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Publications

Publication Type: Conference Paper

Number of items: 112.

Franklin, Joshua D and Guidry, Alicia F and Brinkley, James F (2011) A Partnership Approach for Electronic Data Capture in Small-Scale Clinical Trials.

Wynden, Rob and Solbrig, Harold and Tu, Samson and Brinkley, James F (2011) The Value of Value Sets.

Detwiler, Landon T and Gatterbauer, Wolfgang and Louie, Brenton and Suciu, Dan and Tarczy-Hornoch, Peter (2009) Integrating and Ranking Uncertain Scientific Data.

Cook, Daniel L and Mejino, Jose L V and Neal, Maxwell L and Gennari, John H (2009) Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies.

Gennari, John H and Neal, Maxwell L and Mejino, Jose L V and Cook, Daniel L (2009) Using multiple reference ontologies: Managing composite annotations.

Neal, Maxwell L and Gennari, John H and Arts, Theo and Cook, Daniel L (2009) Advances in semantic representation for multiscale biosimulation: a case study in merging models.

Detwiler, Landon T and Suciu, Dan and Brinkley, James F (2008) Regular Paths in SparQL: Querying the NCI Thesaurus.

Cook, Daniel L and Mejino, Jose L V and Neal, Maxwell L and Gennari, John H (2008) Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology.

Shaw, Marianne and Detwiler, Landon T and Brinkley, James F and Suciu, Dan and Mejino, Jose L V (2008) Generating Application Ontologies from Reference Ontologies.

Mejino, Jose L V and Rubin, Daniel L and Brinkley, James F (2008) FMA-RadLex: An Application Ontology of Radiological Anatomy derived from the Foundational Model of Anatomy Reference Ontology.

John H, Gennari and Maxwell L, Neal and Brian E, Carlson and Daniel L, Cook (2008) Integration of multi-scale biosimulation models via light-weight semantics.

Louie, Brenton and Detwiler, Landon T and Dalvi, Nilesh and Shaker, Ron and Tarczy-Hornoch, Peter and Suciu, Dan (2007) Incorporating Uncertainty Metrics into a General-Purpose Data Integration System.

Brinkley, James F and Suciu, Dan and Detwiler, Landon T and Gennari, John H and Rosse, Cornelius (2006) A framework for using reference ontologies as a foundation for the semantic web.

Li, Hao and Gennari, John H and Brinkley, James F (2006) Model Driven Laboratory Information Management Systems.

Warren, Wayne and Agoncillo, Augusto V and Franklin, Joshua D and Brinkley, James F (2006) Intelligent web-based whole body visualization for anatomy education.

Travillian, Ravensara S and Diatchka, Kremena and Judge, Tejinder K and Wilamowska, Katarzyna and Shapiro, Linda G (2006) A Graphical User Interface for a Comparative Anatomy Information System: Design, Implementation and Usage Scenarios.

Au, Alan and Li, Xiang and Gennari, John H (2006) Differences Among Cell-structure Ontologies: FMA, GO, & CCO.

Benson, Noah and Whipple, Mark and Kalet, Ira J (2006) A Markov Model Approach to Predicting Regional Tumor Spread in the Lymphatic System of the Head and Neck.

Cho, Hansang and Corina, David P and Brinkley, James F and Ojemann, George A and Shapiro, Linda G (2005) A New Template Matching Method using Variance Estimation for Spike Sorting.

Rosse, Cornelius and Kumar, Anand and Mejino, Jose L V and Cook, Daniel L and Detwiler, Landon T and Smith, Barry (2005) A Strategy for Improving and Integrating Biomedical Ontologies.

Detwiler, Landon T and Rosse, Cornelius (2005) Knowledge Base Version Reintegration.

Bales, Nathan and Brinkley, James F and Lee, E. Sally and Mathur, Shobhit and Re, Chris and Suciu, Dan (2005) A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain.

Smith, Barry and Mejino, Jose L V and Schultz, Stefan and Kumar, Anand and Rosse, Cornelius (2005) Anatomical information science.

Warren, Wayne and Brinkley, James F (2005) Knowledge-Based, Interactive, Custom Anatomical Scene Creation for Medical Education: The Biolucida System.

Gennari, John H and Mork, Peter and Li, Hao (2005) Knowledge Transformations between Frame Systems and RDB Systems.

Wang, Kelan and Tarczy-Hornoch, Peter and Shaker, Ron and Mork, Peter and Brinkley, James F (2005) BioMediator data integration: beyond genomics to neuroscience data.

Travillian, Ravensara S and Gennari, John H and Shapiro, Linda G (2005) Of Mice and Men: Design of a Comparative Anatomy Information System.

Smith, Veronica S and Shapiro, Linda G and Hanlon, D. and Martin, Richard F and Brinkley, James F and Poliakov, Andrew V and Ojemann, George A and Corina, David P (2005) Evaluating spatial normalization methods for the human brain.

Smith, Barry and Rosse, Cornelius (2004) The Role of Foundational Relations in the Alignment of Biomedical Ontologies.

Detwiler, Landon T and Chung, Emily and Li, A. and Mejino, Jose L V and Agoncillo, Augusto V and Brinkley, James F and Rosse, Cornelius and Shapiro, Linda G (2004) A Relation-Centric Query Engine for the Foundational Model of Anatomy.

Mejino, Jose L V and Rosse, Cornelius (2004) Symbolic modeling of structural relationships in the Foundational Model of Anatomy.

Re, Chris and Brinkley, James F and Hinshaw, Kevin P and Suciu, Dan (2004) Distributed XQuery.

Gennari, John H and Silberfein, Adam and Wiley, Jesse (2004) Integrating Genomic Knowledge Sources through an Anatomy Ontology.

Rickard, K. L. and Mejino, Jose L V and Martin, Richard F and Agoncillo, Augusto V and Rosse, Cornelius (2004) Problems and Solutions with Integrating Terminologies into Evolving Knowledge Bases.

Cook, Daniel L and Mejino, Jose L V and Rosse, Cornelius (2004) Evolution of a Foundational Model of Physiology: Symbolic Representation for Functional Bioinformatics.

Detwiler, Landon T and Rosse, Cornelius and Shapiro, Linda G (2004) An Intuitive Graphical Query Interface for Protégé Knowledge Bases.

Travillian, Ravensara S and Rosse, Cornelius and Shapiro, Linda G (2003) An Approach to the Anatomical Correlation of Species through the Foundational Model of Anatomy.

Distelhorst, G. M. and Srivastava, V. and Rosse, Cornelius and Brinkley, James F (2003) A Prototype Natural Language Interface to a Large Complex Knowledge Base, the Foundational Model of Anatomy.

Mejino, Jose L V and Agoncillo, Augusto V and Rickard, K. L. and Rosse, Cornelius (2003) Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy.

Tang, Z. and Kadiyska, Y. and Li, Hao and Suciu, Dan and Brinkley, James F (2003) Dynamic XML Based Exchange of Relational Data: Application to the Human Brain Project.

Weng, C. and Kahn, M. and Gennari, John H (2002) Temporal Knowledge Representation for Scheduling Tasks in Clinical Trial Protocols.

Mork, Peter and Shaker, R. and Halevy, A. and Tarczy-Hornoch, Peter (2002) PQL: A Declarative Query Language over Dynamic Biological Schemata.

Shaker, R. and Mork, Peter and Barclay, M. and Tarczy-Hornoch, Peter (2002) A Rule Driven Bi-Directional Translation System for Remapping Queries and Result Sets Between a Mediated Schema and Heterogeneous Data Sources.

Kalet, Ira J and Whipple, Mark and Pessah, S. and Barker, J. and Austin-Seymour, M. M. and Shapiro, Linda G (2002) A Rule-based Model for Local and Regional Tumor Spread.

Teng, C. C. and Austin-Seymour, M. M. and Barker, J. and Kalet, Ira J and Shapiro, Linda G and Whipple, Mark (2002) Head and Neck Lymph Node Region Delineation with 3-D CT Image Registration.

Rosse, Cornelius and Tuttle, M. S. (2001) Explaining the Brain to a Computer.

Campbell, B. and Brinkley, James F and Rosse, Cornelius (2001) The Virtual Anatomy Lab: a Hands-On Anatomy Learning Environment .

Michael, J. and Mejino, Jose L V and Rosse, Cornelius (2001) The Role of Definitions in Biomedical Concept Representation.

Jakobovits, Rex M and Brinkley, James F and Rosse, Cornelius and Weinberger, E. (2001) Enabling Clinicians, Researchers, and Educators to Build Custom Web-Based Biomedical Information Systems.

Kinbar, K. and Martin, Richard F and Hill, J. and Mulligan, K. and Poliakov, Andrew V and Brinkley, James F and Ojemann, George A and Corina, David P (2001) Naming Deficits During Cortical Stimulation Mapping: Functional Specificity Reconsidered.

Lober, W. B. and Trigg, L. J. and Bliss, D. and Brinkley, James F (2001) IML: An Image Markup Language.

Martin, Richard F and Mejino, Jose L V and Bowden, D. M. and Brinkley, James F and Mulligan, K. and Rosse, Cornelius (2001) A Next Generation Knowledge Source: Foundational Model of Neuroanatomy.

Martin, Richard F and Mejino, Jose L V and Bowden, D. M. and Brinkley, James F and Rosse, Cornelius (2001) Foundational Model of Neuroanatomy: Implications for the Human Brain Project.

Poliakov, Andrew V and Albright, Evan M and Corina, David P and Ojemann, George A and Martin, Richard F and Brinkley, James F (2001) Server-Based Approach to Web Visualization of Integrated 3-D Medical Image Data.

Poliakov, Andrew V and Albright, Evan M and Corina, David P and Ojemann, George A and Martin, Richard F and Brinkley, James F (2001) Server-Based Approach to Web Visualization of Integrated 3-D Brain Mapping Data.

Brinkley, James F and Albright, Evan M and Kim, S. and Mejino, Jose L V and Shapiro, Linda G and Rosse, Cornelius (2000) Visible Human, Construct Thyself: The Digital Anatomist Dynamic Scene Generator.

Corina, David P and Poliakov, Andrew V and Steury, K. and Martin, Richard F and Brinkley, James F and Mulligan, K. A. and Ojemann, George A (2000) Correspondences between Language Cortex Identified by Cortical Stimulation Mapping and FMRI.

Jakobovits, Rex M and Soderland, S. and Taira, R. K. and Brinkley, James F (2000) Requirements of a Web-Based Experiment Management System.

Jakobovits, Rex M and Soderland, S. G. and Tiara, R. K. and Brinkley, James F (2000) The Web-Interfacing Repository Manager: A Framework for Developing Web-Based Multimedia Applications for Medical Research.

Lober, W. B. and Brinkley, James F (2000) A Personal Annotated Image Server.

Martin, Richard F and Poliakov, Andrew V and Mulligan, K. A. and Corina, David P and Ojemann, George A and Brinkley, James F (2000) Multi-Patient Mapping of Language Sites on 3-D Brain Models.

Martin, Richard F and Poliakov, Andrew V and Mulligan, K. A. and Kinbar, K. and Corina, David P and Maravilla, K. and Lettich, E. and Ojemann, George A and Brinkley, James F (2000) Multi-Patient Mapping of Language Sites on 3-D Brain Models.

Poliakov, Andrew V and Jakobovits, Rex M and Martin, Richard F and Corina, David P and Brinkley, James F (2000) Software Tools for Visualization and Analysis of Human Brain Data for Language Mapping.

Rosse, Cornelius and Mejino, Jose L V and Shapiro, Linda G and Brinkley, James F (2000) Visible Human, Know Thyself: The Digital Anatomist Structural Abstraction.

Agoncillo, Augusto V and Mejino, Jose L V and Rosse, Cornelius (1999) Influence of the Digital Anatomist Foundational Model on Traditional Representations of Anatomical Concepts.

Stalder, D. S. and Brinkley, James F (1999) The Digital Anatomist Foundational Model Server.

Wong, B. A. and Rosse, Cornelius and Brinkley, James F (1999) Semi-Automatic Scene Generation Using the Digital Anatomist Foundational Model.

Poliakov, Andrew V and Hinshaw, Kevin P and Rosse, Cornelius and Brinkley, James F (1999) Integration and Visualization of Multimodality Brain Data for Language Mapping.

Bowden, D. M. and Robertson, J. E. and Martin, Richard F and Dubach, M. F. and Wu, J. S. and McLean, M. R. and Brinkley, James F (1999) Web-Tools for Neuroscience Based on Neuronames, a Template Brain Atlas, Edgewarp and Geographic Information Systems Software.

Corina, David P and Steury, K. R. and Mulligan, K. A. and Hinshaw, Kevin P and Poliakov, Andrew V and Brinkley, James F and Maravilla, K. R. and Ojemann, George A (1999) A Comparison of Language Cortex Indentified by Cortical Stimulation Mapping and FMRI Techniques.

Kalet, Ira J and Wu, J. and Lease, M. and Austin-Seymour, M. M. and Brinkley, James F and Rosse, Cornelius (1999) Anatomical Information in Radiation Treatment Planning.

Kim, S. and Brinkley, James F and Rosse, Cornelius (1999) Design Features of on-Line Anatomy Information Resources: A Comparison with the Digital Anatomist.

Mejino, Jose L V and Rosse, Cornelius (1999) Conceptualization of Anatomical Spatial Entities in the Digital Anatomist Foundational Model.

Poliakov, Andrew V and Hinshaw, Kevin P and Corina, David P and Steury, K. R. and Maravilla, K. R. and Ojemann, George A and Mulligan, K. A. and Brinkley, James F (1999) Integration and Visualization of Multimodality Brain Data for Language Mapping.

Brinkley, James F (1998) The Use of Anatomical Knowledge in Medical Imaging: An Overview of the University of Washington Structural Informatics Group.

Brinkley, James F and Rosse, Cornelius (1998) Requirements for an on-Line Knowledge-Based Anatomy Information System.

Corina, David P and McBurney, S. L. and Hinshaw, Kevin P and Brinkley, James F and Lettich, E. and Ojemann, George A (1998) Left Hemisphere Specialization for American Sign Language: A Cortical Stimulation Study.

Hinshaw, Kevin P and Brinkley, James F (1998) Incorporating Constraint-Based Shape Models into an Interactive System for Functional Brain Mapping.

Mejino, Jose L V and Rosse, Cornelius (1998) The Potential of the Digital Anatomist Foundational Model for Assuring Consistency in UMLS Sources.

Neal, P. J. and Shapiro, Linda G and Rosse, Cornelius (1998) The Digital Anatomist Spatial Abstraction: A Scheme for the Spatial Description of Anatomical Features.

Rosse, Cornelius and Shapiro, Linda G and Brinkley, James F (1998) The Digital Anatomist Foundational Model: Principles for Defining and Structuring Its Concept Domain.

Brinkley, James F and Myers, L. M. and Prothero, J. S. and Heil, G. H. and Tsuruda, J. S. and Maravilla, K. R. and Ojemann, George A and Rosse, Cornelius (1997) A Structural Information Framework for Brain Mapping.

Hinshaw, Kevin P and Brinkley, James F (1997) Shape-Based Interactive Three-Dimensional Medical Image Segmentation.

Hinshaw, Kevin P and Brinkley, James F (1997) Using 3-D Shape Models to Guide Segmentation of MR Brain Images.

Jakobovits, Rex M and Brinkley, James F (1997) Managing Medical Research Data with a Web-Interfacing Repository Manager.

Modayur, Bharath R and Jakobovits, Rex M and Maravilla, K. and Ojemann, George A and Brinkley, James F (1997) Evaluation of a Visualization-Based Approach to Functional Brain Mapping.

Modayur, Bharath R and Ojemann, George A and Lettich, E. and Jakobovits, Rex M and Sundsten, John W and Brinkley, James F (1997) Information System for Mapping and Studying Cortical Language Organization.

Jakobovits, Rex M and Modayur, Bharath R and Brinkley, James F (1996) A Web-Based Repository Manager for Brain Mapping Data.

Modayur, Bharath R and Prothero, J. and Rosse, Cornelius and Jakobovits, Rex M and Brinkley, James F (1996) Visualization and Mapping of Neurosurgical Functional Data onto a 3-D MR-Based Model of the Brain Surface.

Bradley, S. W. and Rosse, Cornelius and Brinkley, James F (1995) Web-Based Access to an Online Atlas of Anatomy: The Digital Anatomist Common Gateway Interface.

Myers, L. M. and Brinkley, James F (1995) Visualization of Brain Surface Features Using Registered Partially Segmented MRI Scans.

Myers, L. M. and Prothero, J. S. and Brinkley, James F (1995) Volume Rendering of Multi-Spectral MR Data for Brain Language Site Mapping.

Rosse, Cornelius and Said, M. Ben and Eno, Kraig R and Brinkley, James F (1995) Enhancements of Anatomical Information in UMLS Knowledge Sources.

Brinkley, James F (1994) A Distributed, Object-Oriented Framework for Medical Image Management and Analysis: Application to Evaluation of Medical Image Segmentation Techniques.

Shapiro, Linda G and Tanimoto, S. L. and Brinkley, James F and Ahrens, J. P. and Jakobovits, Rex M and Lewis, L. M. (1994) A Visual Database System for Data and Experiment Management in Model-Based Computer Vision.

Brinkley, James F (1994) Educational Systems:Synopsis.

Brinkley, James F (1994) The Digital Anatomist Project.

Dailey, D. J. and Eno, Kraig R and Brinkley, James F (1994) Performance Evaluation of a Distance Learning Program.

Sundsten, John W and Brinkley, James F and Eno, Kraig R (1993) Digital Anatomist Browser: Teaching Neuroanatomy with the Use of Digital and Video-Disc Images Accessed by Computer.

Altman, R. B. and Brinkley, James F (1993) Probabilistic Constraint Satisfaction with Structural Models: Application to Organ Modelling by Radial Contours.

Conley, D. M. and Brinkley, James F and Rauschning, Wolfgang and Rosse, Cornelius (1993) A Multimedia Approach to the Study of the Mediastinum Utilizing a Computer-Generated Three-Dimensional Model.

Dailey, D. J. and Eno, Kraig R and Zick, G. L. and Brinkley, James F (1993) A Network Model for Wide Area Access to Structural Information.

Brinkley, James F (1993) The Potential for Three-Dimensional Ultrasound.

Brinkley, James F (1992) Hierarchical Geometric Constraint Networks as a Representation for Spatial Structural Knowledge.

Sundsten, John W and Brinkley, James F and Eno, Kraig R and Harris, R. M. and Kastella, K. G. (1991) Interactive Use of Videodisc Animations of Computer-Reconstructed Human Brain.

Eno, Kraig R and Sundsten, John W and Brinkley, James F (1991) A Multimedia Anatomy Browser Incorporating a Knowledge Base and 3-D Images.

Greenes, R. G. and Brinkley, James F (1990) Radiology Applications.

Rosse, Cornelius and Brinkley, James F and Prothero, J. (1990) Structural Informatics: The Representation of Anatomical Knowledge in Computer Readable Form.

Brinkley, James F and Prothero, J. S. and Prothero, John W and Rosse, Cornelius (1989) A Framework for the Design of Knowledge-Based Systems in Structural Biology.

Prothero, J. S. and Prothero, John W (1989) A Software Package in C for Interactive 3d Reconstruction and Display of Anatomical Objects from Serial Section Data.

Brinkley, James F (1988) Representing Biologic Objects as Geometric Constraint Networks.

DeVito, J. L. and Graham, J. and Schultz, G. and Sundsten, John W and Prothero, John W (1986) Morphometry of the Developing Brain in Macaca Nemestrina.

This list was generated on Sun Nov 23 07:01:18 PST 2014.