Using multiple reference ontologies: Managing composite annotations

There are a growing number of reference ontologies available across a variety of biomedical domains and current research focuses on their construction, organization and use. An important use case for these ontologies is annotation—where users create metadata that access concepts and terms in reference ontologies. We draw on our experience in physiological modeling to present a compelling use case that demonstrates the potential complexity of such annotations. In the domain of physiological biosimulation, we argue that most annotations require the use of multiple reference ontologies. We suggest that these “composite” annotations should be retained as a repository of knowledge about post-coordination that promotes sharing and interoperation across biosimulation models

Groundwater faunas as indicators of groundwater quality: the South Platte River system

February 1989.Bibliography: pages 33-39

Competing symmetries and broken bonds in superconducting vortex-antivortex molecular crystals

Hall probe microscopy has been used to image vortex-antivortex molecules induced in superconducting Pb films by the stray fields from square arrays of magnetic dots. We have directly observed spontaneous vortex-antivortex pairs and studied how they interact with added free (anti)fluxons in an applied magnetic field. We observe a variety of phenomena arising from competing symmetries which either drive added antivortices to join antivortex shells around dots or stabilize the translationally symmetric antivortex lattice between the dots. Added vortices annihilate antivortex shells, leading first to a stable “nulling state” with no free fluxons and then, at high densities, to vortex shells around the dots stabilized by the asymmetric antipinning potential. Our experimental findings are in good agreement with Ginzburg-Landau calculations

Approximating the Minimum Equivalent Digraph

The MEG (minimum equivalent graph) problem is, given a directed graph, to find a small subset of the edges that maintains all reachability relations between nodes. The problem is NP-hard. This paper gives an approximation algorithm with performance guarantee of pi^2/6 ~ 1.64. The algorithm and its analysis are based on the simple idea of contracting long cycles. (This result is strengthened slightly in ``On strongly connected digraphs with bounded cycle length'' (1996).) The analysis applies directly to 2-Exchange, a simple ``local improvement'' algorithm, showing that its performance guarantee is 1.75.Comment: conference version in ACM-SIAM Symposium on Discrete Algorithms (1994

Impurity relaxation mechanism for dynamic magnetization reversal in a single domain grain

The interaction of coherent magnetization rotation with a system of two-level impurities is studied. Two different, but not contradictory mechanisms, the `slow-relaxing ion' and the `fast-relaxing ion' are utilized to derive a system of integro-differential equations for the magnetization. In the case that the impurity relaxation rate is much greater than the magnetization precession frequency, these equations can be written in the form of the Landau-Lifshitz equation with damping. Thus the damping parameter can be directly calculated from these microscopic impurity relaxation processes

Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology

We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformatics modeling of biological structures and the biosimulation modeling of biological processes. Whereas modeling anatomical entities is relatively wellstudied, representing the physics-based semantics of biosimulation and biological processes remains an open research challenge. The OPB bridges this semantic gap--linking the semantics of biosimulation mathematics to structural bio-ontologies. Our design of the OPB is driven both by theory and pragmatics: we have applied systems dynamics theory to build an ontology with pragmatic use for annotating biosimulation models

Effects of cover crops on phosphatase activity in a clay arable soil in the UK

The effect of five cover crop species (radish, buckwheat, vetch, phacelia and oat) alongside an un-cropped control, on the activity and persistence of soil acid and alkaline phosphatase activity was investigated. There was no effect on alkaline phosphatase activity at the time of cover crop incorporation (March), but by the point of maturation of the following oat cash crop (June) significant differences were detected, with the greatest activity following an oat cover crop. Acid phosphatase activity showed species-related significant differences at both sampling dates, with the magnitude increasing by June. Again, plots following an oat cover crop showed the greatest activity, followed by phacelia. This has shown that soil phosphatase enzymes are affected by the presence of a cover crop, that this effect is apparently species-dependent – and not dependent on the amount of biomass from the cover crop – and that cover crops could be a potential means to enhance soil phosphorus cycling

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies

Abstract—Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies. Here we point out that such simple mappings are inadequate for large-scale multiscale, multidomain integrative “virtual human” projects. For such integrative challenges, we describe a “composite annotation” schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation models to available biomedical ontologies