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Biomedical Informatics books
by Jules J. Berman

  • Jones & Bartlett sales and informational website for Biomedical Informatics
  • Amazon.com U.S. book site for Biomedical Informatics
  • Full Table of Contents from Library of Congress for Biomedical Informatics
  • List of book-related resources
  • Brief author biography on Association for Pathology Informatics Website
  • Quick link to PubMed listing for Jules J. Berman
  • Full list of Publications for Jules J. Berman
  • Dr. Bruce Friedman's review of Biomedical Informatics
  • Perl Programming for Medicine and Biology companion site.
  • Author's blog on data specifications
  • Contact author




  • ASSIGNING TOPOGRAPHY TO MORPHOLOGY:
    RECOMMENDATIONS FOR THE PERPLEXED


    Categorizing tumors can be impossible. Imagine you have a dermatofibroma biopsied from a patient's thigh. Should you consider this a soft tissue lesion (it's included in almost all soft tissue tumor classifications, sometimes called a fibrous histiocytoma), or should you categorize it by its topographic location as a tumor of thigh? Since it came from the skin, maybe it's best to just categorize it among the skin tumors.

    Maybe the best thing to do would be to just call it a dermatofibroma and forget about trying to categorize the lesion. Unfortunately, you can't do that. Tissue databanks, registries, pathology departments and nomenclatures and research protocols often require pathologists to group tumors so that the members of the groups can be counted, compared, retrieved, averaged, whatever.

    Are there standards or recommendations? No. The problem is that most so-called tumor classifications (e.g. tumors of lung, soft tissue tumors, endocrine tumors, etc.) don't help resolve problems of tumor categorization. That's because most of these site-specific classifications are simply lists of tumors that can occur in a given location. So a classification of brain tumors will include lymphomas of brain, endocrine tumors of brain (pituitary tumors), germ cell tumors, etc. Classifications of lymphomas, endocrine tumors, and germ cell tumors will include the same tumors redundantly. So the pathologist is left with no guidelines to help categorize tumors uniquely.

    UNTIL NOW.

    I have made a short and simple categorization for tumors that is comprehensive and attempts to assign a unique and unambiguous slot for every tumor of man.

    Where possible, I tried to separate the different categories according to clinical discipline, so that the categorization would be acceptable to a wide range of clinicians.

    This categorization is public domain, but please use the following citation in any publications that use the categorization.

    Berman JJ. Recommendations for categorizing tumors.
    http://www.pathinfo.com/jjb/ca_topo.htm
    December, 2002.

    Inquiries may be sent to:
    Jules J. Berman, Ph.D., M.D.
    Program Director, Pathology Informatics
    Cancer Diagnosis Program, DCTD, NCI, NIH
    EPN - Room 6028
    6130 Executive Blvd.
    Rockville, MD 20892
    email: bermanj@mail.nih.gov
    Oral Cavity, nasal cavity and accessory sinuses, nasopharynx, pharynx
      and hypopharynx (includes salivary gland tumors, odontogenic tumors,
      soft tissue tumors except from those arising from skin and excludes
      excludes primary)
    Larynx  (includes soft tissue tumors)
    Lung (includes trachea and bronchus and excludes primary tumors of
          visceral pleura)
    Heart
    Digestive system (includes soft tissue tumors arising in submucosa)
      but excludes mucosal and submucosal lymphomas)
      Esophagus
      Stomach
      Small Intestine (includes duodenum and jejunum and ampulla of Vater)
      Large intestine
        Appendix
        Colon
        Rectum
        Anus
      Liver, gall bladder and bile duct
      Pancreas
        exocrine pancreas
        endocrine pancreas
    Pleural/Peritoneal surfaces
      (includes pelvic surfaces and all visceral peritoneal
      surfaces except for the ovarian surfaces)
    Spleen (excludes lymphomas and leukemias of spleen)
    Eyes and Orbit (excludes optic nerve)
    Central Nervous System (includes sella turcica, and brain
      coverings -- meninges and dura -- and soft tissue arising intracranially,
      excludes pituitary)
    Endocrine
      Includes all endocrine organs including pituitary gland and thymus
      but excludes endocrine pancreas, ovaries and testes
    Skin (includes lips, ears and other skin of face, melanomas occurring
      on skin, epithelial tumors of epidermis and appendages, excludes primary
      lymphomas of skin (including Mycosis Fungoides) and includes
      soft tissue tumors of dermis and subcutis (including Kaposi's sarcoma),
      includes non-areolar skin overlying breast, but otherise excludes
      all lesions of breast (including areola)
    Bones and Joints (includes vertebrae, and cartilage but excludes
      larynx and respiratory cartilage and excludes bone marrow)
    Bone marrow (includes hematopoietic tissue within bone, and excludes
      extramedullary hematopoietic tissue, such as spleen)
    Soft Tissue (excludes soft tissue of named organs/anatomic sites, and
      includes soft tissue in extremities and trunk exclusive of skin)
    Breast (requires designations of male or female, left, right or bilateral)
    Gynecologic sites exclusive of breast (excludes germ cell tumors but
      includes soft tissue tumors of these sites)
      Ovaries and appendages
      Uterus
        Corpus
        Cervix
      Vagina
      Vulva (includes accessory structures and perineum)
    Male Genitalia and accessory structures
      Penis (includes penile urethra)
      Scrotum
      Testes
      Vas deferens
      Seminal vesicles
      Prostate (includes prostatic urethra)
    Kidney and Ureters (includes transitional cell lesions)
    Urinary Bladder
    Lymphoid tissue: includes lymph nodes and lymphoid collections in
      any organ, icluding spleen, gi tract, skin, orbit
    

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