Symbolic modeling of structural relationships in the Foundational Model of Anatomy

The need for a sharable resource that can provide deep anatomical knowledge and support inference for biomedical applications has recently been the driving force in the creation of biomedical ontologies. Previous attempts at the symbolic representation of anatomical relationships necessary for such ontologies have been largely limited to general partonomy and class subsumption. We propose an ontology of anatomical relationships beyond class assignments and generic part-whole relations and illustrate the inheritance of structural attributes in the Digital Anatomist Foundational Model of Anatomy. Our purpose is to generate a symbolic model that accommodates all structural relationships and physical properties required to comprehensively and explicitly describe the physical organization of the human body

Short-range Magnetic interactions in the Spin-Ice compound Ho2_{2}Ti2_{2}O7_{7}

Magnetization and susceptibility studies on single crystals of the pyrochlore Ho$_{2}$Ti$_{2}$O$_{7}$ are reported for the first time. Magnetization isotherms are shown to be qualitatively similar to that predicted by the nearest neighbor spin-ice model. Below the lock-in temperature, $T^{\ast }\simeq 1.97$ K, magnetization is consistent with the locking of spins along [111] directions in a specific two-spins-in, two-spins-out arrangement. Below $T^{\ast}$ the magnetization for $B||[111]$ displays a two step behavior signalling the breaking of the ice rules.Comment: 4 pages, 3 figure

The Foundational Model of Anatomy Ontology

Anatomy is the structure of biological organisms. The term also denotes the scientific discipline devoted to the study of anatomical entities and the structural and developmental relations that obtain among these entities during the lifespan of an organism. Anatomical entities are the independent continuants of biomedical reality on which physiological and disease processes depend, and which, in response to etiological agents, can transform themselves into pathological entities. For these reasons, hard copy and in silico information resources in virtually all fields of biology and medicine, as a rule, make extensive reference to anatomical entities. Because of the lack of a generalizable, computable representation of anatomy, developers of computable terminologies and ontologies in clinical medicine and biomedical research represented anatomy from their own more or less divergent viewpoints. The resulting heterogeneity presents a formidable impediment to correlating human anatomy not only across computational resources but also with the anatomy of model organisms used in biomedical experimentation. The Foundational Model of Anatomy (FMA) is being developed to fill the need for a generalizable anatomy ontology, which can be used and adapted by any computer-based application that requires anatomical information. Moreover it is evolving into a standard reference for divergent views of anatomy and a template for representing the anatomy of animals. A distinction is made between the FMA ontology as a theory of anatomy and the implementation of this theory as the FMA artifact. In either sense of the term, the FMA is a spatial-structural ontology of the entities and relations which together form the phenotypic structure of the human organism at all biologically salient levels of granularity. Making use of explicit ontological principles and sound methods, it is designed to be understandable by human beings and navigable by computers. The FMA’s ontological structure provides for machine-based inference, enabling powerful computational tools of the future to reason with biomedical data

The Potential of the Digital Anatomist Foundational Model for Assuring Consistency in UMLS Sources

Inconsistent anatomical concept representation can be identified in anatomy textbooks and hard copy term lists, as well as in UMLS source vocabularies and other controlled medical terminologies. In this report we select some examples of inconsistent representations of anatomical concepts, and illustrate how these inconsistencies can be explained and reconciled by the Digital Anatomist Foundational Model1. We use this process for gaining a measure of the validity of the logic-based Model

The Role of Definitions in Biomedical Concept Representation

The Foundational Model (FM) of anatomy, developed as an anatomical enhancement of UMLS, classifies anatomical entities in a structural context. Explicit definitions have played a critical role in the establishment of FM classes. Essential structural properties that distinguish a group of anatomical entities serve as the differentiae for defining classes. These, as well as other structural attributes, are introduced as template slots in Protege, a frame-based knowledge acquisition system, and are inherited by descendants of the class. A set of desiderata has evolved during the instantiation of the FM for formulating definitions. We contend that 1. these desiderata generalize to non-anatomical domains and 2. satisfying them in constituent vocabularies of UMLS would enhance the quality of information retrievable through UMLS

Context-Dependent Memory under Stressful Conditions: The Case of Skydiving

Two experiments examined the effect of differing levels of emotional arousal on learning and memory for words in matching and mismatching contexts. In Experiment 1, experienced skydivers learned words either in the air or on the ground and recalled them in the same context or in the other context. Experiment 2 replicated the stimuli and design of the first experiment except that participants were shown a skydiving video in lieu of skydiving. Recall was poor in air-learning conditions with actual skydiving, but when lists were learned on land, recall was higher in the matching context than in the mismatching context. In the skydiving video experiment, recall was higher in matching learn-recall contexts regardless of the situation in which learning occurred. We propose that under extremely emotionally arousing circumstances, environmental and/or mood cues are unlikely to become encoded or linked to newly acquired information and thus cannot serve as cues to retrieval. Results can be applied to understanding variations in context-dependent memory in occupations (e.g., police, military special operations, and Special Weapons and Tactics teams) in which the worker experiences considerable emotional stress while learning or recalling new information

Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy

The Foundational Model of Anatomy (FMA) is a frame-based ontology that represents declarative knowledge about the structural organization of the human body. Part-whole relationships play a particularly important role in this representation. In order to assure that knowledge-based applications relying on the FMA as a resource can reason about anatomy, we have modified and enhanced currently available schemes of meronymic relationships. We have introduced and defined distinct partitions for decomposing anatomical structures and attributed the part relationships in order to eliminate ambiguity and enhance specificity in the richness of meronymic relationships within the FMA