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)

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 (...) class='Hi'>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)

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 (...) class='Hi'>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 (...) class='Hi'>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. (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)

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)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged (...) class='Hi'>behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

So-called “traditional epistemology” and “Bayesian epistemology” share a word, but it may often seem that the enterprises hardly share a subject matter. They differ in their (...) class='Hi'>central concepts. They differ in their main concerns. They differ in their main theoretical moves. And they often differ in their methodology.However, in the last decade or so, there have been a number of attempts to build bridges between the two epistemologies. Indeed, many would say that there is just one branch of philosophy here—epistemology. There is a common subject matter after all.In this paper, we begin by playing the role of a “bad cop,” emphasizing many apparent points of disconnection, and even conflict, between the approaches to epistemology. We then switch role, playing a “good cop” who insists that the approaches are engaged in common projects after all. We look at various ways in which the gaps between them have been bridged, and we consider the prospects for bridging them further. We conclude that this is an exciting time for epistemology, as the two traditions can learn, and have started learning, from each other. (shrink)

Metaphysical rationalism, the doctrine which affirms the Principle of Sufficient Reason (the PSR), is out of favor today. The best argument against it is that it appears (...) to lead to necessitarianism, the claim that all truths are necessarily true. Whatever the intuitive appeal of the PSR, the intuitive appeal of the claim that things could have been otherwise is greater. This problem did not go unnoticed by the great metaphysical rationalists Spinoza and Leibniz. Spinoza’s response was to embrace necessitarianism. Leibniz’s response was to argue that, despite appearances, rationalism does not lead to necessitarianism. This paper examines the debate between these two rationalists and concludes that Leibniz has persuasive grounds for his opinion. This has significant implications both for the plausibility of the PSR and for our understanding of modality. (shrink)

Locke is often thought to have introduced the topic of personal identity into philosophy when, in the second edition of the Essay, he distinguished the person from (...) both the human being and the soul. Each of these entities differs from the others with respect to their identity conditions, and so they must be ontologically distinct. In particular, Locke claimed, a person cannot survive total memory loss, although a human being or a soul can. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics (...) class='Hi'>fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Material from this paper appears in Chap. 7 of my book Reason and Being, but there is also stuff here that isn't in the book. In (...) class='Hi'>particular, it discusses the claims that, for Spinoza, conceiving implies explaining and that existence is identical to or reducible to conceivability. So, if you're interested in those issues, this paper might be worth a read. (shrink)

This paper presents five studies on the development and validation of a scale of intellectual humility. This scale captures cognitive, affective, behavioral, and motivational components of the (...) construct that have been identified by various philosophers in their conceptual analyses of intellectual humility. We find that intellectual humility has four core dimensions: Open-mindedness (versus Arrogance), Intellectual Modesty (versus Vanity), Corrigibility (versus Fragility), and Engagement (versus Boredom). These dimensions display adequate self-informant agreement, and adequate convergent, divergent, and discriminant validity. In particular, Open-mindedness adds predictive power beyond the Big Six for an objective behavioral measure of intellectual humility, and Intellectual Modesty is uniquely related to Narcissism. We find that a similar factor structure emerges in Germanophone participants, giving initial evidence for the model’s cross-cultural generalizability. (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 (...) class='Hi'>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 desire-satisfaction theory of welfare says that what is basically good for a subject is the satisfaction of his desires. One challenge to this view is (...) class='Hi'>the existence of quirky desires, such as a desire to count blades of grass. It is hard to see why anyone would desire such things, and thus hard to believe that the satisfaction of such desires could be basically good for anyone. This suggests that only some desires are basically good when satisfied, and that desire satisfactionists owe us an account of which desires these are, and why. In "Quirky Desires and Well-Being," Donald Bruckner proposes such an account: a desire is welfare-relevant (i.e., such that its satisfaction would be basically good for its subject) if and only if and because its subject could describe its object in a way that makes it comprehensible what about the object attracts him or appeals to him. We are inclined to view quirky desires as welfare-irrelevant because we assume that their objects cannot be described in such a way. But if there were a quirky desire whose object could be so described by the subject whose desire it is, then this desire would be relevant to that subject's welfare. I will argue that while Bruckner's view delivers plausible verdicts about the cases to which it is meant to apply, its account of what makes a desire welfare-relevant is unmotivated and implausible. Desire satisfactionists can retain what is plausible about his view while endorsing a better explanation of why welfare-relevant desires have that status if they accept the following account instead: a desire is welfare-relevant if and only if and because something about its object attracts, or appeals to, the subject who has the desire. (shrink)

As robots slip into more domains of human life-from the operating room to the bedroom-they take on our morally important tasks and decisions, as well as (...) class='Hi'> create new risks from psychological to physical. This book answers the urgent call to study their ethical, legal, and policy impacts. (shrink)

This paper attempts to revive interest in the speech act theory of literature by looking into Monroe C. Beardsley's account in particular. Beardsley's view in this (...) class='Hi'> respect has received, surprisingly, less attention than deserved. I first offer a reconstruction of Beardsley's account and then use it to correct some notable misconceptions. Next, I show that the reformulation reveals a hitherto unnoticed discrepancy in Beardsley's position and that this can be explained away by a weak version of intentionalism that Beardsley himself actually tolerates. Finally, I assess the real difficulty of Beardsley's theory and its relevance today. (shrink)

This paper addresses the always online behavior of the data owner in proxy re- encryption schemes for re-encryption keys issuing. We extend and adapt multi-authority ciphertext (...) class='Hi'> policy attribute based encryption techniques to type-based proxy re-encryption to build our solution. As a result, user authentication and user authorization are moved to the cloud server which does not require further interaction with the data owner, data owner and data users identities are hidden from the cloud server, and re-encryption keys are only issued to legitimate users. An in depth analysis shows that our scheme is secure, flexible and efficient for mobile cloud computing. (shrink)

Cover Date: July 2006.Source Info: 115(3), 317-354. Language: English. Journal Announcement: 41-2. Subject: ACTION; CAUSATION; METAPHYSICS; REPRESENTATION; TELEOLOGY. Subject Person: SPINOZA, BENEDICT DE (BARUCH). (...) class='Hi'>Update Code: 20130315. (shrink)

: Perhaps the central problem which preoccupies Spinoza as a moral philosopher is the conflict between reason and passion. He belongs to a long tradition that sees the (...) class='Hi'> key to happiness and virtue as mastery and control by reason over the passions. This mastery, however, is hard won, as the passions often overwhelm its power and subvert its rule. When reason succumbs to passion, we act against our better judgment. Such action is often termed 'akratic'. Many commentators have complained that the psychological principles that Spinoza appeals to in his account of akrasia are mere ad hoc modifications to his philosophical psychology. I show, on the contrary, that these principles follow from some of the most important and interesting aspects of Spinoza's philosophy of mind. (shrink)

죽고 다시 태어나는 반복의 과정을 논하는 불교의 윤회설은 끊임없이 변화하는 생명현상의 본래 모습을 그대로 보여준다. 어느 생명체도 변하지 않고 영구한 것은 없다. 오래된 개체의 삶이 끝나고 새로운 (...) 삶이 시작되는 반복의 자연현상이 윤회이다. 본고는 윤회를 생명과학적으로 해석하며 삼라만상에서 일어나는 윤회란 개체들뿐만 아니라 세포와 분자선상에서도 일어나는 자연스런 생명현상임을 밝히겠다. (shrink)