led to calls for fundamental political change and to modern representative politics.

“主体性”是哲学中一个十分重大的课题，在20世纪80年代至90年代，“主体性”观念在中国当代哲学的进程中产生了十分特殊的作用，对于推动思想解放、观念变革居功至伟。今天我们究竟应该怎样理解和评估“主体性 ”原则？马克思哲学的“主体性”思想在哲学史上所具有的重大意义究竟是什么？对我们今天重新阐释“主体性”思想有什么价值？本书正是试图围绕上述问题，在当代哲学的历史语境中对“主体性”观念进行专门研究和当代阐 释。.

何定生是顧頡剛在廣州中山大學任教時的學生，早年即已有文章收錄於《古史辨》中，而享有古史辨學者的光環。一九四九年隨國民政府來臺，任教於臺大中文系。生前出版有《詩經今論》一書，收錄三篇《詩經》研究論文，為 臺灣學界所仰重。一九七○去世後，其弟子何寄澎、曾志雄整理遺稿，出版《定生論學集──詩經與孔學研究》，收錄四篇論著。《何定生著作集》即在此二書的基礎上，復廣泛蒐求其論著、書信與相關資料，編為二冊。第一冊 為《何定生著作集一：詩經、孔學及其他》，第二冊為《何定生著作集二：尚書與文法》，雖尚未能將何氏著作網羅殆盡，但已足將何氏學術的主要面向及研究精華充分展現出來。 何定生深受五四以來新文化運動的影響，繼承顧頡剛及古史辨的學風，將此學風在戰後的臺灣學界持續發皇。何定生的學問主要表現在《詩經》，強調復古解放的精神，他呼籲今日的《詩經》研究，應從清學的漢學壁壘中出來， 以復於原始的樂歌地位。他認為惟有站在《儀禮》的樂歌地位來讀《詩經》，從人性的同類意識來接觸人性，才有碰到詩人靈感的可能。.

Spinoza est-il un adversaire de la religion? Rien n'est moins sûr. Dès la correspondance avec Guillaume de Blyenbergh, il admet l'existence de deux voies de salut hétérogènes : par la philosophie et par la religion, par l'intelligence et par la charité. Y a-t-il là quelque incohérence? Rien n'est moins sûr. Il s'agit dans cet essai de montrer pourquoi et comment coexistent ces deux voies de salut hétérogènes. Par là même, Spinoza s'avérera unique, un hapax dans la constellation des grands philosophes (...) du XVIIe siècle, et s'éclairera l'accusation d'athéisme prononcée de manière récurrente à son encontre. (shrink)

Dans la pensée pascalienne, la sagesse revêt plusieurs significations. Elle peut se définir comme la sagesse des philosophes, mais aussi comme la sagesse divine. La vraie sagesse est celle des saints et se situe dans l'ordre de la charité. En confrontant ces deux sortes de sagesse, l'ouvrage pose les questions suivantes : la sagesse des saints s'oppose-t-elle à la sagesse naturelle des philosophes ou bien peut-on accorder les deux? Comment définir le rapport entre l'amour de la sagesse et la sagesse (...) de l'amour dans la pensée pascalienne? Les études recueillies dans cet ouvrage traitent cette problématique. (shrink)

In this multidisciplinary book, mathematician Matthew He provides integrative perspectives of algebraic biology, cognitive informatics, and poetic expressions of the human mind. Using classical Pythagorean Theorem and contemporary Category Theory, the proposed matrix models of the human mind connect three domains of the physical space of objective matters, mental space of subjective meanings, and emotional space of bijective modes; draws the connections between neural sparks and idea points, between synapses and idea lines, and between action potentials and frequency curves.

本书以道教神仙思想的演变为中心, 发掘不同时期相对突出的道教社会伦理思想, 回答了道教在面对世俗社会时有什么样的伦理思考和规范, 旨在对道教深层价值作重新认识和评价, 向人们展示一种更全面的道教.本书结合时代, 融入了当今时代理念, 更具有现代意义.

Heideggers Philosophie stellt die Frage nach dem Sein. Das Sein betrifft das Seiende im Ganzen, es ist in allem Seienden durchgangig das allem Gemeine und so das Gemeinste, aber es ist zugleich auch das Leerste. Wenn Heidegger das Ganze bedenkt, bedenkt er zugleich auch das Nichts. Das Sein versteht er dementsprechend als Sein-lassen. Was aber ist der Sinn von Sein? Sowohl phanomenologisch als auch fundamentalontologisch entfaltet Heidegger eine Analytik des Daseins, in der Zeit als Horizont eines jeden Seinsverstandnisses leitend ist. (...) Von diesem Horizont her versteht sich das Dasein als Sein zum Tode und als Mitsein mit dem Anderen - bis hin zur vorausspringend-befreienden Fursorge. (shrink)

The standard Lewis–Stalnaker semantics of counterfactuals, given the Strong Centering Thesis, implies that all true–true counterfactuals are trivially true. McGlynn developed a theory, based on Penczek, to rehabilitate the non-triviality of true–true counterfactuals. I show here that counterfactuals with true but irrelevant components are counterexamples to McGlynn’s account. I argue that an extended version of the connection hypothesis is sustainable, and grounds a full theory of counterfactuals explicable in a broadly standard way, if an indispensable asymmetry between semifacuals and other (...) counterfactuals is acknowledged. (shrink)

本书厘清了何谓历史,何谓历史学,何谓历史学家等基本概念;认为历史的发展有其必然性与偶然性,而人类的历史是由自由人的自由意志作用的结果;历史学家对过去所构思出来的那幅历史图像,乃是他自己思想的外烁.

本书收录何兆武先生的读书心得,通过回忆与师友一起读书,交流,工作的岁月,从一个侧面回顾了20世纪上半叶中国历史上一代学者的思想成就,桥接了新旧两个时代的思想与历史,触摸到一个历史时代的灵魂.

Drawing on his extensive experience as both a medical practitioner and a patient, acclaimed author, award-winning physician, and ethicist Philip Hébert creates a brave and intimate portrait of the complex ethical questions raised by revolutionary advances in medical diagnosis and treatment. Philip Hébert addresses the complex ethical questions raised by revolutionary advances in medical treatment. This work expands upon Hébert's previous book, "Doing Right," and extends his knowledge of the field beyond medical professionals to reach the patients they treat.

Over the past half-century, China has experienced some incredible human dramas, ranging from Red Guard fanaticism and the loss of education for an entire generation during the Cultural Revolution, to the Tiananmen tragedy, the economic miracle, and its accompanying fad of money worship and the rampancy of official corruption. _Social Ethics in a Changing China: Moral Decay or Ethical Awakening?_ provides a rich empirical narrative and thought-provoking scholarly arguments, highlighting the imperative for an ethical discourse in a country that is (...) increasingly seen by many as both a materialistic giant and a spiritual dwarf. Professor He Huaihong was not only an extraordinary firsthand witness to all of these dramas, he played a distinct role as a historian, an ethicist, and a social critic exploring the deeper intellectual and sociological origins of these events. Incorporating ethical theories with his expertise in culture, history, religion, literature, and politics of the country, He reviews the remarkable transformation of ethics and morality in the People's Republic of China and engages in a global discourse about the major ethical issues of our time. The book aims to reconstruct Chinese social ethics in an innovative philosophical framework, reflecting China's search for new virtues. Contents 1. Reconstructing China's Social Ethics 2. Historical and Sociological Origins of Chinese Cultural Norms 3. The Transformation of Ethics and Morality in the PRC 4. China's Ongoing Moral Decay? 5. Ethical Discourse in Reform Era China 6. Chinese Ethical Dialogue with the West and the World. (shrink)