{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T05:27:57Z","timestamp":1770355677586,"version":"3.49.0"},"reference-count":8,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,3,29]],"date-time":"2005-03-29T00:00:00Z","timestamp":1112054400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,3,29]],"date-time":"2005-03-29T00:00:00Z","timestamp":1112054400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. Our objective was to establish an automated text-mining system for OMIM that will identify genetically-related cancers and cancer-related genes. We developed the computer program CGMIM to search for entries in OMIM that are related to one or more cancer types. We performed manual searches of OMIM to verify the program results.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>In the OMIM database on September 30, 2004, CGMIM identified 1943 genes related to cancer. BRCA2 (OMIM *164757), BRAF (OMIM *164757) and CDKN2A (OMIM *600160) were each related to 14 types of cancer. There were 45 genes related to cancer of the esophagus, 121 genes related to cancer of the stomach, and 21 genes related to both. Analysis of CGMIM results indicate that fewer than three gene entries in OMIM should mention both, and the more than seven-fold discrepancy suggests cancers of the esophagus and stomach are more genetically related than current literature suggests.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>CGMIM identifies genetically-related cancers and cancer-related genes. In several ways, cancers with shared genetic etiology are anticipated to lead to further etiologic hypotheses and advances regarding environmental agents. CGMIM results are posted monthly and the source code can be obtained free of charge from the BC Cancer Research Centre website <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.bccrc.ca\/ccr\/CGMIM\">http:\/\/www.bccrc.ca\/ccr\/CGMIM<\/jats:ext-link>.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-78","type":"journal-article","created":{"date-parts":[[2005,3,30]],"date-time":"2005-03-30T06:16:11Z","timestamp":1112163371000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes"],"prefix":"10.1186","volume":"6","author":[{"given":"Chris D","family":"Bajdik","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Byron","family":"Kuo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shawn","family":"Rusaw","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven","family":"Jones","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angela","family":"Brooks-Wilson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,3,29]]},"reference":[{"key":"403_CR1","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/nrc1299","volume":"4","author":"PA Futreal","year":"2004","unstructured":"Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR: A census of human cancer genes. Nat Rev Cancer 2004, 4: 177\u2013183. 10.1038\/nrc1299","journal-title":"Nat Rev Cancer"},{"key":"403_CR2","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1093\/nar\/30.1.52","volume":"30","author":"A Hamosh","year":"2002","unstructured":"Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, McKusick VA: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research 2002, 30: 52\u201355. 10.1093\/nar\/30.1.52","journal-title":"Nucleic Acids Research"},{"key":"403_CR3","doi-asserted-by":"publisher","first-page":"D35","DOI":"10.1093\/nar\/gkh073","volume":"32","author":"DL Wheeler","year":"2004","unstructured":"Wheeler DL, Church DM, Edgar R, Federhen S, Helmberg W, Madden TL, Pontius JU, Schuler GD, Schrimi LM, Sequeira E, Suzek TO, Tatusova TA, Wagner L: Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Research 2004, 32: D35\u201340. 10.1093\/nar\/gkh073","journal-title":"Nucleic Acids Research"},{"key":"403_CR4","volume-title":"Data Mining: Concepts and Techniques","author":"J Han","year":"2001","unstructured":"Han J, Kamber M: Data Mining: Concepts and Techniques. First edition. Morgan Kaufmann Publishers; 2001.","edition":"First"},{"key":"403_CR5","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/S1386-5056(02)00050-3","volume":"67","author":"B de Bruin","year":"2002","unstructured":"de Bruin B, Martin J: Getting to the (c)ore of knowledge: mining biomedical literature. Int J Medical Informatics 2002, 67: 7\u201318. 10.1016\/S1386-5056(02)00050-3","journal-title":"Int J Medical Informatics"},{"key":"403_CR6","volume-title":"Canadian Cancer Statistics Toronto","author":"National Cancer Institute of Canada","year":"2004","unstructured":"National Cancer Institute of Canada: Canadian Cancer Statistics Toronto. 2004."},{"key":"403_CR7","volume-title":"International Classification of Diseases for Oncology","author":"A Fritz","year":"2000","unstructured":"Fritz A, Percy C, Jack A, Shanmugaratnam K, Sobin L, Parkin DM, Whelan S: International Classification of Diseases for Oncology. Third edition. World Health Organization; 2000.","edition":"Third"},{"key":"403_CR8","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1108\/eb046814","volume":"14","author":"MF Porter","year":"1980","unstructured":"Porter MF: An algorithm for suffix stripping. Program 1980, 14: 130\u2013137. It has since been reprinted in Sparck Jones, Karen, and Peter Willet (1997) Readings in Information Retrieval San Francisco. Morgan Kaufmann","journal-title":"Program"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-78.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-78\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-78.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:09:36Z","timestamp":1728302976000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-78"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,3,29]]},"references-count":8,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["403"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-78","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,3,29]]},"assertion":[{"value":"29 October 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"78"}}