Internet Autopsy Database
Prototype Autopsy Diagnosis
UMLS Paragraph Translator.


All text is in the public domain, and may be used freely without restriction.
Please select the desired sentence, and click on the SUBMIT button:


1 Postpartum hepatitis. Pancytopenia of unknown etiology.
2 Infiltrating ductal carcinoma, right breast. Right modified radical mastectomy, with negative axillary lymph node dissection.
3 High-dose adriamycin and cytoxan, granulocyte monocyte-colony stimulating factor. Tamoxifen therapy. Jaundice; low-grade fever; anorexia; myalgias; arthralgias.
4 Admission to HOSPITALNAME, PLACENAME.
5 Markedly elevated aspartate and alanine aminotransferases; hyperbilirubinemia; anemia; thrombocytopenia; elevated white blood cell count. Negative hepatitis A, B, and C; Negative human immunodeficiency virus; Negative antinuclear antibody and Monospot tests.
6 Focal atelectasis, lower lobes, right and left lungs, and calcified nodes, mediastinum and lower lobe, right lung (per chest x-ray).

7 Non-specific hepatitis, per liver biopsy. Hepatic encephalopathy; coagulopathy; nasal and buccal ecchymoses.
8 Replacement of normal marrow by non-specific lymphoid infiltrates, per bone marrow biopsy. Progressive pancytopenia; diarrhea; ascites.
9 Invasive fungal infection, sphenoid sinuses and cribriform plate, cranium. Diffuse, brown-green discoloration and focal necrosis, bilateral orbitofrontal cortices, brain. Focal petechial hemorrhages and opacification, dura mater. Thrombosis, basilar artery, brain.
10 Well-defined, circular ecchymosis, nasal and medial buccal region, face. Multiple, brown-green, discoid plaques, with focal extension into lung parenchyma, visceral pleura, right and left lungs.
11 Calcified nodules, hilum, right and left lungs, and lower lobe, right lung. Several scattered thromboemboli, middle-sized vessels, right and left lungs. Moderate congestion and edema, right and left lungs. Serous effusions, right and left pleural cavities. Serous ascites.
12 Subcapsular hemorrhages, liver. Capsular scar, right lobe, liver. Jaundice, skin, mucosal surfaces, and sclerae.

13 Multiple ulcerations with brown-green bases and hemorrhagic rims, esophagus, stomach, and small bowel.
14 Lymphadenopathy, mediastinum, mesentery, and retroperitoneum.
15 Mild atherosclerosis, left main coronary artery and left circumflex artery. Status post splenectomy.
16 Diffuse alveolar damage and focally accentuated fibrosis, right and left lungs. Serous effusions, right and left pleural cavities. Hemorrhagic infarct, posterior lower lobe, left lung. Status post: tracheostomy tube placement.
17 Scattered, multiple infarcts, liver and spleen. Splenomegaly. Circumscribed hemorrhage and necrosis with acute inflammation, distal duodenum and jejunum.
18 Bilateral hemorrhagic infarcts with hemosiderin-laden macrophages, mammillary bodies, brain. Focal hemorrhage, left globus pallidus, brain.

19 Postmortem autolysis, including extensive desquamation. Green-brown discoloration and opacification, fetal membranes. Enlarged placenta.
20 Severe complicated atherosclerosis, thoracic and abdominal aorta, bilateral renal arteries, bilateral external iliac arteries, celiac artery, and splenic artery. Arterial and arteriolonephrosclerosis, right and left kidneys. Cardiomegaly, heart. Myocardial infarct, well-healed, left ventricle.
21 Multifocal and confluent necrotizing pneumonia and bronchopneumonia, lungs. Hemorrhage, lower lobe, left lung. Multiple adhesions, heart to pericardium, right and left lungs to rib cage, and pericardium to rib cage.
22 Mild to moderate focal necrosis with congestion, liver. Subcapsular infarct, spleen.
23 Acoustic neuroma, right eighth cranial nerve, brain. Multiple Schwannomas, nerve roots, Spinal cord and caudal equina Mild, nonstenotic atherosclerosis, circle of Willis, brain.
24 Diverticular disease, sigmoid colon. Tubulovillus adenoma, sigmoid colon. Thinned and hemorrhagic mucosa, small intestine.




Introduction to the UMLS Paragraph Translator.

      1. In autopsy pathology, the final results are typically summarized as diagnostic PARAGRAPHS in a standarized format. This summary form appears at the beginning of the autopsy report, and is called the AUTOPSY FACESHEET. Usually each medical institution or private pathology practice has its own reporting form. In the United States Government, all pathology results are reported on U. S. Standard Form 515, an uncopyrighted, publicly available document.

      2. The most popular coding vocabulary for pathology specimens is SNOMED, the Systematized Nomenclature of Human and Veterinary Medicine SNOMED is a copyrighted product of the College of American Pathologists (CAP). There are restrictions on the distribution of SNOMED code numbers, which must be negotiated with CAP, and typically require the payment of a user fee.

      3. The concepts within SNOMED have been contributed to the Unified Medical Language System (UMLS) of the United States National Library of Medicine (USNLM). The UMLS is a metathesaurus, containing over 600,000 concepts, with over 2 million synonymous terms, partial translations into German, French, Spanish, Italian, Portuguese, Danish, Finnish, Swedish, Norwegian, Dutch, Hungarian, and Romanized-Russian, and linked to over 50 contributed biomedical terminologies. In research investigations, such as the Internet Autopsy Database, the concept unique identifiers (CUIs) of the UMLS may be discussed and copied freely in public forums.

      7. The paragraph translator is a public-domain computer translator, with source code available in PERL and M, formerly MUMPS.

      8. In the translator, each word or multiple-word term is pointed to its corresponding UMLS concept. In general, the longest consecutive sequence of words is translated by the translator.

      9. For foreign language translation, each concept may be mapped to a part-of-speech, and the stereotypical word order of the source language is rearranged into the stereotypical word order of the target language, using a set of parsing formulas. Since the source language (medical English) and the target language (UMLS, whose base language is English) have the same stereotypical word order, there is no word order rearrangement required.

Syntax Considerations for the UMLS Paragraph Translator.

      1. Within UMLS, there are atomic concepts, e.g., "acute" (C0205178), "inflammation" (C0021368), and "appendix" (C0003617), and compound concepts, e.g., "acute appendicitis" (C0085693).

      2. In the IAD-UMLS lexicon, "acute appendicitis" may be defined as C0085693 or alternatively as C0205178!C0021368!C0003617, using ! (ASCII 33) as a connecting character. Cases are indexed redundantly as: C0085693, C0205178, C0021368, C0003617.

      3. The IAD-UMLS translator contains additional definitions not authorized by the USNLM, including: Punctuation and linguistic particles are classified as FULL STOP (C9999999), as NULL (C0000000), or as COMMA (C9999998). FULL STOP includes: . [period] : [colon] ; [semicolon] ! [exclamation point] ? [question mark] ( [left parenthesis] ) [right parenthesis] . NULL includes: - the a these this that those I we you he she it they them. In addition, medical concepts that we think should be added to UMLS are designated as EMERGENT (C9999997). Concepts which have not yet received a dictionary entry (an error on our part) are designated as: CXXXXXXX .

Files in the IAD UMLS Paragraph Translator.

      1. U. S. Government Tissue Examination Form (U. S. Standard Form 515). http://www.autopsydb.org/iadbs515.htm

      2. Suite of PERL Translation Programs. http://www.autopsydb.org/imarperl.htm

      3. Suite of MUMPS Translation Programs. http://www.autopsydb.org/imarmump.htm

      4. List of Barrier Words. http://www.autopsydb.org/imarbarr.htm

      5. List of Keywords. http://www.autopsydb.org/imarkeyw.htm

      6. MRCON Subset. http://www.autopsydb.org/imarmrco.htm

      7. List of Parts-of-speech. http://www.autopsydb.org/imarposp.htm

      8. List of Medical Word Roots. http://www.autopsydb.org/imarroot.htm

      9. List of UMLS Pathology vocabulary. http://www.autopsydb.org/umlslexi.htm

For further information, please contact: G. William Moore, M.D., Ph.D., moore.md.george.w@baltimore.va.gov

Last updated: May 22, 1999.