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)
This introduction to the Common Knowledge symposium titled “Comparative Relativism” outlines a variety of intellectual contexts where placing the unlikely companion terms comparison and relativism in conjunction offers analytical purchase. If comparison, in the most general sense, involves the investigation of discrete contexts in order to elucidate their similarities and differences, then relativism, as a tendency, stance, or working method, usually involves the assumption that contexts exhibit, or may exhibit, radically different, incomparable, or incommensurable traits. Comparative studies are required to (...) treat their objects as alike, at least in some crucial respects; relativism indicates the limits of this practice. Jensen argues that this seeming paradox is productive, as he moves across contexts, from Lévi-Strauss's analysis of comparison as an anthropological method to Peter Galison's history of physics, and on to the anthropological, philosophical, and historical examples offered in symposium contributions by Barbara Herrnstein Smith, Eduardo Viveiros de Castro, Marilyn Strathern, and Isabelle Stengers. Comparative relativism is understood by some to imply that relativism comes in various kinds and that these have multiple uses, functions, and effects, varying widely in different personal, historical, and institutional contexts that can be compared and contrasted. Comparative relativism is taken by others to encourage a “comparison of comparisons,” in order to relativize what different peoples—say, Western academics and Amerindian shamans—compare things “for.” Jensen concludes that what is compared and relativized in this symposium are the methods of comparison and relativization themselves. He ventures that the contributors all hope that treating these terms in juxtaposition may allow for new configurations of inquiry. (shrink)
A number of researchers have begun to demonstrate that the widely discussed ?Knobe effect? (wherein participants are more likely to think that actions with bad side-effects are brought about intentionally than actions with good or neutral side-effects) can be found in theory of mind judgments that do not involve the concept of intentional action. In this article we report experimental results that show that attributions of knowledge can be influenced by the kinds of (non-epistemic) concerns that drive the Knobe effect. (...) Our findings suggest there is good reason to think that the epistemic version of the Knobe effect is a theoretically significant and robust effect, and that the goodness or badness of side-effects can often have greater influence on participant knowledge attributions than explicit information about objective probabilities. Thus, our work sheds light on important ways in which participant assessments of actions can affect the epistemic assessments participants make of agents? beliefs. (shrink)
K.J. Devlin has extended Jensen's construction of a model ofZFC andCH without Souslin trees to a model without Kurepa trees either. We modify the construction again to obtain a model with these properties, but in addition, without Kurepa trees inccc-generic extensions. We use a partially defined ◊-sequence, given by a fine structure lemma. We also show that the usual collapse ofκ Mahlo toω 2 will give a model without Kurepa trees not only in the model itself, but also inccc-extensions.
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)
We study type 1 premice equipped with supercomplete extenders. In this paper, we show that such premice are normally iterable and all normal iteration trees of type 1 premice has a unique cofinal branch. We give a construction of an KC type model using supercomplete type 1 extenders.
In the 1999 Galton Lecture for the annual conference of The Galton Institute, the author summarizes the main elements of Galtongenerals original and largely intuitive ideas, which still inspire mainstream scientific research on intelligence.
Acquisition of word meanings, or vocabulary, reflects general mental ability (psychometric g) more than than do most abilities measured in test batteries. Among diverse subtests, vocabulary is especially high on indices of genetic influences. Bloom's exposition of the psychological complexities of understanding words, involving the primacy of concepts, the theory of mind, and other processes, explains vocabulary's predominant g saturation.