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

An Ontology-based Image Repository for a Biomedical Research Lab

We have developed a prototype web-based database for managing images acquired during experiments in a biomedical research lab studying the factors controlling cataract development. Based on an evolving ontology we are developing for describing the experimental data and protocols used in the lab, the image repository allows lab members to organize image data by multiple attributes. The use of an ontology for developing this and other tools will facilitate intercommunication among tools, and eventual data sharing with other researchers

The Digital Anatomist Spatial Abstraction: A Scheme for the Spatial Description of Anatomical Features

In this paper, we propose a generalized scheme for the symbolic description of the spatial attributes of anatomical entities. The power of the scheme lies in the ability to model the spatial objects at the highest level of granularity: information can be obtained at the desired level of detail needed for a given application. This scheme uses the topological classes of point, line, surface, and volume to represent zero-D, one- D, two-D and three-D objects. A spatial object participates as a node in three complementary networks; the topology network, the part-of network, and the spatial associations network. The topology network describes a spatial object in terms of its boundaries, the part-of network describes a spatial object in terms of its parts, and the spatial associations network describes the spatial object in terms of its relationships to other spatial objects. All three of the networks can be used in combination or alone to answer queries to the spatial information system. The Digital Anatomist Structural Abstraction together with the other components of the Digital Anatomist Foundational Model1 will provide the information for describing and reasoning about anatomical entities

Observation of the lowest energy gamma-ray in any superdeformed nucleus : 196Bi

New results on the superdeformed $^{196}$Bi nucleus a re reported. We have observed with the EUROBALL IV $\gamma$-ray spectrometer array a superdeformed trans ition of 124 keV which is the lowest observed energy $\gamma$-ray in any superdeformed nucleus. We have de velopped microscopic cranked Hartree-Fock-Bogoliubov calculations using the SLy4 effective force and a realistic surface p airing which strongly support the $K^\pi=2^-$($\pi$[651]1/2$\otimes \nu$[752]5/2) assignment of this su perdeformed band

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

The SOFG Anatomy Entry List (SAEL):an annotation tool for functional genomics data

A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies

Large Deformation Effects in the N = Z 44Ti Compound Nucleus

The N = Z 44Ti* nucleus has been populated in Fusion Evaporation process at very high excitation energies and angular momenta using two entrance channels with different mass-asymmetry. The deformation effects in the rapidly rotating nuclei have been investigated through the energy distribution of the alpha-particle combined to statistical-model calculations. In the case of low-multiplicity events, the ratio between first particle emitted has been measured and shows significant disagreement with the predictions of the statistical-model. This may explain The large discrepancies observed in proton energy spectra measured in previous experiments performed in the same mass region.Comment: Proceeding of the 10th International Conference on Nuclear Reaction Mechanisms, Varenna Italy, June 9-13 2003. 10 pages, 6 figures, 1 tabl

Analytic Metaphysics versus Naturalized Metaphysics: The Relevance of Applied Ontology

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field

Primary chronic cold agglutinin disease: An update on pathogenesis, clinical features and therapy

Chronic cold agglutinin disease (CAD) is a subgroup of autoimmune hemolytic anemia. Primary CAD has traditionally been defined by the absence of any underlying or associated disease. The results of therapy with corticosteroids, alkylating agents and interferon-a have been poor. Cold reactive immunoglobulins against erythrocyte surface antigens are essential to pathogenesis of CAD. These cold agglutinins are monoclonal, usually IgMκ auto antibodies with heavy chain variable regions encoded by the VH4-34 gene segment. By flowcytometric and immunohistochemical assessments, a monoclonal CD20+κ+B-lymphocyte population has been demonstrated in the bone marrow of 90% of the patients, and lymphoplasmacytic lymphoma is a frequent finding. Novel attempts at treatment for primary CAD have mostly been directed against the clonal B-lymphocytes. Phase 2 studies have shown that therapy with the chimeric anti-CD20 antibody rituximab produced partial response rates of more than 50% and occasional complete responses. Median response duration, however, was only 11 months. In this review, we discuss the clinical and pathogenetic features of primary CAD, emphasizing the more recent data on its close association with clonal lymphoproliferative bone marrow disorders and implications for therapy. We also review the management and outline some perspectives on new therapy modalities