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Open Access Database

Tumor taxonomy for the developmental lineage classification of neoplasms

Jules J Berman

Author Affiliations

Cancer Diagnosis Program, National Cancer Institute, Bethesda, USA

BMC Cancer 2004, 4:88  doi:10.1186/1471-2407-4-88

Published: 30 November 2004

Additional files

Additional File 1:

Neoplasia classification structure (XML version) Neoclxml.gz is a compressed (gzipped) XML file. The downloaded file should be renamed neoclxml.gz so that the .gz suffix can be recognized by unzip utilities. Unzip the file (using a free, open source utility such as gunzip.exe [23], or a proprietary utility such as Winzip). Once unzipped, the file should be renamed neocl.xml, so that it will have an .xml suffix. If the file is too large for viewing on your web browser, it can be viewed on plain-text word processors.

Format: GZ Size: 515KB Download file

Open Data

Additional File 2:

Neoplasia classification with taxonomy (flat-file plain-text version) Neoself.gz is a compressed (gzipped) ascii flat-file. If the filename is changed during download, it should be renamed neoself.gz so that the .gz suffix can be recognized by unzip utilities. Unzip the file (using an open source utility such as gunzip.exe [23], or a proprietary utility such as Winzip). Once unzipped, the file is 19+ Mbytes in length. The expanded file should be renamed neoself.txt.

Format: GZ Size: 828KB Download file

Open Data

Additional File 3:

Taxonomy validating Perl script The validating Perl script is xmlvocab.pl. Perl scripts will execute on any computer with a Perl interpreter. It requires the external taxonomy file named "neocl.xml" residing in the same subdirectory as xmlvocab.pl.

Format: PL Size: 4KB Download file

Open Data

Additional File 4:

Perl script for transforming taxonomy XML file to a plain-text flat file The Perl script neoself.pl transforms the XML database file (neocl.xml) to a flat file (neoself.txt).

Format: PL Size: 4KB Download file

Open Data

Additional File 5:

Perl script for extracting neoplasm codes and terms from UMLS The Perl script ca_mrrec.pl produces a file (neomrcxt.txt) containing all UMLS codes and terms with a neoplasm relationship. This script requires the external files MRCXT and MRCON (available at no cost from the National Library of Medicine) to reside in the same directory as ca_mrrec.pl. This script may take more than one-half hour to execute.

Format: PL Size: 2KB Download file

Open Data

Additional File 6:

Perl script for extracting UMLS codes for SNOMED-derived terms The Perl script snomout.pl produces a file (snomout.txt) containing all UMLS terms with a SNOMED-CT vocabulary relationship It requires the external file MRCXT (available at no cost from the National Library of Medicine) to reside in the same directory as snomout.txt. It produces an output file, snomout.txt that has a size of 1,895,054,040 bytes. This script may take more than one-half hour to execute.

Format: PL Size: 2KB Download file

Open Data

Additional File 7:

Perl script for extracting neoplasm concepts and terms from the SNOMED-CT subset of UMLS The Perl script ca_snrec.pl produces a file (neosnom.txt) containing all UMLS terms derived from SNOMED-CT having a neoplasm relationship. It requires the external file MRCON (available at no cost from the National Library of Medicine) and snomout.txt (produced by snomout.pl) [see 6], both residing in the same directory as ca_snrec.pl. This script may take more than one-half hour to execute.

Format: PL Size: 2KB Download file

Open Data