Jules J Berman

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Tumor taxonomy for the developmental lineage classification of neoplasms
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, Bethesda, USA
    BMC Cancer 4:88. 2004
  2. pmc Doublet method for very fast autocoding
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    BMC Med Inform Decis Mak 4:16. 2004
  3. ncbi request reprint Pathology data integration with eXtensible Markup Language
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA
    Hum Pathol 36:139-45. 2005
  4. pmc Resources for comparing the speed and performance of medical autocoders
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    BMC Med Inform Decis Mak 4:8. 2004
  5. pmc Tumor classification: molecular analysis meets Aristotle
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, Bethesda, USA
    BMC Cancer 4:10. 2004
  6. pmc The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA
    BMC Bioinformatics 5:19. 2004
  7. ncbi request reprint Zero-check: a zero-knowledge protocol for reconciling patient identities across institutions
    Jules J Berman
    Pathology Informatics, Cancer Diagnosis Program NCI NIH, Rockville, MD 20892, USA
    Arch Pathol Lab Med 128:344-6. 2004
  8. ncbi request reprint Pathology abbreviated: a long review of short terms
    Jules J Berman
    Pathology Informatics, Cancer Diagnosis Program NCI NIH, Rockville, MD 20892, USA
    Arch Pathol Lab Med 128:347-52. 2004
  9. ncbi request reprint Biomedical data integration: using XML to link clinical and research data sets
    Jules J Berman
    Pathology Informatics, Cancer Diagnosis Program, National Cancer Institute, Rockville, MD 20892, USA
    Expert Rev Mol Diagn 5:329-36. 2005
  10. ncbi request reprint Nomenclature-based data retrieval without prior annotation: facilitating biomedical data integration with fast doublet matching
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Insititute, National Institutes of Health, Bethesda, Maryland, USA
    In Silico Biol 5:313-22. 2005

Collaborators

Detail Information

Publications32

  1. pmc Tumor taxonomy for the developmental lineage classification of neoplasms
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, Bethesda, USA
    BMC Cancer 4:88. 2004
    ..A taxonomy is a list of the instances that populate a classification. The taxonomy of neoplasia attempts to list every known term for every known tumor of man...
  2. pmc Doublet method for very fast autocoding
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    BMC Med Inform Decis Mak 4:16. 2004
    ..The purpose of this paper is to describe the doublet method, a new algorithm for very fast autocoding...
  3. ncbi request reprint Pathology data integration with eXtensible Markup Language
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA
    Hum Pathol 36:139-45. 2005
    ..This manuscript gives pathologists a glimpse into how XML allows pathology data to be linked to other types of biomedical data and reduces our dependence on centralized proprietary databases...
  4. pmc Resources for comparing the speed and performance of medical autocoders
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    BMC Med Inform Decis Mak 4:8. 2004
    ....
  5. pmc Tumor classification: molecular analysis meets Aristotle
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, Bethesda, USA
    BMC Cancer 4:10. 2004
    ..The growing question facing cancer researchers is, "How can we successfully integrate the molecular, morphologic and clinical characteristics of human cancer to produce a helpful tumor classification?"..
  6. pmc The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, USA
    BMC Bioinformatics 5:19. 2004
    ..The purpose of this paper is to demonstrate how the TMA Data Exchange Specification is implemented in a prostate cancer TMA...
  7. ncbi request reprint Zero-check: a zero-knowledge protocol for reconciling patient identities across institutions
    Jules J Berman
    Pathology Informatics, Cancer Diagnosis Program NCI NIH, Rockville, MD 20892, USA
    Arch Pathol Lab Med 128:344-6. 2004
    ..Unless patient identities can be reconciled across institutions, individuals with records held in different institutions will be falsely "counted" as multiple persons when databases are merged...
  8. ncbi request reprint Pathology abbreviated: a long review of short terms
    Jules J Berman
    Pathology Informatics, Cancer Diagnosis Program NCI NIH, Rockville, MD 20892, USA
    Arch Pathol Lab Med 128:347-52. 2004
    ..During the past decade, the author has collected more than 12 000 medical abbreviations, concentrating on terms used or interpreted by pathologists...
  9. ncbi request reprint Biomedical data integration: using XML to link clinical and research data sets
    Jules J Berman
    Pathology Informatics, Cancer Diagnosis Program, National Cancer Institute, Rockville, MD 20892, USA
    Expert Rev Mol Diagn 5:329-36. 2005
    ..The article also discusses some of the most important challenges that block the widespread availability of annotated biomedical data sets...
  10. ncbi request reprint Nomenclature-based data retrieval without prior annotation: facilitating biomedical data integration with fast doublet matching
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Insititute, National Institutes of Health, Bethesda, Maryland, USA
    In Silico Biol 5:313-22. 2005
    ..Perl scripts for implementing the algorithm and testing execution speed are provided as open source documents available from the Association for Pathology Informatics (www.pathologyinformatics.org/informatics_r.htm)...
  11. pmc Threshold protocol for the exchange of confidential medical data
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, Bethesda, Maryland, USA
    BMC Med Res Methodol 2:12. 2002
    ..The author describes and implements a novel threshold protocol that can be used to search, annotate or transform confidential data without breaching patient confidentiality...
  12. ncbi request reprint Confidentiality issues for medical data miners
    Jules J Berman
    Pathology Informatics Cancer Diagnosis Program, DCTD, NCI, NIH, EPN Room 6028, 6130 Executive Building, Rockville, MD 20892, USA
    Artif Intell Med 26:25-36. 2002
    ..This article also describes some of the innovative computational remedies that will permit researchers to conduct research AND share their data without risk to patient or institution...
  13. ncbi request reprint Concept-match medical data scrubbing. How pathology text can be used in research
    Jules J Berman
    Pathology Informatics, Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
    Arch Pathol Lab Med 127:680-6. 2003
    ..This article addresses the problem of data scrubbing...
  14. pmc The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, Bethesda, MD, USA
    BMC Med Inform Decis Mak 3:5. 2003
    ..In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification...
  15. pmc A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, NIH, Rockville, MD, USA
    BMC Med Inform Decis Mak 3:6. 2003
    ..However, a subset of the UMLS vocabularies, designated Category 0 by UMLS, can be used to annotate and share data sets without violating the UMLS License Agreement...
  16. pmc Classifying the precancers: a metadata approach
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, NIH, Rockville, Maryland, USA
    BMC Med Inform Decis Mak 3:8. 2003
    ..As a novel approach to disease classification, terms and classes were annotated with metadata (data that describes the data) so that the classification could be used to link precancer terms to data elements in other biological databases...
  17. pmc Automatic extraction of candidate nomenclature terms using the doublet method
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    BMC Med Inform Decis Mak 5:35. 2005
    ....
  18. ncbi request reprint Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reports
    Kevin J Mitchell
    Centers for Pathology and Oncology Informatics, University of Pittsburgh, UPMC Shadyside, 5230 Centre Avenue, Pittsburgh, PA 15232, USA
    Stud Health Technol Inform 107:663-7. 2004
    ..Further work will focus on refining the Negation Tagger and UMLS Tagger and adding additional processing resources for annotating free-text pathology reports...
  19. pmc An informatics model for tissue banks--lessons learned from the Cooperative Prostate Cancer Tissue Resource
    Ashokkumar A Patel
    Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
    BMC Cancer 6:120. 2006
    ..Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control...
  20. pmc The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experience
    Ashokkumar A Patel
    Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
    BMC Cancer 5:108. 2005
    ..To facilitate this effort, it was critical to arrive at agreed upon common data elements (CDEs) that could be used to collect demographic, pathologic, treatment and clinical outcome data...
  21. ncbi request reprint Precancer: a conceptual working definition -- results of a Consensus Conference
    Jules J Berman
    Cancer Diagnosis Program, National Cancer Institute, NIH, Bethesda, MD, USA
    Cancer Detect Prev 30:387-94. 2006
    ..Precancers are lesions that precede the appearance of invasive cancers. The successful prevention or treatment of precancers has the potential to eliminate deaths due to cancer...
  22. pmc Availability and quality of paraffin blocks identified in pathology archives: a multi-institutional study by the Shared Pathology Informatics Network (SPIN)
    Ashokkumar A Patel
    Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
    BMC Cancer 7:37. 2007
    ..This paper examines if tissue blocks, identified by localized computer searches at participating institutions, can be retrieved in adequate quantity and quality to support medical researchers...
  23. ncbi request reprint Borderline ovarian tumors: diverse contemporary viewpoints on terminology and diagnostic criteria with illustrative images
    Jeffrey D Seidman
    Department of Pathology, Washington Hospital Center, Washington DC 20010, USA
    Hum Pathol 35:918-33. 2004
    ..For those issues where there is disagreement, the terminology and diagnostic approaches reflecting the differing views are presented...
  24. ncbi request reprint Dangerous abbreviations
    David L Booker
    Hum Pathol 35:529-31. 2004
  25. ncbi request reprint Racing to share pathology data
    Jules J Berman
    Am J Clin Pathol 121:169-71. 2004
  26. ncbi request reprint The precancers: waiting for a classification
    Jules J Berman
    Hum Pathol 34:833-4. 2003
  27. ncbi request reprint Gastrointestinal stromal tumors: answers and questions
    Timothy O'Leary
    Department of Cellular Pathology and Genetics, Armed Forces Institute of Pathology, Washington, DC 20306 6000, USA
    Hum Pathol 33:456-8. 2002
  28. ncbi request reprint Prostate cancer in patients with screening serum prostate specific antigen values less than 4.0 ng/dl: results from the cooperative prostate cancer tissue resource
    Milton W Datta
    Departments of Pathology, New York University School of Medicine, New York, New York, USA
    J Urol 173:1546-51. 2005
    ..0 ng/ml). It is currently unclear whether these tumors are different from prostate cancer in patients with high PSA levels (greater than 4.0 ng/ml)...
  29. ncbi request reprint Prostate cancer with low PSA levels
    Milton W Datta
    N Engl J Med 351:1802-3. 2004
  30. ncbi request reprint Borderline Ovarian Tumor Workshop, Bethesda, Maryland, August 27-28, 2003
    Jules J Berman
    Hum Pathol 35:907-9. 2004
  31. ncbi request reprint The cooperative prostate cancer tissue resource: a specimen and data resource for cancer researchers
    Jonathan Melamed
    Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
    Clin Cancer Res 10:4614-21. 2004
    ..This communication describes the CPCTR to investigators interested in obtaining prostate cancer tissue samples...
  32. doi request reprint Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Eric W Deutsch
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Biotechnol 26:305-12. 2008
    ..This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal...