Supplemental Book Resources for:
Developmental Lineage Classification and Taxonomy of Neoplasms
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The Developmental Lineage Classification and Taxonomy of Neoplasms
is an open source computer-parsable data set that can be used to organize,
collect, merge, share, analyze, understand, develop and test hypotheses,
and discover new information related to neoplasia. The classification is
used extensively in software projects linked
from my home page.
The Classification and taxonomy contains about 6,000 classified
types of neoplasms and over 130,000 neoplasm names.
It is the largest cancer nomenclature in existence and has
been described in several journal articles:
Berman JJ.
Tumor classification: molecular analysis meets Aristotle
BMC Cancer, BMC Cancer 2004, 4:10.Download manuscript
This article is among the all-time
most-viewed articles in BMC Cancer, and,
as of September 2008, has been downloaded about 15,000 times from BiomedCentral.
Statistics Page
Berman JJ. Tumor taxonomy for the developmental lineage
classification of neoplasms. BMC Cancer. 2004 Nov 30;4(1):88. Download manuscript
Berman JJ. Modern classification of neoplasms: reconciling
differences between morphologic and molecular approaches.
BMC Cancer 2005, 5:100. Download manuscript
The classification is available in several different file formats.
The RDF (Resource Description Framework) version of the classification
is about 10 Megabytes in length and is so large that some
browsers cannot parse the entire file, with all of its child nodes.
I am providing the file as a simple text file. This way your
browser will not try parse the nodal hierarchy.
Whenever you want to parse the
file as an RDF document, you can just rename
the file "neordf.xml".
A primer on RDF is
available.
Download RDF file:
http://www.julesberman.info/neordf.txt
A short sampling of the RDF file is available at: http://www.julesberman.info/plainrdf.htm
The RDF file was validated using the W3C validator service
at http://www.w3.org/rdf/validator/, with a caveat. The
full ontology file (10+ Mbytes) was too large for the
validator, so I truncated the ontology, validated the
truncated file (that contained all of the classes,
subclasses, properties), and left out the repetitive
list of terms. Then I took the entire file and validated
it with an XML parser to verify that the file was well-formed).
The gzipped version of the RDF file (under 1 Megabyte)
Download gzipped RDF file:
http://www.julesberman.info/neordf.gz
A short sampling of the RDF file is available at: http://www.julesberman.info/plainrdf.htm
The zipped version of the RDF file (under 1 Megabyte)
Download zipped RDF file:
http://www.julesberman.info/neordf.zip
A short sampling of the RDF file is available at: http://www.julesberman.info/plainrdf.htm
The flat file version, listing each term followed by its lineage (gzipped file).
Download gzipped flat-file:
http://www.julesberman.info/neoself.gz
A short sampling of the flat-file version is available at: http://www.julesberman.info/plaintxt.htm
The flat file version, listing each term followed by its lineage (zipped file).
Download zipped flat-file:
http://www.julesberman.info/neoself.zip
A short sampling of the flat-file version is available at: http://www.julesberman.info/plaintxt.htm
The plain old XML version, with no RDF semantics (compressed gzip file).
Download gzipped XML file:
http://www.julesberman.info/neoclxml.gz
A short sampling of the XML version is available at: http://www.julesberman.info/plainxml.htm
The plain old XML version, with no RDF semantics (compressed zip file).
Download zipped XML file:
http://www.julesberman.info/neoclxml.zip
A short sampling of the XML version is available at: http://www.julesberman.info/plainxml.htm
The schematic for the classification is illustrated below.
The classification also serves as the dataset underlying a neoplasm
search engine that provides synonyms and related terms for phrases
entered into a query box. This is available at:
http://www.julesberman.info/neoget.htm
The classification is described in Neoplasms: Principles of Development
and Diversity, by Jules J. Berman
Last modified: July 27, 2008
