Daniel L Rubin

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc MScanner: a classifier for retrieving Medline citations
    Graham L Poulter
    UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
    BMC Bioinformatics 9:108. 2008
  2. pmc Comparison of concept recognizers for building the Open Biomedical Annotator
    Nigam H Shah
    Centre for Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
    BMC Bioinformatics 10:S14. 2009
  3. pmc Ontology-assisted analysis of Web queries to determine the knowledge radiologists seek
    Daniel 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
  4. pmc Computational neuroanatomy: ontology-based representation of neural components and connectivity
    Daniel L Rubin
    Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
    BMC Bioinformatics 10:S3. 2009
  5. pmc The caBIG annotation and image Markup project
    David 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
  6. pmc Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer
    Viswam S Nair
    Division of Pulmonary and Critical Care Medicine, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
    Cancer Res 72:3725-34. 2012
  7. pmc Creating and curating a terminology for radiology: ontology modeling and analysis
    Daniel 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
  8. pmc Informatics in radiology: An open-source and open-access cancer biomedical informatics grid annotation and image markup template builder
    Pattanasak Mongkolwat
    Department of Radiology, Feinberg School of Medicine, Northwestern University, 737 N Michigan Ave, Suite 1600, Chicago, IL 60611, USA
    Radiographics 32:1223-32. 2012
  9. ncbi request reprint Biomedical ontologies: a functional perspective
    Daniel L Rubin
    Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
    Brief Bioinform 9:75-90. 2008
  10. pmc Protégé: a tool for managing and using terminology in radiology applications
    Daniel 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

Detail Information

Publications49

  1. pmc MScanner: a classifier for retrieving Medline citations
    Graham L Poulter
    UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
    BMC Bioinformatics 9:108. 2008
    ....
  2. pmc Comparison of concept recognizers for building the Open Biomedical Annotator
    Nigam 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...
  3. pmc Ontology-assisted analysis of Web queries to determine the knowledge radiologists seek
    Daniel 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...
  4. pmc Computational neuroanatomy: ontology-based representation of neural components and connectivity
    Daniel L Rubin
    Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
    BMC Bioinformatics 10:S3. 2009
    ....
  5. pmc The caBIG annotation and image Markup project
    David 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...
  6. pmc Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer
    Viswam S Nair
    Division of Pulmonary and Critical Care Medicine, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
    Cancer Res 72:3725-34. 2012
    ..Together, our findings suggest that leveraging tumor genomics with an expanded collection of PET-FDG imaging features may enhance our understanding of FDG uptake as an imaging biomarker beyond its association with glycolysis...
  7. pmc Creating and curating a terminology for radiology: ontology modeling and analysis
    Daniel 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...
  8. pmc Informatics in radiology: An open-source and open-access cancer biomedical informatics grid annotation and image markup template builder
    Pattanasak Mongkolwat
    Department of Radiology, Feinberg School of Medicine, Northwestern University, 737 N Michigan Ave, Suite 1600, Chicago, IL 60611, USA
    Radiographics 32:1223-32. 2012
    ....
  9. ncbi request reprint Biomedical ontologies: a functional perspective
    Daniel L Rubin
    Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
    Brief Bioinform 9:75-90. 2008
    ....
  10. pmc Protégé: a tool for managing and using terminology in radiology applications
    Daniel 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...
  11. ncbi request reprint Use of microcalcification descriptors in BI-RADS 4th edition to stratify risk of malignancy
    Elizabeth 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
    ....
  12. doi request reprint Computing human image annotation
    David 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...
  13. pmc Integration of imaging signs into RadLex
    Matthew W Shore
    Department of Radiology, Medical College of Wisconsin, 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...
  14. pmc Annotation and query of tissue microarray data using the NCI Thesaurus
    Nigam 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...
  15. pmc A prototype symbolic model of canonical functional neuroanatomy of the motor system
    Ion 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...
  16. pmc Automated semantic indexing of figure captions to improve radiology image retrieval
    Charles 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...
  17. pmc The ACR BI-RADS experience: learning from history
    Elizabeth 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...
  18. ncbi request reprint A resource to acquire and summarize pharmacogenetics knowledge in the literature
    Daniel L Rubin
    Department of Genetics, Stanford University, Stanford, CA 94305 5210, USA
    Stud Health Technol Inform 107:793-7. 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)...
  19. ncbi request reprint Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models
    Daniel L Rubin
    Department of Genetics, Stanford Medical Informatics, MSOB X 215, Stanford, CA 94305 5479, USA
    Bioinformatics 18:S207-15. 2002
    ..As experimental and analytical methods change, and as biological knowledge advances, the data storage requirements and types of queries needed may also change...
  20. pmc The role of informatics in health care reform
    Yueyi I Liu
    Department of Radiology, Stanford University, Richard M Lucas Center, CA 94305 5488, USA
    Acad Radiol 19:1094-9. 2012
    ..We also discuss informatics related to the increasing imperatives of state and local regulations (such as radiation dose tracking) and quality initiatives...
  21. pmc Semantic reasoning with image annotations for tumor assessment
    Mia 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...
  22. pmc Informatics in radiology: an information model of the DICOM standard
    Charles E Kahn
    Department of Radiology, Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, Wis 53226, USA
    Radiographics 31:295-304. 2011
    ....
  23. doi request reprint A bayesian network for differentiating benign from malignant thyroid nodules using sonographic and demographic features
    Yueyi 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
    ....
  24. pmc A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge
    Daniel 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...
  25. ncbi request reprint Using ontologies linked with geometric models to reason about penetrating injuries
    Daniel 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...
  26. ncbi request reprint Indexing pharmacogenetic knowledge on the World Wide Web
    Russ B Altman
    Department of Genetics, Stanford Medical Informatics, Stanford University, Stanford, California, USA
    Pharmacogenetics 13:3-5. 2003
  27. pmc Informatics in radiology: improving clinical work flow through an AIM database: a sample web-based lesion tracking application
    Aaron C Abajian
    Departments of Radiology and Medicine, Stanford University School of Medicine, Richard M Lucas Center, Stanford University, Stanford, CA 94305, USA
    Radiographics 32:1543-52. 2012
    ....
  28. pmc Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results
    Olivier Gevaert
    Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Radiology 264:387-96. 2012
    ....
  29. doi request reprint Informatics in radiology: RADTF: a semantic search-enabled, natural language processor-generated radiology teaching file
    Bao 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...
  30. doi request reprint Toward best practices in radiology reporting
    Charles 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...
  31. pmc Evaluation of negation and uncertainty detection and its impact on precision and recall in search
    Andrew 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...
  32. pmc An ontology for PACS integration
    Charles 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...
  33. doi request reprint Informatics in radiology: Measuring and improving quality in radiology: meeting the challenge with informatics
    Daniel 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...
  34. pmc Automated temporal tracking and segmentation of lymphoma on serial CT examinations
    Jiajing Xu
    Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
    Med Phys 38:5879-86. 2011
    ..In this paper, we show a method to automatically and reproducibly identify and segment abnormal lymph nodes in serial computed tomography (CT) exams...
  35. doi request reprint A picture is worth a thousand words: needs assessment for multimedia radiology reports in a large tertiary care medical center
    Lina Nayak
    Department of Radiology, Stanford University Medical Center, Stanford, CA
    Acad Radiol 20:1577-83. 2013
    ..The purposes of this study are to identify referring physicians' preferences about radiology reports and to quantify their perceived value of multimedia reports (with embedded images) compared with narrative text reports...
  36. pmc Modeling perceptual similarity measures in CT images of focal liver lesions
    Jessica Faruque
    Electrical Engineering Department, Stanford University, James H Clark Center, 318 Campus Drive S 324, Stanford, CA 94305, USA
    J Digit Imaging 26:714-20. 2013
    ..Our objective was to develop a statistical model that predicts the number of readers (N) necessary to achieve acceptable levels of variability...
  37. doi request reprint Informatics methods to enable patient-centered radiology
    Daniel 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
    ....
  38. pmc A Controlled Vocabulary to Represent Sonographic Features of the Thyroid and its application in a Bayesian Network to Predict Thyroid Nodule Malignancy
    Yueyi 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...
  39. pmc Automated retrieval of CT images of liver lesions on the basis of image similarity: method and preliminary results
    SANDY 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
    ....
  40. ncbi request reprint National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge
    Daniel L Rubin
    Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA
    OMICS 10:185-98. 2006
    ....
  41. doi request reprint A data warehouse for integrating radiologic and pathologic data
    Daniel L Rubin
    Stanford Medical Informatics, Stanford, California 94305, USA
    J Am Coll Radiol 5:210-7. 2008
    ....
  42. pmc Dynamic contrast-enhanced MRI-based biomarkers of therapeutic response in triple-negative breast cancer
    Daniel I Golden
    Department of Radiology, Stanford University Medical Center, Stanford, California, USA
    J Am Med Inform Assoc 20:1059-66. 2013
    ..To predict the response of breast cancer patients to neoadjuvant chemotherapy (NAC) using features derived from dynamic contrast-enhanced (DCE) MRI...
  43. pmc Automated drusen segmentation and quantification in SD-OCT images
    Qiang Chen
    Department of Radiology, Stanford University, Stanford, CA 94305, USA School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China Electronic address
    Med Image Anal 17:1058-72. 2013
    ....
  44. pmc Snake model-based lymphoma segmentation for sequential CT images
    Qiang Chen
    Department of Radiology, Stanford University, Stanford, CA, USA
    Comput Methods Programs Biomed 111:366-75. 2013
    ..58s. The proposed segmentation algorithm for lymph nodes is fast and can achieve high segmentation accuracy, which may be useful to automate the tracking and evaluation of cancer therapy. ..
  45. pmc PharmGKB: the Pharmacogenetics Knowledge Base
    Micheal 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...
  46. ncbi request reprint Bayesian network to predict breast cancer risk of mammographic microcalcifications and reduce number of benign biopsy results: initial experience
    Elizabeth 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
    ....
  47. ncbi request reprint Using an ontology of human anatomy to inform reasoning with geometric models
    Daniel 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...
  48. ncbi request reprint A probabilistic expert system that provides automated mammographic-histologic correlation: initial experience
    Elizabeth 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
    ....
  49. ncbi request reprint Using a Bayesian network to predict the probability and type of breast cancer represented by microcalcifications on mammography
    Elizabeth 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
    ....