OBJECTIVE The objective of this paper is to demonstrate how a formal spatial theory can be used as an important tool for disambiguating the spatial information embodied in biomedical ontologies and for enhancing their automatic reasoning capabilities. METHOD AND MATERIALS This paper presents a formal theory of parthood and location relations among individuals, called Basic Inclusion Theory (B...

We describe the need for a Foundational Model of Physiology (FMP) as a reference ontology for "functional bioinformatics". The FMP is intended to support symbolic lookup, logical inference and mathematical analysis by integrating descriptive, qualitative and quantitative functional knowledge. The FMP will serve as a symbolic representation of biological functions initially pertaining to human p...

This paper presents a theoretical framework for defining corecursive functions safely in a total setting, based on corecursion up-to and relational parametricity. The end product is a general corecursor that allows corecursive (and even recursive) calls under wellbehaved operations, including constructors. Corecursive functions that are well behaved can be registered as such, thereby increasing...

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 ...