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CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes

BACKGROUND: 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 identi...

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Autores principales: Bajdik, Chris D, Kuo, Byron, Rusaw, Shawn, Jones, Steven, Brooks-Wilson, Angela
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274267/
https://www.ncbi.nlm.nih.gov/pubmed/15796777
http://dx.doi.org/10.1186/1471-2105-6-78
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author Bajdik, Chris D
Kuo, Byron
Rusaw, Shawn
Jones, Steven
Brooks-Wilson, Angela
author_facet Bajdik, Chris D
Kuo, Byron
Rusaw, Shawn
Jones, Steven
Brooks-Wilson, Angela
author_sort Bajdik, Chris D
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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 .
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spelling pubmed-12742672005-10-29 CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes Bajdik, Chris D Kuo, Byron Rusaw, Shawn Jones, Steven Brooks-Wilson, Angela BMC Bioinformatics Software BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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 . BioMed Central 2005-03-29 /pmc/articles/PMC1274267/ /pubmed/15796777 http://dx.doi.org/10.1186/1471-2105-6-78 Text en Copyright © 2005 Bajdik et al; licensee BioMed Central Ltd.
spellingShingle Software
Bajdik, Chris D
Kuo, Byron
Rusaw, Shawn
Jones, Steven
Brooks-Wilson, Angela
CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
title CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
title_full CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
title_fullStr CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
title_full_unstemmed CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
title_short CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes
title_sort cgmim: automated text-mining of online mendelian inheritance in man (omim) to identify genetically-associated cancers and candidate genes
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274267/
https://www.ncbi.nlm.nih.gov/pubmed/15796777
http://dx.doi.org/10.1186/1471-2105-6-78
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