UW-SIG Publications
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Subject based institutional repository for materials produced or associated with this structural biological computing research group. Not all items are available as full text, and are only displayed as bibliographic entries on the site. In addition to the search and browse functions conference papers are highlighted for the years 1998-2004.
Mostrando recursos 1 - 20 de 206
1.
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration - Smith, Barry; Ashburner, Michael; Rosse, Cornelius; Bard, Jonathan; Bug, William; Ceusters, Werner; Goldberg, Louis J; Eilbeck, Karen; Ireland, Amelia; Mungall, Christopher J; OBI Consortium, The; Leontis, Neocles; Rocca?Serra, a b
Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Shah, Migam; Whetzel, Patricia L; Lewissi, Suzanna
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...
2.
Of Mice and Men: Design of a Comparative Anatomy Information System - Travillian, Ravensara S; Gennari, John H; Shapiro, Linda G
In previous work, we proposed an approach called the Structural Difference Method (SDM) to correlating the anatomy of Homo sapiens with selected species, using the Foundational Model of Anatomy (FMA) as a framework and graph matching as a method, for determining similarities and differences between species. In this paper, we present the design of a comparative anatomy information system that utilizes the SDM and allows users to issue queries to determine the similarities and differences between two species. Our system will serve as a pilot project for cross-species anatomical information collection, storage, and retrieval. The underlying data structure of a...
3.
Evaluating spatial normalization methods for the human brain - Smith, Veronica S; Shapiro, Linda G; Hanlon, D.; Martin, Richard F; Brinkley, James F; Poliakov, Andrew V; Ojemann, George A; Corina, David P
Cortical stimulation mapping (CSM) studies have shown cortical locations for language function are highly variable from one subject to the next. If individual variation can be normalized, patterns of language organization may emerge that were heretofore hidden. In order to uncover this pattern, computer-aided spatial normalization to a common atlas is required. Our problem was how to determine which spatial normalization method was best for the given research application. We developed key metrics to measure accuracy of a surface-based (Caret) and volume-based (SPM2) method. We specified that the optimal method would i) minimize variation as measured by spread reduction between...
4.
Classification of functional brain data for multimedia retrieval - Cho, Hansang
This study introduces new signal processing methods for extracting meaningful information from brain signals (functional magnetic resonance imaging and single unit recording) and proposes a content-based retrieval system for functional brain data. First, a new method that combines maximal overlapped discrete wavelet transforms (MODWT) and dynamic time warping (DTW) is presented as a solution for dynamically detecting the hemodynamic response from fMRI data. Second, a new method for neuron spike sorting is presented that uses the maximal overlap discrete wavelet transform and rotated principal component analysis. Third, a procedure to characterize firing patterns of neuron spikes from the human brain,...
5.
Custom Views of Reference Ontologies - Detwiler, Landon T; Brinkley, James F
Generating views over reference ontologies allows them to be customized for use within specific application contexts. In this project we investigated the operations necessary to generate one such custom ontology view. We catalogued the involved operations as a first step in defining the requirements of a formal view definition language.
6.
A framework for using reference ontologies as a foundation for the semantic web - Brinkley, James F; Detwiler, Landon T; Gennari, John H; Rosse, Cornelius; Suciu, Dan
The semantic web is envisioned as an evolving set of local ontologies that are gradually linked together into a global knowledge network. Many such local application ontologies are being built, but it is difficult to link them together because of incompatibilities and lack of adherence to ontology standards. Reference ontologies are an emerging ontology type that attempt to represent deep knowledge of basic science in a principled way that allows them to be re-used in multiple ways, just as the basic sciences are re-used in clinical applications. As such they have the potential to be a foundation for the semantic...
7.
Model Driven Laboratory Information Management Systems - Li, Hao; Gennari, John H.; Brinkley, James F
Scientists in small research labs need more robusttools than spreadsheets to manage their data.However, no suitable laboratory informationmanagement systems (LIMS) are readily available;they are either too costly or too complex. We havetherefore developed Seedpod, a model driven LIMSthat allows users to create an integrated model of aLIMS without programming. Seedpod then automaticallyproduces a relational database from the model,and dynamically generates a web-based graphicaluser interface. Our goal is to make LIMS easier touse by decreasing development time and cost, therebyallowing researchers to focus on producing andcollecting data.
8.
CELO: A System for Efficiently Building Informatics Solutions to Manage Biomedical Research Data - Fong, Christine
Traditional data management methods are unable to sufficiently support growing trends in biomedical research such as collection of larger data sets, use of diverse data types, and sharing of data among multiple laboratories. Although many technologies are readily available to help laboratories build data management solutions, many laboratories are not taking advantage of them. This may be due to hardware and software costs, the need for an informaticist to build customized solutions, and long development times.
Several systems already exist which attempt to address the informatics needs of biomedical researchers. A review of these systems has revealed the benefits and...
9.
Customizable Electronic Laboratory Online (CELO): A Web-based Data Management System Builder for Biomedical Research Laboratories - Fong, Christine; Brinkley, James F
A common challenge among todays biomedical research labs is managing growing amounts of research data. In order to reduce the time and resource costs of building data management tools, we designed the Customizable Electronic Laboratory Online (CELO) system. CELO automatically creates a generic database and web interface for laboratories that submit a simple web registration form. Laboratories can then use a collection of predefined XML templates to assist with the design of a database schema. Users can immediately utilize the web-based system to query data, manage multimedia files, and securely share data remotely over the internet.
10.
Surface Projection Method for Visualizing Volumetric Data - Lincoln, Peter
The goal of this project was to explore, develop, and implement additional visualization methods for volumetric data within MindSeer. This paper discusses the implementation of one such visualization method, the surface projection method, and compares it to other existing methods.
11.
A performant XQuery to SQL translator - Re, Chris; Brinkley, James; Suciu, Dan
We describe a largely complete and efficient XQuery to SQL translation for XML publishing. Our translation supports the entire XQuery language, except for functions, if statements and upwards navigation axes. The system has three important properties. First, it preserves the correct XQuery semantics. This is accomplished by first translating XQuery into core-XQuery, using a complete XQuery implementation, Galax. Second, we optimize the resulting SQL queries. We develop a comprehensive framework for optimizing the XQuery to SQL translation, which is effective for a wide range of XQuery workloads. Third, our translation is platform independent. Our system achieves high degree of efficiency...
12.
Contrast Masking and Differential fMRI Brain Responses Relative to a Rest Condition - Johnson, Clark L; Richards, Todd L; Poliakov, Andrew V; Aylward, Elizabeth H
Analysis of an fMRI protocol often involves a comparison of the fMRI brain signal between task A (e.g., zero-back working memory task) and task B (e.g., 2-back working memory). When a third reference condition such as fixation is included then comparisons between the main tasks and this reference are also possible (e.g. 2-back versus fixation). In this case, the fMRI signal from each voxels response with regard to fixation can be classified into one of six possible response patterns (1), three for A > B (both A and B > fixation; both A and B < fixation; A > fixation...
13.
Intelligent web-based whole body visualization for anatomy education - Warren, W.V.; Agoncillo, A.; Franklin, J.D.; Brinkley, J.F.
In this report, we describe a process of applying intelligent scene generation to a newly acquired complete set of 3D models representing the whole human body.
14.
XGI: A Graphical Interface for XQuery Creation and XML Schema Visualization - Li, Xiang
XML (Extensible Markup Language) is used in many contexts of modern information technology to facilitate sharing of information between heterogeneous data sources and inter-platform applications. The prevalence of XML implementation in data storage and exchange necessitates a method to adequately query XML data. The World Wide Web Consortium (W3C) is proposing XQuery as the standard querying language for semistructured XML data. XQuery is designed for experienced database programmers, since its syntax and capabilities are analogous to the SQL relational query language. Therefore, the inherent complexity of formulating XQuery statements makes it an intimidating task for anyone, except an expert in...
15.
Lightweight XML-based query, integration and visualization of distributed, multimodality brain imaging data - Brinkley, JF; Poliakov, AV; Moore, EB; Detwiler, LT; Franklin, JD; Corina, DP; Ojemann, GA
A need of many neuroimaging researchers is to integrate multimodality brain data that may be stored in separate databases. To address this need we have developed a framework that provides a uniform XML-based query interface across multiple online data sources. The development of this framework is driven by the need to integrate neurosurgical and neuroimaging data related to language. The data sources for the language studies are 1) a web-accessible relational database of neurosurgical cortical stimulation mapping data (CSM) that includes patient-specific 3-D coordinates of each stimulation site mapped to an MRI reconstruction of the patient brain surface; and 2)...
16.
Relations in biomedical ontologies - Smith, Barry; Werner, Ceusters; Bert, Klagges; Jacob, Köhler; Anand, Kumar; Jane, Lomax; Chris, Mungall; Fabian, Neuhaus; Alan L, Rector; Cornelius, Rosse
To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
17.
A Graphical User Interface for a Comparative Anatomy Information System: Design, Implementation and Usage Scenarios - Travillian, Ravensara S; Diatchka, Kremena; Judge, Tejinder K; Wilamowska, Katarzyna; Shapiro, Linda G
Building on our previous design work in the development of the Structural Difference Method (SDM) for describing anatomical similarities and differences across species, we describe the design and implementation of the associated comparative anatomy information system (CAIS) interface and provide scenarios from the literature for its use by research scientists.
18.
The Foundational Model of Anatomy Ontology - Rosse, Cornelius; Mejino, Jose L V
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...
19.
The Digital Anatomist Information System and Its Use in the Generation and Delivery of Web-Based Anatomy Atlases - Brinkley, James F; Bradley, S. W.; Sundsten, John W; Rosse, Cornelius
Advances in network and imaging technology, coupled with the availability of 3-D datasets
such as the Visible Human, provide a unique opportunity for developing information systems
in anatomy that can deliver relevant knowledge directly to the clinician, researcher or educator. A software framework is described for developing such a system within a distributed architecture that includes spatial and symbolic anatomy information resources, Web and custom servers, and authoring and end-user client programs. The authoring tools have been used to create 3-D atlases of the brain, knee and thorax that are used both locally and throughout the world. For the one and a...
20.
Differences Among Cell-structure Ontologies: FMA, GO, & CCO - Au, Alan; Li, Xiang; Gennari, John
When different groups create models or ontologies of the same knowledge domain, this creates challenges for knowledge sharing. To identify these challenges, we compare cellular structure as modeled by the Foundational Model of Anatomy (FMA), the Gene Ontology (GO), and the Cell Component Ontology (CCO). Although these ontologies all model the physical anatomy of a cell, the actual differences among them are substantial. In this paper, we provide a description and analysis of these differences.
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