In previous chapters we have discussed how making use of a formal (or top-level or domain-neutral) ontology can be helpful in constructing domain ontologies that are interoperable, rigorous, and ...clear. We argued that issues such as terminology selection, term definition, and classification can all be better addressed in the context of a top-level ontology, and also suggested that use of a top-level ontology brings benefits when it comes to sharing ontology content, governance of ontology development, and developing expertise.
Multiple ontologies working together within the framework of the OBO Foundry initiative utilize Basic Formal Ontology (BFO) as a starting point
Basic Formal Ontology at Work Spear, Andrew D; Smith, Barry; Arp, Robert
Building Ontologies with Basic Formal Ontology,
08/2015
Book Chapter
Odprti dostop
All good ontology building, in our view, starts with thinking. The author of an ontology should first assemble a collection of the major terms he will need to use, and use careful thinking to ensure ...that he understands the meanings of these terms within the context of the associated science, and then further careful thinking to ensure that he can define these terms using words that other human beings will understand and in ways conformant to the BFO ontology and to the other principles set forth in the foregoing.
At some point, however, the ontology builder will need to embark
Having presented thecontinuantcategories of BFO, we will now focus on theoccurrentcategories starting, again, with the most general, and then working downward through their respective subtypes. The ...occurrent portion of BFO represents entities that occur, happen, unfold, or develop in time. In commonsensical terms, these entities are occurrences or happenings or the processes of change; they are the ontological counterparts of present participles (runnings, swimmings, dividings, orbitings).
A BFO:occurrentis, more precisely, either an entity that unfolds itself in time, or it is the instantaneous boundary of such an entity (for example, a beginning or an
The Ontology of Relations Spear, Andrew D; Smith, Barry; Arp, Robert
Building Ontologies with Basic Formal Ontology,
08/2015
Book Chapter
Odprti dostop
In chapter 6, we introduced the basic categories of BFO:continuantand BFO:occurrent, and their respective subtypes. In this chapter we will introduce the central ontological relations in BFO, and ...provide examples of how definitions for such relations are to be formulated.
As has been noted in earlier chapters, providing definitions of the terms representing universals and defined classes alone is normally not sufficient to capture all of the important scientific information about a given domain. The relations that obtain between and among them need to be defined also, and we further need to provide axioms, for example, representing
I motivate the need for and begin developing an account of internalist foundationalist a priori justification. This view of a priori justification is committed to the thesis that there is a ...phenomenon, reason-based intuition or rational insight, which involves the non-inferential and non-empirical (in the sense of relying essentially on sensory experience) acquisition of epistemic justification for beliefs based purely on adequate reflection on or understanding of the concepts, propositions or things that are the objects of beliefs so justified. In Chapter 1 I motivate the need for an account of a priori justification by considering three arguments against strict empiricism: the generality argument, the argument from modality, and the metajustification argument. I argue that debates between rationalism and empiricism are best understood in the context of foundationalist internalism. I then appeal to plausible commitments of foundationalist internalism in conjunction with plausible theses about the nature of the content of sensory experience to argue that each of the three arguments against strict empiricism is sound, despite recent objections to the contrary. Strict empiricism in conjunction with plausible epistemic principles and assumptions entails skepticism about justification for belief in the majority of propositions of the sciences, logic and mathematics. If one is committed to some version of foundationalist internalism, and skepticism about the majority of general and modal beliefs in science, mathematics and logic is implausible, then one should be committed to the existence of at least some a priori justification. In Chapter 2 I introduce what I call the "traditional conception of intentionality", which has roots in the phenomenological tradition of Franz Brentano and Edmund Husserl. I characterize this view of the nature of thought, its content and its objects as a version of content internalism and discuss three major implications of the view: that thought is "conception dependent", "existence independent", and admits of "indeterminacy". I consider recent arguments against internalism about content and argue that the conception of intentionality I am developing can be understood in such a way that these arguments do not compromise it. I then argue that certain versions of content externalism involve the denial of the conception dependence, existence independence and indeterminacy of thought advocated by the traditional view. Each of these denials leads to a problem for externalism: the qua problem, the problem of thought about the non-existent, and problems involving knowledge and self-knowledge respectively. This being the case, the traditional conception of intentionality is a plausible version of internalism and represents a significant alternative to externalism about content. In Chapter 3 I develop accounts of indexical and demonstrative content, and of propositions, all of which are motivated by the traditional conception of intentionality. I argue that the best way for the traditional conception of intentionality to respond to recent arguments against content internalism is by developing an account of indexical and demonstrative intentional content. I offer such an account, then discuss its implications for a neo-Fregean view of propositions. In Chapter 4 I identify a key desideratum for any account of distinctively epistemic justification, and develop an account of epistemic internalism intended to meet this desideratum. I argue that the primary task in developing an account of epistemic justification is to establish the existence of a modal tie of "making likely" or "probable" between reasons for belief (whether these be "production by reliable cognitive processes" or "internally accessible mental states") and the truth of what is believed on their basis. I then introduce and articulate two notions, the notion of identity-sensitive phenomenology and the notion of an identity-sensitive thought type, as candidates for basic internalist justification. I conclude by attempting to motivate the intuition that experiences with identity-sensitive phenomenology are more likely than not to be instances of identity-sensitive thought types, and that experiences that are identity-sensitive thought types can plausibly be understood as involving the kind of modal tie between reasons and the likely truth of things believed on their basis that the first part of the chapter proposed as a desideratum for accounts of epistemic justification.
In the last decades, Ingvar Johansson has made a formidable contribution to the development of philosophy and particularly that of metaphysics. This volume consists of original papers written by 50 ...philosophers from all over the world to celebrate his 70th birthday. The papers cover traditional issues in metaphysics and the philosophy of mind, applied ethics, applied metaphysics, the nature of human rights, the philosophy of economics and sports.
The field of landscape genetics has great potential to identify habitat features that influence population genetic structure. To identify landscape correlates of genetic differentiation in a ...quantitative fashion, we developed a novel approach using geographical information systems analysis. We present data on blotched tiger salamanders (Ambystoma tigrinum melanostictum) from 10 sites across the northern range of Yellowstone National Park in Montana and Wyoming, USA. We used eight microsatellite loci to analyse population genetic structure. We tested whether landscape variables, including topographical distance, elevation, wetland likelihood, cover type and number of river and stream crossings, were correlated with genetic subdivision (FST). We then compared five hypothetical dispersal routes with a straight‐line distance model using two approaches: (i) partial Mantel tests using Akaike's information criterion scores to evaluate model robustness and (ii) the BIOENV procedure, which uses a Spearman rank correlation to determine the combination of environmental variables that best fits the genetic data. Overall, gene flow appears highly restricted among sites, with a global FST of 0.24. While there is a significant isolation‐by‐distance pattern, incorporating landscape variables substantially improved the fit of the model (from an r2 of 0.3 to 0.8) explaining genetic differentiation. It appears that gene flow follows a straight‐line topographic route, with river crossings and open shrub habitat correlated with lower FST and thus, decreased differentiation, while distance and elevation difference appear to increase differentiation. This study demonstrates a general approach that can be used to determine the influence of landscape variables on population genetic structure.
Numerous developmental changes occur across levels of personal organization (eg, changes related to puberty, brain and cognitive-affective structures and functions, and family and peer relationships) ...in the age period of 10 to 15 years. Furthermore, the onset and escalation of alcohol use commonly occur during this period. This article uses both animal and human studies to characterize these multilevel developmental changes. The timing of and variations in developmental changes are related to individual differences in alcohol use. It is proposed that this integrated developmental perspective serve as the foundation for subsequent efforts to prevent and to treat the causes, problems, and consequences of alcohol consumption.
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