A logical and principled representation of cell types and their component parts could serve as a framework for correlating the various ontologies that are emerging in bioinformatics with a focus on cells and subcellular biological entities. In order to address this need we have extended the Foundational Model of Anatomy (FMA)1,2 from macroscopic to cellular and subcellular anatomical entities. ...

The objective of this study is to provide an operational definition of principles with which well-formed ontologies should comply. We define 15 such principles, related to classification (e.g., no hierarchical cycles are allowed; concepts have a reasonable number of children), incompatible relationships (e.g., two concepts cannot stand both in a taxonomic and partitive relation), dependence amo...

Proof-carrying code is a framework for the mechanical verification of safety properties of machine language programs, but the problem arises of quis custodiat ipsos custodes—who will verify the verifier itself? Foundational proof-carrying code is verification from the smallest possible set of axioms, using the simplest possible verifier and the smallest possible runtime system. I will describe ...

In this paper, I address the what, the how, and the why of moral phenomenology. I consider first the question What is moral phenomenology?, secondly the question How to pursue moral phenomenology?, and thirdly the question Why pursue moral phenomenology? My treatment of these questions is preliminary and tentative, and is meant not so much to settle them as to point in their answers’ direction.

Integrating property-based testing with a proof assistant creates an interesting opportunity: reusable or tricky testing code can be formally verified using the proof assistant itself. In this work we introduce a novel methodology for formally verified property-based testing and implement it as a foundational verification framework for QuickChick, a port of QuickCheck to Coq. Our framework enab...

Implementations of logical reasoning systems are invariably based on the foundational theory of justification. The AGM logic is based on the coherence theory and the principle of minimal change, but this presents difficulties in its implementation. We show that both the foundational and coherence styles of reasoning are necessary for practical reasoning and that both can be achieved in the AGM ...

It has been shown that using a foundational ontology for domain ontology development is beneficial in theory and practice. However, developers have difficulty with choosing the appropriate foundational ontology, and why. In order to solve this problem, a comprehensive set of criteria that influence foundational ontology selection has been compiled and the values for each parameter determined fo...

How can one possibly analyze computation in general? The task seems daunting if not impossible. There are too many different kinds of computation, and the notion of general computation seems too amorphous. As in quicksand, one needs a rescue point, a fulcrum. In computation analysis, a fulcrum is a particular viewpoint on computation that clarifies and simplifies things to the point that analys...