The Blood Ontology: An ontology in the domain of hematology

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some of its anticipated uses

Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base

<p>Abstract</p> <p>Background</p> <p>The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO).</p> <p>Results</p> <p>We define the Saliva Ontology (SALO; <url>http://www.skb.ucla.edu/SALO/</url>) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry.</p> <p>Conclusions</p> <p>The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB.</p

Cold Induces Micro- and Nano-Scale Reorganization of Lipid Raft Markers at Mounds of T-Cell Membrane Fluctuations

Whether and how cold causes changes in cell-membrane or lipid rafts remain poorly characterized. Using the NSOM/QD and confocal imaging systems, we found that cold caused microscale redistribution of lipid raft markers, GM1 for lipid and CD59 for protein, from the peripheral part of microdomains to the central part on Jurkat T cells, and that cold also induced the nanoscale size-enlargement (1/3- to 2/3-fold) of the nanoclusters of lipid raft markers and even the colocalization of GM1 and CD59 nanoclusters. These findings indicate cold-induced lateral rearrangement/coalescence of raft-related membrane heterogeneity. The cold-induced re-distribution of lipid raft markers under a nearly-natural condition provide clues for their alternations, and help to propose a model in which raft lipids associate themselves or interact with protein components to generate functional membrane heterogeneity in response to stimulus. The data also underscore the possible cold-induced artifacts in early-described cold-related experiments and the detergent-resistance-based analyses of lipid rafts at 4°C, and provide a biophysical explanation for recently-reported cold-induced activation of signaling pathways in T cells. Importantly, our fluorescence-topographic NSOM imaging demonstrated that GM1/CD59 raft markers distributed and re-distributed at mounds but not depressions of T-cell membrane fluctuations. Such mound-top distribution of lipid raft markers or lipid rafts provides spatial advantage for lipid rafts or contact molecules interacting readily with neighboring cells or free molecules

Using web mining to discover learning patterns in course management systems

Title from PDF of title page (University of Missouri--Columbia, viewed on Sept.8, 2010).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Dissertation advisor: Dr. James Laffey.Vita.Ph. D. University of Missouri--Columbia 2009.[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Since E-learning in Course Management System (CMS) is a growing form for learning and teaching in higher education, it is key for us to identify and describe student behavior and patterns of activity in CMS. Understanding student behaviors and patterns of activities may lead to better approaches for supporting online learning. These approaches in turn can support more effective teaching and improve learning outcomes. Data mining (including web mining) is a recognized approach for building knowledge and value in business and commercial information systems. Multiple data mining techniques have potential for application in a comprehensive course management system. Three main web mining methods (Classification, Association Rule and Clustering) have been used on the data from a CMS (WebCT).The primary finding of this research was to suggest that web mining can be an approach that educational researchers can use, and when combined with other forms of data collection, has potential for adding to the way we build knowledge about e-learning. A second contribution of the current study was to draw implications for how to improve the process of web mining e-learning data sets.Includes bibliographical references

Integrated Omics Analysis of Sjogren’s Syndrome

Sjögren's syndrome (SS) is a chronic autoimmune disorder clinically characterized by dry mouth and eyes. The pathogenic mechanism of SS is inadequately understood and a long delay from the start of the symptoms to final diagnosis has been frequently observed. In this paper, we aim to provide an overview about using omics technologies to discover biomarkers for SS diagnosis and understand potential pathways underlying SS pathogenesis. Omics databases relevant to SS such as Sjögren’s Syndrome Knowledge Base,  Saliva Ontology and SDxMart are also discussed

Towards a Body Fluids Ontology: A unified application ontology for basic and translational science

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with a description of how the body fluids ontology initiative may provide support to basic and translational science