Professional Miscellanea, Jules J. Berman, Ph.D., M.D.
for a list of all published papers, with links to many of the full-text documents.
Recent meetings attended or presented
NCI Specimen Resources Committee Meeting, Holiday Inn Bethesda, Bethesda, Maryland,
Invited speaker: Informatics in support of Specimen Resources, Jan 13, 1999.
1999 Health Information Infrastructure (HII99) Conference. Improving Health in a Digital World, Renaissance Washington Hotel, Washington, D.C., April 26-28, 1999.
Internet2 Spring Members Meeting, Non-member observer, Washington, D.C., April 28, 1999.
Translating Comprehensive Molecular Technologies to the Clinic: Issues and Barriers, Rockville, MD, May 6-7, 1999.
Cooperative Breast Cancer Tissue Resource group meeting: Jackson Memorial Hospital, Miami, Florida, Feb 4-5, 1999.
Basic Project Officer Training, with Honors Commendation, Rockville, MD, March 8-11, 1999.
Invited Lecture: "Informatics Issues Related to Pathology Practice," Department of Pathology, Washington Hospital Center, Washington, D.C., April 26, 1999.
College of American Pathologists Conference. Solid Tumor Prognostic Factors: which, how, and so what?" Westin Hotel, Chicago, Illinois, Jun 10-13, 1999.
NCI Specimen Resources Committee meeting. Speaker: "Informatics for Pathology Based Specimen Resources," Double Tree Hotel, Rockville, MD, July 15, 1999.
Association of Pathology Chairs, Boulder, Colorado,
Invited speaker: "NCI activities in pathology informatics," July 21-23, 1999.
Cooperative Breast Cancer Tissue Resource site visit: Sugarloaf Conference Center, 9230 Germantown Ave., Philadelphia, PA 19118 Aug. 26-27, 1999.
Symposium - Detection of HER2/neu (erbB2) Antigen overexpression Bethesda Marriott, Bethesda, MD, Oct 7-8, 1999.
APIII Advancing Pathology Informatics: Imaging and the Internet, Marriott City Center, Pittsburgh, PA,
Invited speaker: "Automatic Indexing of a Pathology Image Archive using UMLS," October 14-16, 1999.
Conference on Confidentiality, Data Security and Cancer Research: Best Practices Workshop. Renaissance Hotel, Washington, D.C., October 20, 1999.
SNOMED Users' Group Conference, Omni Shoreham Hotel, Washington, D.C., November 5, 1999.
NCI Working Group Meeting on Tissue Microarrays, DoubleTree Hotel, Rockville, MD, Dec 16-17, 1999.
SNOMED RT Vendor - End User Open Dialogue, New Orleans Hilton Riverside, March 25, 2000.
U.S.-Canadian Academy of Pathology Meeting, New Orleans Hilton Riverside Hotel, March 26-28, 2000.
Leukemia Vocabulary Meeting, Sponsored by the Mouse Models of Human Cancers Consortium, Doubletree Hotel, Rockville, MD, June 9, 2000.
NCI SPORE Intergroup Common Data Element Meeting. Westfields Marriott, Chantilly, Virginia.
Invited speaker: "CDEs and the Shared Pathology Informatics Network," July 8-9, 2000.
Association of Pathology Chairs, Boulder, Colorado.
Invited speaker: "Pathology information, privacy, and research progress - Are they compatible?", July 26-28, 2000.
Health Informatics Standards Board (HISB). Non-member observer, Arlington, VA, September 7, 2000.
University of Illinois at Chicago, Department of Pathology.
Invited speaker: "Confidentiality issues and models for Pathology Research," September 25, 2000.
Early Detection Research Network First Annual Scientific Workshop, Chicago, Illinois
Invited Speaker: "Sharing Pathology Data: Confidentiality and Data Representation Issues," September 26-27, 2000.
NCI Mouse Models of Human Cancers Consortium. Workshop on the Classification of Hematopoietic Neoplasms of the Mouse. Rockville, MD, Oct 11, 2000
Emerging Opportunities in Prostate Cancer Epidemiology. National Cancer Institute. Washington, D.C., Oct. 12-13, 2000
2000 ASCP/CAP Annual Meeting, San Diego, CA. Invited workshop speaker: "Data Mining and Data Warehousing," Oct 17, 2000.
Full Text of Handout
Advancing Pathology Informatics and the Internet (APIII), Pittsburgh, PA. Invited workshop speaker: "Anatomic Pathology Data Mining," Oct 27, 2000.
Universities Associated for Research and Education in Pathology (UAREP). In conjunction with Advancing Pathology Informatics and the Internet (APIII), Pittsburgh, PA. Invited focus session speaker: "Bioinformatics Data: Confidentiality Issues," Oct 27, 2000.
A Molecular Classification for Precancerous Lesions Report of an EDRN (Early Dectection Research Network) Working Group Meeting Summary February 1-2, 2001, Rockville, Maryland
Invited Speaker: "Informatics Opportunities for a Molecular Taxonomy of Precancer,"
Confidential Health Information and the Public Good: Balancing Needs and Priorities. A Roundtable for the Pfizer Journal. Pointe Hilton Tapatio Cliffs Resort, Phoenix, Arizona, Feb 22-23, 2001. The meeting summary was reported in, The Pfizer Journal. Perspectives on Health Care and Biomedical Research: Balancing Medical Innovation and Patient Confidentiality, editor SJ Giorgianni. Volume 5, number 3, 2001.
Early Lung Cancer Screening Workshop National Cancer Institute / American Cancer Society. Attendee. March 7-8, 2001, Rockville, MD.
Invited Speaker: "Sharing Large Pathology Datasets." Pathology Grand Rounds, Department of Pathology, East Carolina University School of Medicine, Greenville, North Carolina, April 9, 2001.
Informatics Committee, College of American Pathologists. Attendee. May 4-5, 2001, Chicago, IL.
19th Annual Automated Information Management in the Clinical Laboratory (AIMCL) Symposium. Invited Speaker for the Tissue Microarray (TMA) Infostructure Workshop. May 30, 2001, Ann Arbor, MI.
First TMA Workshop Summary
APIII 2001, Advancing Pathology Informatics, Imaging and the Internet," Chair of breakout session B3 entitled, "Practical Solutions to Confidentiality Issues and IRB Requirements in Pathology Research: Lessons for Pathologists, Tissue Bankers, and Data Archivists," October 5, 2001, Pittsburgh, PA.
Full Text of Discussion Hand-out
NCI Enterprise Vocabulary System Vocabulary Executive Board Quarterly Meeting. April 3, 2002. Invited speaker.
Presentation, PDF file
APIII 2001, Advancing Pathology Informatics, Imaging and the Internet," Moderator and break-out session co-chair for Tissue Microarray Data Exchange Standards Workshop, October 6, 2001, Pittsburgh, PA.
Second TMA Workshop Summary
Community Standards for Publication-Related Data and Materials. Feb. 25, 2002, National Academy of Sciences. Washington, D.C.
This workshop resulted in UPSIDE (Universal Principle of Sharing Integral Data Expeditiously), explained in the NAS publication,
Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences (2003).
See Acknowledgement page (xi) for list of conference contributors.
Clinical Information System / Life science Roundtable, Cerner Vision Center, April 9-10, 2002, Kansas City, Missouri
International Symposium on Antimutagenesis and Anticarcinogenesis, New York Medical College, April 26-27, 2002, Valhalla, New York.
20th Annual Automated Information Management in the Clinical Laboratory (AIMCL) Symposium.
May 22-24, 2002, Ann Arbor, MI.
Invited Speaker: Confidentiality and Privacy of Lab Data: An IRB Perspective.
Roundtable discussant: The NCI-Supported Shared Pathology Informatics Network (SPIN): Secure Web-Based Searching of Heterogeneous De-identified Pathology Data at Multiple Institutions
Workshop faculty: The Tissue Microarray (TMA) Infostructure: Planning, Development, and Data Exchange.
Sarcoma State of the Science: Building on Molecular and Clinical Progress, June 17-18, 2002, Bethesda, Marriott
APIII 2002, Advancing Pathology Informatics Imaging and the Internet, October 2-4, 2002, Pittsburgh, Pennsylvania
Invited speaker: Perl workshop.
Oct 3, 2002. Programming for Informatics: Why Should I learn to program?
Oct 4, 2002. Programming for Informatics: Perl Programming Tutorial - Tools for Pathology Informatics
National Dialogue on Cancer (NDC) Research Team "Tissue Access Working Group Meeting," January 7, 2003, Hyatt Regency Capitol Hill, Washington, D.C.
C-Kit Meeting. College of American Pathologists. Feb. 5, 2002. 1350 I Street, Washington, D.C.
Invited Speaker: The Tissue Microarray Data Exchange Specification. For: Specimen Processing Workshop. Sponsored by the Epidemiology and Carcinogenesis faculty, NCI. February 24, 2003, Rockville, MD.
Invited speaker. Health Sciences Informatics Research-in-Progress Seminar. Johns Hopkins University Medical Institutions, March 7, 2003, Johns Hopkins Hospital, Meyer B-105, Baltimore, MD.
Non-Invasive Autopsy Workshop. March 12-13, 2003, Neurosciences Building, NCI, NIH, Rockville, Maryland.
Open Source for National and local eGovernment Programs in the U.S. and European Union, March 17-19, 2003, The George Washington University, Washington, D.C.
U.S.-Canadian Academy of Pathology. March 22-28, 2003, Washington, D.C.
Abstract 1 text
Abstract 2 text
Standards in pathology informatics and experimental pathology (lecture). To be presented in the "Mining Datasets" session of Experimental Biology: Translating the Genome, 2004. Washington, D.C. April 17, 2004.
Tissue Microarray Data Exchange Specification (lecture). Microarrays in Medicine, Cambridge Health Institute (CHI), April 26-27, 2004, Boston MA.
What is pathology informatics? Massachusetts General Hospital Pathology Grand Rounds, May 20, 2004.
Opportunities and Rewards for Pathology Data Sharing. Associationfor Pathology Chairs (APC/PRODS/PDAS/GRIPE) Annual summer meeting. July 23, 2004, Mont-Tremblant, Quebec, Canada.
Sharing, merging and querying pathology data. ASCP teleconference. October 27, 2004.
Outline of discussion
Pathology data sharing. United States Military Cancer Institute (USMCI), Walter Reed Army Medical Center (WRAMC), Washington, D.C., November 16, 2004.
The Development of Imaging Standards for Pathology (lecture). Lab InfoTech Summit. March 2-4, 2005. Venetian Hotel, Las Vegas, Nevada.
Invited panelist: President's Cancer Panel. Assessing progress, advancing change: Challenges in Cancer Survivorship. Washington, D.C., Aug. 25, 2005.
Modern Neoplasm Classification (lecture). Department of Pathology. University of Maryland. Baltimore, Maryland. October 12, 2005.
Modern Neoplasm Classification (lecture). Department of Pathology. University of Michigan. Ann Arbor, Michigan. October 27, 2005.
Shared Pathology Informatics Network Meeting (Consultant). Boston MA. January 23, 2006.
Lab InfoTech Summit. March 1-3, 2006. Venetian Hotel, Las Vegas, Nevada.
Advancing Practice, Instruction and Innovation through Informatics (APIII) 2004, August 15-18, 2006, Vancouver, British Columbia.
Informatics Laboratory Digital Imaging Project, Session F2, Friday, August 18, 2006, 10:30 A.M. to noon
API Imaging Working Group Thursday, August 17, 2006 11:30 A.M. To 1:00 P.M.
Imaging white paper
caBIG 2007 Annual Meeting. Panelist, "Digital Imaging: How It Relates to Pathology." Tuesday, February 6, 2007, Marriott Wardman Park Hotel, Washington, D.C.
Han-Mo Koo Seminar, April 25, 2007. "The Evils of Complexity." Van Andel Research Institute, Grand Rapids, Michigan.
Advancing Practice, Instruction and Innovation through Informatics (APIII) 2007, September 9-12, 2007, Pittsburgh, PA.
Monday, September 10, 2007, 7:30 am - 8:30 am
Implementing an RDF Schema for Pathology Images, From the Association for Pathology Informatics
White paper (about 45 pages)
Tuesday, September 11, 2007, 11:30 am - 12:30 pm
Book Publishing in Biomedical Informatics
Invited speaker. 2008 ISBER Annual Meeting. Special session: Informatics for Repositories: How Pathology's Data and Clinical Tissue Flow Can be Harnessed to the Mission of Biospecimen Repositories. Talk title: Informatics Open Source Tools for Tissue Banking and Annotation. Wednesday, May 21, 2008. Bethesda North Marriott Hotel, 5701 Marinelli Road, Bethesda, Maryland 20852
Invited panelist for the U.S. Office of Civil Rights (HHS), Workshop on the HIPAA Privacy Rule's De-identification Standard, March 8-9, 2010, Washington, D.C.
Meeting Powerpoint Presentation
Pathology informatics in support of specimen-based cancer research. May 13-14, 1999, Annapolis, Maryland.
GastroIntestinal Stromal Tumors (GIST). Co-hosted by The Office of Rare Diseases, NIH, and the Armed Forces Institute of Pathology (AFIP). Organizers: Dr. Jules Berman and Dr. Timothy O'Leary. April 2-3, 2001, Bethesda, MD.
November 29, 1999 application for funding for GIST Workshop
GIST Workshop Summary
Introduction, GIST Workshop Papers
. Programming for pathology informatics: Perl programming tutorial - Tools for pathology informatics. Advancing Pathology Informatics, Imaging and the Internet, Pittsburgh, PA, Friday, October 4, 2002.
Pathology Workshop on Borderline Ovarian Tumors. Sponsored by the NIH Office of Rare Diseases and the NIH Office of Women's Health. Held in the Bethesda Hyatt Regency Hotel, August 27-28, 2003. Co-chaired with Steven Silverberg, Department of Pathology, University of Maryland Medical Center.
Advancing Practice, Instruction and Innovation through Informatics (APIII) 2003, October 7-9, 2003, Pittsburgh, Pennsylvania
Organizer and speaker: Perl/Python XML workshop.
Short Workshop Description
Advancing Practice, Instruction and Innovation through Informatics (APIII) 2004, October 6-8, 2004, Pittsburgh, Pennsylvania.
Co-Organizer and speaker: API Working Group Session: Open Discussion of Pathology Digital Imaging Standards.
Precancer Workshop. Sponsored by The Division of Cancer Biology, National Cancer Institute, and by the George Washington University. November 8-9, 2004. Marvin Center, George Washington University, Washington, D.C.
Statement of purpose
Published federal announcements/public documents
Request for Application CA-99-012, "Cooperative prostate cancer tissue resource," April 29, 1999
Text of RFA
Request for Application CA-01-006, "Shared Pathology Informatics Network", March 27, 2000
Concept, Nov. 9, 1999
Text of RFA
Pre-Application Meeting Notice, May 4, 2000
Pre-Application Meeting Transcript, May 22, 2000
Web sites/software with contributions from Jules Berman
International Foundation for Ethical Research
Precancer draft paper
Precancer terms - meta data
Inherited cancer syndrome list
Tumor Sites: Recommendations
Abbreviations and Acronyms Page
Assoc. for Pathology Informatics Call for Technical Reports (FAQ)
Tissue micro array (tissue array, tissue microarray) data exchange project
Summary of 1st TMA workshop
Summary of 2nd TMA workshop
Tissue Microarray Data Standard first draft
Tissue Microarray Data Standard second draft
First Tissue Micro array Data Standards FAQ
Second Tissue Micro array Data Standards FAQ
Validating Perl script
Tissue Micro-Array Common Data Elements (CDEs)
TMA Specification article (BMC Med. Inform. Dec. Making)
TMA Implementation article (BMC Bioinformatics)
LABORATORY DIGITAL IMAGING PROJECT DOCUMENTS
Implementing an RDF Schema for Pathology Images (September 10, 2007)
Instructions for submitting CDEs to LDIP [May 8, 2006, ldip_cde.txt]
Minutes of April 28, 2006 LDIP Conference Call [4-28-06.txt]
Minutes of the March 31, 2006 LDIP Conference Call [03-31-06.txt]
Minutes of the February 24, 2006 LDIP Conference Call [2-24-06.txt]
Minutes of the January 27, 2006 LDIP Conference Call [1-27-06.txt]
Minutes of the December 30, 2005 LDIP Conference Call [12-30-05.txt]
Minutes of the September 30, 2005 LDIP Conference Call [9-30-05.txt]
First (and very preliminary) draft of RDF namespace for LDIP, adapted from OME (Open Microscopy Environment) [ldip.xml]
Minutes of the July 29, 2005 LDIP Conference Call
Minutes of the June 24, 2005 LDIP Conference Call [6-24-05.txt]
Dr. Jules Berman's presentation at the API session of Laboratory InfoTech Summit in Las Vegas (March 4, 2005)
Minutes of the Feb. 25, 2005 LDIP Conference Call
Minutes of the January 28, 2005 LDIP Conference Call
Minutes of the December 17, 2004 LDIP Conference Call
LDIP Blog for Lab IntoTech Summit, December 7, 2004, by Berman JJ and Friedman BA
Minutes of the November 19, 2004 LDIP Conference Call
Minutes of the November 2, 2004 LDIP Conference Call with the Veterans Administration DICOM implementers
Minutes of the October 29, 2004 LDIP Conference Call
Draft of LDIP task document (Updated October 29, 2004)
Minutes of second LDIP open workshop (October 6, 2004)
Dr. Jules Berman's presentation at APIII LDIP open workshop (October 6, 2004)
LDIP Charter document (draft revised January 25, 2005)
Minutes of first LDIP Conference Call (May 3, 2004)
Eric Skjei. CAP Today Feature Story.
Arraying the data.
Laura Lane. Tissue Microarrays Coming of Age. The Scientist. Volume 17, Issue 42, September 8, 2003.
Stephanie De Ritis. Impact of information overload. Advance for Administrators of the Laboratory. pp. 24-27, October, 2003.
Eric Skjei. CAP Today Feature Story
Bringing order to data chaos.
Ann Paxton. CAP Today Feature Story.
Swinging for the fences with prostate cancer tissue bank,
Laura Lane. The Scientist Feature Story.
TMA Buyers' Guide: Tissue microarrays come in various sizes and shapes; here's what you need to know before making your first purchase.
Volume 18, Issue 5, p 44, Mar. 15, 2004.
Last modified: March 22, 2010