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Items submitted by Franklin, Joshua Daniel

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Number of items submitted by this user: 55

Moore, Eider B and Poliakov, Andrew V and Brinkley, James F (2005) Web-enabled 3D Multimodality Brain Visualization in Java. In Proceedings, Society for Neuroscience Annual Meeting, Washington, DC.

Detwiler, Landon T and Rosse, Cornelius and Shapiro, Linda G (2004) An Intuitive Graphical Query Interface for Protégé Knowledge Bases. In Proceedings, 7th International Protégé Conference, Bethesda, MD.

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. In Proceedings, XSym 2005, pages pp. 207-221, Trondheim, Norway.

Smith, Barry and Mejino, Jose L V and Schultz, Stefan and Kumar, Anand and Rosse, Cornelius (2005) Anatomical information science. In Proceedings, Seventh International Conference on Spatial Information Theory COSIT 2005 Lecture Notes in Computer Science 3693, pages pp. 149-164.

Warren, Wayne and Brinkley, James F (2005) Knowledge-Based, Interactive, Custom Anatomical Scene Creation for Medical Education: The Biolucida System. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 789-793, Washington, DC.

Gennari, John H and Mork, Peter and Li, Hao (2005) Knowledge Transformations between Frame Systems and RDB Systems. In Proceedings, 3rd International Conference on Knowledge Capture (K-CAP’05), pages pp. 197-198, Banff, Alberta, Canada.

Travillian, Ravensara S and Gennari, John H and Shapiro, Linda G (2005) Of Mice and Men: Design of a Comparative Anatomy Information System. In Proceedings, American Medical Informatics Association Fall Symposium.

Detwiler, Landon T and Brinkley, James F (2006) Custom Views of Reference Ontologies. In Proceedings, American Medical Informatics Association Fall Symposium, Bethesda, MD.

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. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 96-100, Bethesda, MD.

Li, Hao and Gennari, John H and Brinkley, James F (2006) Model Driven Laboratory Information Management Systems. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 484-488, Bethesda, MD.

Fong, Christine (2005) CELO: A System for Efficiently Building Informatics Solutions to Manage Biomedical Research Data. Master's Thesis, Medical Education and Biomedical Informatics, University of Washington.

Fong, Christine and Brinkley, James F (2006) Customizable Electronic Laboratory Online (CELO): A Web-based Data Management System Builder for Biomedical Research Laboratories. In Proceedings, American Medical Informatics Association Fall Symposium, Bethesda, MD.

Lincoln, Peter (2006) Surface Projection Method for Visualizing Volumetric Data. BS with Departmental Honors, Computer Science and Engineering, University of Washington.

Li, Xiang (2006) XGI: A Graphical Interface for XQuery Creation and XML Schema Visualization. Master's Thesis, Medical Education and Biomedical Informatics, University of Washington.

Smith, Barry and Ceusters, Werner and Klagges, Bert and Köhler, Jacob and Kumar, Anand and Lomax, Jane and Mungall, Chris and Neuhaus, Fabian and Rector, Alan L and Rosse, Cornelius (2005) Relations in biomedical ontologies. Genome Biology 6(5):R46.1-R46.15.

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. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 774-778, Bethesda, MD.

Poliakov, Andrew V and McLaughlin, Judy and Valentine, Geoffry and Pitkanen, Ilona and Osterhout, Lee (2007) Intrinsic Variability of GM Density Maps and its Implications to VBM Studies. In Proceedings, Human Brain Mapping, Chicago, IL.

Smith, Barry and Ashburner, Michael and Rosse, Cornelius and Bard, Jonathan and Bug, William and Ceusters, Werner and Goldberg, Louis J and Eilbeck, Karen and Ireland, Amelia and Mungall, Christopher J and OBI Consortium, The and Leontis, Neocles and Rocca‐Serra, a b and Ruttenberg, Alan and Sansone, Susanna-Assunta and Shah, Migam and Whetzel, Patricia L and Lewissi, Suzanna (2007) The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology 25(11):pp. 1251-1255. doi:10.1038/nbt1346.

Detwiler, Landon T and Brinkley, James F (2007) Querying Non-Materialized Ontology Views. In Proceedings, American Medical Informatics Association Fall Symposium, Chicago, IL.

Mejino, Jose L V and Martin, Richard F and Detwiler, Landon T and Brinkley, James F (2007) Challenges in Reconciling Different Views of Neuroanatomy in a Reference Ontology of Anatomy. In Proceedings, American Medical Informatics Association Fall Symposium, Chicago, IL.

Li, Xiang and Gennari, John H and Brinkley, James F (2007) XGI: A Graphical Interface for XQuery Creation. In Proceedings, American Medical Informatics Association Fall Symposium, Chicago, IL.

Moore, Eider B and Poliakov, Andrew V and Lincoln, Peter and Brinkley, James F (2007) MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data. BMC Bioinformatics 8:389.

Brinkley, James F and Ach, Daniel and Franklin, Joshua D and Anderson, Nicholas R and Stevens, Anne and Tarczy-Hornoch, Peter (2007) Tools for Clinical Trials Management: Handling the Norm and the Outliers. In Proceedings, American Medical Informatics Association Fall Symposium, pages 5, Chicago, IL. From Clinical Research Informatics Expo.

Yngve, Gary and Brinkley, James F and Cook, Daniel L and Shapiro, Linda G (2007) A Model Browser for Biosimulation. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 836-840, Chicago, IL.

Poliakov, Andrew V and X., Hertzenberg and Moore, Eider B and Corina, David P and Ojemann, George A and Brinkley, James F (2008) Unobtrusive Integration of Data Management With fMRI Analysis. NeuroInformatics 5(1):pp. 3-10.

Donnelly, Maureen and Bittner, Thomas and Rosse, Cornelius (2006) A formal theory for spatial representation and reasoning in biomedical ontologies. Artificial Intelligence in Medicine 36(1):pp. 1-27.

Detwiler, Landon T and Suciu, Dan and Brinkley, James F (2008) Regular Paths in SparQL: Querying the NCI Thesaurus. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 161-165, Washington, DC.

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. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 136-140, Washington, DC.

Guidry, Alicia F and Brinkley, James F and Anderson, Nicholas R and Tarczy-Hornoch, Peter (2008) Concept Mapping to Develop a Framework for Characterizing Electronic Data Capture (EDC) Systems. In Proceedings, American Medical Informatics Association Fall Symposium, pages 960, Washington, DC.

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. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 672-676, Washington, DC.

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. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 465-469, Washington, DC.

Franklin, Joshua D and Mejino, Jose L V and Detwiler, Landon T and Rubin, Daniel L and Brinkley, James F (2008) Web Service Access to Semantic Web Ontologies for Data Annotation. In Proceedings, American Medical Informatics Association Fall Symposium, pages 946, Washington, DC.

Detwiler, Landon T and Gatterbauer, Wolfgang and Louie, Brenton and Suciu, Dan and Tarczy-Hornoch, Peter (2009) Integrating and Ranking Uncertain Scientific Data. In Proceedings, International Conference on Data Engineering, Shanghai, China.

Kalet, Ira J (2009) Principles of Biomedical Informatics. Academic Press.

Detwiler, Landon T and Suciu, Dan and Franklin, Joshua D and Moore, Eider B and Poliakov, Andrew W and Lee, E Sally and Corina, David P and Ojemann, George A and Brinkley, James F (2009) Distributed XQuery-based integration and visualization of multimodality data: Application to brain mapping. . Frontiers in Neuroinformatics.

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. In Proceedings, Engineering in Medicine and Biology Conference, Montreal.

Gennari, John H and Neal, Maxwell L and Mejino, Jose L V and Cook, Daniel L (2009) Using multiple reference ontologies: Managing composite annotations. In Proceedings, International Conference on Biomedical Ontology, pages pp. 83-86, Buffalo, N.Y..

Detwiler, Landon T and Shaw, Marianne and Cook, Daniel L and Gennari, John H and Brinkley, James F (2009) Post-Coordinating Orthogonal Ontologies for Data Annotation. In Proceedings, Annual Symposium of the American Medical Informatics Association, pages 815, San Fransisco, CA.

Franklin, Joshua D and Detwiler, Landon T and Brinkley, James F (2009) Lightweight distributed XML-based integration of translational data. In Proceedings, Annual Symposium of the American Medical Informatics Association, pages 847, San Fransisco, CA.

Gu, Huanying and Wei, Duo and Mejino, Jose L V and Elhanan, Gai (2009) Relationship auditing of the FMA ontology. Journal of Biomedical Informatics 42(3):pp. 540-549.

Kalet, Ira and Mejino, Jose L V and Wang, Vania and Whipple, Mark and Brinkley, James F (2009) Content-specific auditing of a large scale anatomy ontology. Journal of Biomedical Informatics 42(3):pp. 540-549.

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. In Proceedings, Pacific Symposium on Biocomputing, pages pp. 304-315.

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. In Proceedings, Pacific Symposium on Biocomputing, Hawaii.

Turner, Jessica A and Mejino, Jose L V and Brinkley, James F and Detwiler, Landon T and Lee, Hyo Jong and Martone, Maryann E and Rubin, Daniel L (2010) Application of neuroanatomical ontologies for neuroimaging data annotation. Frontiers in Neuroinformatics 4(10):pp. 1-12.

Shen, Terry H and Detwiler, Landon T and Tarczy-Hornoch, Peter and Cadag, Eithon and Carlson, Christopher S (2010) Evaluation of probabilistic and logical inference for a SNP annotation system. Journal of Biomedical Informatics 43(3):pp. 407-418.

Nichols, Nolan and Perlmutter, Aaron and Mejino, Jose L V and Brinkley, James F (2010) Representing Neural Connectivity in the Foundational Model of Anatomy Ontology. In Proceedings, Annual Symposium of the American Medical Informatics Association, Washington, DC.

Mejino, Jose L V and Detwiler, Landon T and Turner, Jessica A and Martone, Maryann E and Rubin, Daniel L and Brinkley, James F (2010) Enabling RadLex with the Foundational Model of Anatomy Ontology to Organize and Integrate Neuro-imaging Data. In Proceedings, Annual Symposium of the American Medical Informatics Association, pages 1171, Washington, DC.

Detwiler, Landon T and Shaw, Marianne and Brinkley, James F (2010) Ontology View Query Management. In Proceedings, Annual Symposium of the American Medical Informatics Association, pages 1023, Washington, DC.

Brinkley, James F and Turner, Jessica A and Detwiler, Landon T and Mejino, Jose L V and Martone, Maryanne E and Rubin, Daniel L (2010) Intelligent Queries over BIRN Data using the Foundational Model of Anatomy and a Distributed Query-Based Data Integration System. In Proceedings, Annual Symposium of the American Medical Informatics Association, pages 989, Washington, DC.

Oldenkamp, Paul (2010) Guide to Low Cost Electronic Data Capture Systems for Clinical Trials. Technical Report, Center for Clinical and Translational Research, Seattle Children's Research Institute.

Franklin, Joshua D and Guidry, Alicia F and Brinkley, James F (2011) A Partnership Approach for Electronic Data Capture in Small-Scale Clinical Trials. In Proceedings, Clinical Research Informatics Summit of the American Medical Informatics Association, pages 10, San Francisco, CA.

Detwiler, Landon T and Brinkley, James F (2011) Value Sets via Ontology Views. In Proceedings, Clinical Research Informatics Summit of the American Medical Informatics Association, pages 100, San Francisco, CA.

Nichols, Nolan and Detwiler, Landon T and Franklin, Joshua D and Brinkley, James F (2011) Distributed Queries for Quality Control Checks in Clinical Trials. In Proceedings, Clinical Research Informatics Summit of the American Medical Informatics Association, pages 115, San Francisco, CA.

Wynden, Rob and Solbrig, Harold and Tu, Samson and Brinkley, James F (2011) The Value of Value Sets. In Proceedings, Clinical Research Informatics Summit of the American Medical Informatics Association, pages pp. 162-163, San Francisco, CA.

Shaw, Marianne and Detwiler, Landon T and Noy, N. F. and Brinkley, James F and Suciu, Dan (2011) vSPARQL: A View Definition Language for the Semantic Web. Journal of Biomedical Informatics 44(1):pp. 102-117.