Research Topics
| Daniel L RubinSummaryAffiliation: Stanford University Country: USA Publications
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Detail Information
Publications
MScanner: a classifier for retrieving Medline citationsGraham L Poulter
UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
BMC Bioinformatics 9:108. 2008....- Comparison of concept recognizers for building the Open Biomedical AnnotatorNigam H Shah
Centre for Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 10:S14. 2009..The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data... - Computational neuroanatomy: ontology-based representation of neural components and connectivityDaniel L Rubin
Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
BMC Bioinformatics 10:S3. 2009.... - Ontology-assisted analysis of Web queries to determine the knowledge radiologists seekDaniel L Rubin
Department of Radiology, Stanford University, Richard M Lucas Center, 1201 Welch Road, Office P285, Stanford, CA 94305 5488, USA
J Digit Imaging 24:160-4. 2011..0001). We conclude that RadLex can enable processing and categorization of user queries of Web resources and enable understanding the types of information users seek from radiology knowledge resources on the Web... - The caBIG annotation and image Markup projectDavid S Channin
Department of Radiology, Feinberg School of Medicine, Northwestern University, 737 N Michigan Avenue, Suite 1600, Chicago, IL 60611, USA
J Digit Imaging 23:217-25. 2010..The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM... - Creating and curating a terminology for radiology: ontology modeling and analysisDaniel L Rubin
Section of Medical Informatics, Stanford University, MSOB X 215, 251 Campus Drive, Stanford, CA 94305, USA
J Digit Imaging 21:355-62. 2008..We believe that adopting an ontology representation of RadLex will permit more widespread use of the terminology and make it easier to collect feedback from the community that will ultimately lead to improving RadLex... - Biomedical ontologies: a functional perspectiveDaniel L Rubin
Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
Brief Bioinform 9:75-90. 2008.... - Use of microcalcification descriptors in BI-RADS 4th edition to stratify risk of malignancyElizabeth S Burnside
Department of Radiology, University of Wisconsin Medical School, E3 311 Clinical Science Center, 600 Highland Ave, Madison, WI 53792 3252, USA
Radiology 242:388-95. 2007.... - Protégé: a tool for managing and using terminology in radiology applicationsDaniel L Rubin
Section of Medical Informatics, Stanford University, MSOB X 215, 251 Campus Drive, Stanford, CA 94305, USA
J Digit Imaging 20:34-46. 2007..In this report, we describe Protégé's features and its particular advantages in the radiology domain in the creation, maintenance, and use of radiology terminology... - Computing human image annotationDavid S Channin
Department of Radiology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
Conf Proc IEEE Eng Med Biol Soc 2009:7065-8. 2009..This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities... - Annotation and query of tissue microarray data using the NCI ThesaurusNigam H Shah
Stanford Medical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 8:296. 2007..These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult... - A resource to acquire and summarize pharmacogenetics knowledge in the literatureDaniel L Rubin
Department of Genetics, Stanford University, Stanford, CA 94305-5210, USA
Medinfo 11:793-7. 2004..This resource is growing, containing entries for 138 genes and 215 drugs of pharmacogenetics significance, and is a core component of PharmGKB, a pharmacogenetics knowledge base (http://www.pharmgkb.org)... - The ACR BI-RADS experience: learning from historyElizabeth S Burnside
Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53792 3252, USA
J Am Coll Radiol 6:851-60. 2009..The history of this lexicon illustrates a series of challenges and instructive successes that provide a valuable guide for other groups that aspire to develop similar lexicons in the future... - Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational modelsDaniel L Rubin
Department of Genetics, Stanford Medical Informatics, MSOB X 215, Stanford, CA 94305 5479, USA
Bioinformatics 18:S207-15. 2002.... - A prototype symbolic model of canonical functional neuroanatomy of the motor systemIon Florin Talos
Department of Radiology, Brigham and Women s Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
J Biomed Inform 41:251-63. 2008..Although the scope of our current prototype ontology is limited to a particular functional system in the brain, it may be possible to adapt this approach for modeling other brain functional systems as well... - Automated semantic indexing of figure captions to improve radiology image retrievalCharles E Kahn
Division of Informatics, Department of Radiology, Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, WI 53226, USA
J Am Med Inform Assoc 16:380-6. 2009..We explored automated concept-based indexing of unstructured figure captions to improve retrieval of images from radiology journals... - Semantic reasoning with image annotations for tumor assessmentMia A Levy
Stanford University, Stanford, CA, USA
AMIA Annu Symp Proc 2009:359-63. 2009..Our methods enable automated inference of semantic information about cancer lesions in images... - Indexing pharmacogenetic knowledge on the World Wide WebRuss B Altman
Department of Genetics, Stanford Medical Informatics, Stanford University, Stanford, California, USA
Pharmacogenetics 13:3-5. 2003 - A bayesian network for differentiating benign from malignant thyroid nodules using sonographic and demographic featuresYueyi I Liu
Department of Radiology, Stanford University School of Medicine, Richard M Lucas Center, CA 94305, USA
AJR Am J Roentgenol 196:W598-605. 2011.... - A statistical approach to scanning the biomedical literature for pharmacogenetics knowledgeDaniel L Rubin
Section of Medical Informatics, MSOB X 215, Stanford, CA 94305, USA
J Am Med Inform Assoc 12:121-9. 2005..The goal of the authors was to develop an automated method to identify articles in Medline citations that contain pharmacogenetics data pertaining to gene-drug relationships... - Using ontologies linked with geometric models to reason about penetrating injuriesDaniel L Rubin
Stanford Medical Informatics, MSOB X 215, Stanford University, Stanford, CA 94305, USA
Artif Intell Med 37:167-76. 2006..We are developing a methodology to automate reasoning about penetrating injuries using canonical knowledge combined with specific subject image data... - Informatics in radiology: an information model of the DICOM standardCharles E Kahn
Department of Radiology, Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, Wis 53226, USA
Radiographics 31:295-304. 2011.... - Informatics in radiology: RADTF: a semantic search-enabled, natural language processor-generated radiology teaching fileBao H Do
Department of Radiology, Stanford University Hospitals and Clinics, 300 Pasteur Dr, Room H1307, Stanford, CA 94305, USA
Radiographics 30:2039-48. 2010..RADTF combines a compact representation of the teaching-relevant content in radiology reports and a versatile search engine with the scale of the entire RIS-PACS collection of case material... - Toward best practices in radiology reportingCharles E Kahn
Department of Radiology, Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, WI 53226, USA
Radiology 252:852-6. 2009..The committee's charter provides an opportunity to improve the organization, content, readability, and usefulness of the radiology report and to advance the efficiency and effectiveness of the reporting process... - An ontology for PACS integrationCharles E Kahn
Division of Informatics, Department of Radiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
J Digit Imaging 19:316-27. 2006..Ontologies can represent radiological and clinical knowledge to integrate PACS with the clinical enterprise and to support the radiology interpretation process... - Evaluation of negation and uncertainty detection and its impact on precision and recall in searchAndrew S Wu
Department of Radiology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA
J Digit Imaging 24:234-42. 2011..Our approach may be useful to adopt into current report retrieval systems to help radiologists to more accurately search for radiology reports... - Informatics in radiology: Measuring and improving quality in radiology: meeting the challenge with informaticsDaniel L Rubin
Department of Radiology, Stanford University, Richard M Lucas Center, 1201 Welch Rd, Office P285, Stanford, CA 94305 5488, USA dlrubin stanford edu
Radiographics 31:1511-27. 2011..Institutions can tackle the challenges of assessing and improving quality in radiology by means of informatics... - Automated temporal tracking and segmentation of lymphoma on serial CT examinationsJiajing Xu
Department of Electrical Engineering, Stanford University, Stanford, California 94305
Med Phys 38:5879. 2011..It potentially will be useful to streamline and improve cancer lesion measurement and tracking and to improve assessment of cancer treatment response... - A Controlled Vocabulary to Represent Sonographic Features of the Thyroid and its application in a Bayesian Network to Predict Thyroid Nodule MalignancyYueyi I Liu
Department of Radiology, Stanford University, Stanford, CA
Summit on Translat Bioinforma 2009:68-72. 2009..Controlled terminology for describing thyroid radiology findings could be useful to characterize thyroid nodules and could enable decision support applications... - Automated retrieval of CT images of liver lesions on the basis of image similarity: method and preliminary resultsSANDY A NAPEL
Department of Radiology, Stanford University School of Medicine, James H Clark Center S323, Stanford, CA 94305 5450, USA
Radiology 256:243-52. 2010.... - Informatics methods to enable patient-centered radiologyDaniel L Rubin
Department of Radiology and the Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305, USA
Acad Radiol 16:524-34. 2009.... - A data warehouse for integrating radiologic and pathologic dataDaniel L Rubin
Stanford Medical Informatics, Stanford, California 94305, USA
J Am Coll Radiol 5:210-7. 2008.... - National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledgeDaniel L Rubin
Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA
OMICS 10:185-98. 2006.... - Integration of Imaging Signs into RadLexMatthew W Shore
Department of Radiology, Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, WI, 53226, USA
J Digit Imaging 25:50-5. 2012..The addition of imaging signs to RadLex augments its use to index the radiology literature, create and interpret clinical radiology reports, and retrieve relevant cases and images... - Bayesian network to predict breast cancer risk of mammographic microcalcifications and reduce number of benign biopsy results: initial experienceElizabeth S Burnside
Department of Radiology, University of Wisconsin Medical School, E3 311 Clinical Science Center, 600 Highland Ave, Madison, WI 53792 3252, USA
Radiology 240:666-73. 2006.... - Using an ontology of human anatomy to inform reasoning with geometric modelsDaniel L Rubin
Stanford Medical Informatics, Stanford, California 94305 5479, USA
Stud Health Technol Inform 111:429-35. 2005..To accomplish this, we needed to develop an architecture to combine geometric data with anatomic knowledge and reasoning services that use this information to predict the consequences of injuries... - PharmGKB: the Pharmacogenetics Knowledge BaseMicheal Hewett
Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford, CA 94305 5479, USA
Nucleic Acids Res 30:163-5. 2002..The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001... - Using a Bayesian network to predict the probability and type of breast cancer represented by microcalcifications on mammographyElizabeth S Burnside
Department of Radiology, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA
Stud Health Technol Inform 107:13-7. 2004.... - A probabilistic expert system that provides automated mammographic-histologic correlation: initial experienceElizabeth S Burnside
Department of Radiology, University of California School of Medicine, Box 1667, San Francisco, CA 94143 1667, USA
AJR Am J Roentgenol 182:481-8. 2004....