Research Topics
| Jules J BermanSummaryAffiliation: National Institutes of Health Country: USA Publications
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Detail Information
Publications
Tumor taxonomy for the developmental lineage classification of neoplasmsJules 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...- Doublet method for very fast autocodingJules 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... - Pathology data integration with eXtensible Markup LanguageJules 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... - Resources for comparing the speed and performance of medical autocodersJules J Berman
Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
BMC Med Inform Decis Mak 4:8. 2004.... - Tumor classification: molecular analysis meets AristotleJules 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?".. - The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue ResourceJules 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... - Zero-check: a zero-knowledge protocol for reconciling patient identities across institutionsJules 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... - Pathology abbreviated: a long review of short termsJules 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... - Biomedical data integration: using XML to link clinical and research data setsJules 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... - Nomenclature-based data retrieval without prior annotation: facilitating biomedical data integration with fast doublet matchingJules 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)... - Threshold protocol for the exchange of confidential medical dataJules 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... - Concept-match medical data scrubbing. How pathology text can be used in researchJules 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... - The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray dataJules 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... - A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabulariesJules 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... - Classifying the precancers: a metadata approachJules 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... - Confidentiality issues for medical data minersJules 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... - Automatic extraction of candidate nomenclature terms using the doublet methodJules J Berman
Cancer Diagnosis Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
BMC Med Inform Decis Mak 5:35. 2005.... - Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reportsKevin 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... - An informatics model for tissue banks--lessons learned from the Cooperative Prostate Cancer Tissue ResourceAshokkumar 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... - Precancer: a conceptual working definition -- results of a Consensus ConferenceJules J Berman
Cancer Diagnosis Program, National Cancer Institute, NIH, Bethesda, MD, USA
Cancer Detect Prev 30:387-94. 2006..This manuscript reviews the proposed definition of precancers and suggests how pathologists, oncologists and cancer researchers may determine when these criteria are satisfied... - The development of common data elements for a multi-institute prostate cancer tissue bank: the Cooperative Prostate Cancer Tissue Resource (CPCTR) experienceAshokkumar 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... - 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... - Borderline ovarian tumors: diverse contemporary viewpoints on terminology and diagnostic criteria with illustrative imagesJeffrey 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... - Dangerous abbreviationsDavid L Booker
Hum Pathol 35:529-31. 2004 - Racing to share pathology dataJules J Berman
Am J Clin Pathol 121:169-71. 2004 - The precancers: waiting for a classificationJules J Berman
Hum Pathol 34:833-4. 2003 - Gastrointestinal stromal tumors: answers and questionsJules J Berman
Department of Cellular Pathology and Genetics, Armed Forces Institute of Pathology, Washington, DC 20306-6000, USA
Hum Pathol 33:456-8. 2002 - Prostate cancer in patients with screening serum prostate specific antigen values less than 4.0 ng/dl: results from the cooperative prostate cancer tissue resourceMilton 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 had smaller, lower grade tumors and lower recurrence rates than patients with PSA 4.0 ng/ml or greater. This was not true for those older than 62 years and for black men... - Prostate cancer with low PSA levelsMilton W Datta
N Engl J Med 351:1802-3. 2004 - Borderline Ovarian Tumor Workshop, Bethesda, Maryland, August 27-28, 2003Jules J Berman
Hum Pathol 35:907-9. 2004 - The cooperative prostate cancer tissue resource: a specimen and data resource for cancer researchersJonathan Melamed
Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
Clin Cancer Res 10:4614-21. 2004..Interested investigators are encouraged to apply for use of this material (www.prostatetissues.org)... - 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...