Books by Jules J. Berman, covers

Specified Life

The Specified Life Blog is concerned with the topic of data specification (including data organization, data description, data retrieval and data sharing) in the life sciences and in medicine. Beyond data sharing issues, it covers a range of topics that might be of interest to biomedical researchers. Titles, with links, to all posted blogs, are listed below, in order of their chronologic occurrence (i.e., oldest on top).

Protecting standards from embedded patents
Bad ideas to stop patent farmers
Standards developers can help the Patent Office
Don't ask the government to write your standard
Specifications versus Standards
Protecting the basic uses of a Standard
Why governments rarely create data standards
Data standards should not be monopolistic
Data standards can be coercive
Searching for U.S. patents that encumber a
Searching patents that may encumber a standard
Patenting the uses of the DICOM medical image
More Introduction to RDF
Expressing triples in RDF
Intro to RDF biomedical specifications
Tissue Microarray Data Exchange Specification
Ex Parte Reexamination of Patents
Consequences of open access to clinical trial data
Funding opportunity in precancer research
Obviousness in Patents
"Precancer" versus "early cancer"
Embryological specifications
Newest version of Neoplasm Classification now
Neoplasm classification introspection
Unclassified terms in the Neoplasm Classification
Synonymy in the Neoplasm Classification
New Ontology research funding opportunity at NIH
Tutorial document on image annotation
LUA programming language gaining popularity
Ruby moves up on TIOBE Programming Index
List of inherited syndromes associated with
Ruby scripts from Ruby Programming for Medicine
Updates to my web site
Specifying a classification with GraphViz
Annotating a PDF image
Merging and splitting pdf images while preserving
New schema for the Neoplasm Classification
National Cancer Institute Thesaurus
Developmental Classification of Neoplasms now an
The high level classes in the Developmental
Medical Abbreviations
Google preview of Perl Programming for Medicine
Deidentification with one-way hash algorithms
Concept-match deidentification
Zipf law for surgical pathology
Possessive forms of eponymous neoplasms
Rhabdoid tumors, a sui generis class in the
Failure to rescue
Complex Hospital Information Systems (HISs)
Perl implementation of doublet deidentifier
Parsable Doublets List now available in public
Medical record de-identifier (using the doublet
Easy method for building public domain medical
Minimum Necessary Provision (HIPAA) and
Fast deidentifier that preserves punctuation
De-identifying a public domain book with the
Corrections to Perl scripts
Computerized physician order entry (CPOE)
Comments sent to the "Specified Life" blog
Arcane "iform" words in UMLS
More on "iform" words in UMLS
Update of Neoplasm Classification
Correction to Ruby Programming for Medicine and
Fast, accurate medical autocoding with Ruby
Medical autocoding with Perl
Ruby, Perl and Python medical autocoders
The importance of having a FAST medical autocoding
Dangerous medical abbreviations
Before you create a new standard....
Informatics issues for consenting medical data
JCAHO policy on abbreviations
Ruby, Perl, and Python medical autocoding
Confused medical terms
Medical autocoder circa 1994
Ambiguous disease names
A fast (combined) medical autocoder and scrubber
The linguistic basis for the doublet medical
Medical linguistics, Part 2
Ruby Programming for Medicine and Biology limited
Medical Linguistics, Part 3
Medical Linguistics, Part 4
Medical Linguistics, Part 5
Gaucher cells occurring in diseases other than
MISFISHIE Specification (for in situ hybridization
Updated files for the Neoplasm Classification now
RDF Schemas and directed graphs
Generating Prime numbers in Ruby, Python and Perl
A web site for viewing the phylogeny of organisms
Ruby script for building phylogenetic lineages
Python script to extract phylogenetic lineages
Medical Informatics has barely advanced in 50
Perl script for extracting lineages of organisms
MeSH (Medical Subject Headings) more complex than
Diagnostic errors in medicine: excellent paper
Precancer: small representation in the literature
Precancer versus Intraepithelial neoplasia
Precancer principles
Precancer: one to many relationships
Precancers: counter-arguments
Biomedical Ruby Programming
Arguments for precancer research: 1
Defending Precancer Research: 2
Defending the precancers: 3
Defending Precancer Research: 4
Biomedical Informatics Book
Biomedicine for the Post-Information Age: 1
Biomedicine in the Post-Information Age: 2
Biomedicine in the Post-Information Age: 3
Biomedicine in the Post-Information Age: 4
Biomedicine in the Post-Informatics Age: 5
Biomedicine in the Post-Information Age: 6
Biomedical Informatics "Search Inside"
Neoplasms: 1
Neoplasms: 2
Neoplasms: 3
Neoplasms: 4
Neoplasms: 5
Neoplasms: 6
Neoplasms: 7
Neoplasms: 8
Neoplasms: 9
Neoplasms: 9
Neoplasms: 10
Neoplasms: 11
Neoplasms: 12
Neoplasms: 13
Neoplasms: 15
Neoplasms: 16
Neoplasms: 17
Neoplasms: 18
Neoplasms: 19
Neoplasms: 20
Neoplasms: 21
Neoplasms: 22
Appeals Court Ruling on Open Source License
Neoplasm synonym look-up
Inherited disorders associated with neoplasms: web
Update of Medical Abbreviation Web Page
Books versus Google: Comment on Nicholas Carr's
New version of the Developmental Lineage
New version of Precancer nomenclature now
Sample pages for formatted versions of Neoplasm
Journal articles on the Developmental Lineage
Tumor Speciation in Neoplasms book
Neoplasms: Short excerpt from Preface
Neoplasms: More on Tumor Speciation
Neoplasms: Excerpt from Chapter 1
Neoplasms: Excerpts
Neoplasms: Excerpts
Neoplasms: Excerpt 4
Neoplasms: Excerpt 4
Neoplasms: Excerpt 5
Neoplasms: Excerpt 6
Book discount at Amazon
Neoplasms: Excerpt 7
Neoplasms: Excerpt 8
Neoplasms: Excerpt 9
Neoplasms: Book discussion
U.S. Cancer Death Rates: The Crude Reality
Using SEER Public Use Data: 1
Using SEER Public Use Data: 3
Using SEER Public Use Data: 2
Using SEER Public Use Data: 4
Using SEER Public Use Data: 5
Using SEER Public-Use Data: 6
Using SEER Public-Use Data: 7
Using SEER Public-Use Data: 9
Using SEER Public-Use Data: 8
Neoplasms: Excerpt 10
CDC Mortality data: 1
CDC Mortality data: 2
CDC Mortality data: 2
Latest version of Neoplasms Classification now
CDC Mortality Data: 4
CDC Mortality Data: 5
CDC Mortality Data: 5
CDC Mortality Data: 6
Ruby Programming for Medicine and Biology
CDC Mortality Data: 7
CDC Mortality Data: 8
CDC Mortality Data: 8
CDC Mortality Data: 10
CDC Mortality data: 3
CDC Mortality Data: 10
Cancer occurrence by age: distributions and
Is the incidence of sickle cell disease rising?
Updated cancer occurrence document now available
Pleural versus Peritoneal Mesotheliomas
Updated and new file on neoplasm occurrences, by
Cancers with two peaks in age distribution
Corrections site for Neoplasms book
Medical importance of bimodal cancers
Biomedical Informatics
Precancers: 1
PRECANCERS: 2 Inducing regression in precancers
Precancers 3: All Myeloma Preceded by MGUS
Precancers 4: Agents that cause precancers are
New mammogram recommendations
New mammogram recommendations
More on new mammographic screening recommendations
New guidelines for cervical (Pap Smear) screening
New guidelines for cervical (Pap Smear) screening
Cancer prevention better than cancer screening
Happy Thanksgiving
Quarter century anniversary of Bhopal disaster
Batch image conversions
Grabbing, Testing Web Links
Familial and Heritable Neoplasm Syndromes
Scripts for fetching and testing web pages
Chronology of Earth Website Updated
One-way hash: Perl, Python, Ruby
Reviews are in on Precancer book
Cover art design with PovRay
Cover art design with PovRay 2
Cover art design with PovRay 4
Cover art design with PovRay 3
Cover art design with PovRay 5
Cover art design with PovRay 6
Updated web pages
Machiavelli's Laboratory updated
Anatomic adjectival forms
New book coming in September
New book coming in September
Image montage with Perl Ruby Python
Medical abbreviation nightmare
Precancer properties
Precancer: missed opportunities for diagnosis
Mystery of the missing prelymphomas
Treating breast precancers saves lives
Treating breast precancers saves lives
Precancer time machine
Naming rocks, minerals, and gems
Methods in Medical Informatics
Perl script for moving files
Melanoma and the precancer time machine
Tumor speciation revisited
Germ cell tumors: the problems

Created January 20, 2010; last modified April 8, 2014
By Jules J. Berman, Ph.D., M.D.
Web site:
Specified Life blog site:
Books by Jules J. Berman, covers