Literature-related discovery: common factors for Parkinson’s Disease and Crohn’s Disease
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Literature-related discovery (LRD) is the linking of two or more literature concepts that have heretofore not been linked (i.e., disjoint), in order to produce novel, interesting, and intelligible knowledge (i.e., potential discovery). The mainstream software for assisting LRD is Arrowsmith. It uses text-based linkage to connect two disjoint literatures, and it generates intermediate linking literatures by matching Title phrases from two disjoint literatures (literatures that do not share common records). Arrowsmith then prioritizes these linking phrases through a series of text-based filters. The present study examines citation-based linkage in addition to text-based linkage to link disjoint literatures through a process called bibliographic coupling. Two disjoint literatures were selected for the demonstration: Parkinson’s Disease (PD) (neurodegeneration) and Crohn’s Disease (CD) (autoimmune). Three cases were examined: (1) matching phrases in records with no shared references (text-based linkage only); (2) shared references in records with no matching phrases (citation-based linkage only); (3) matching phrases in records with shared references (text-based and citation-based linkages). In addition, the main themes in the body of shared references were examined through grouping techniques to identify the common themes between the two literatures. All the high-level concepts in the Case 1) records could be found in Case 3) records Some new concepts (at the sub-set level of the main themes) not found in the Case 3) records were identified in the Case 2) records. The synergy of matching phrases and shared references provides a strong prioritization to the selection of promising matching phrases as discovery mechanisms. There were three major themes that unified the PD and CD literatures: Genetics; Neuroimmunology; Cell Death. However, these themes are not completely independent. For example, there are genetic determinants of the inflammatory response. Naturally occurring genetic variants in important inflammatory mediators such as TNF-alpha appear to alter inflammatory responses in numerous experimental and a few clinical models of inflammation. Additionally, there is a strong link between neuroimmunology and cell death. In PD, for example, neuroinflammatory processes that are mediated by activated glial and peripheral immune cells might eventually lead to dopaminergic cell death and subsequent disease progression.
KeywordsLiterature-related discovery Text mining Scientometrics Parkinson’s Disease Crohn’s Disease Neurodegeneration Autoimmunity Inflammation
This project was supported by MITRE internal research funding.
The views in this report are solely those of the author, and do not necessarily represent the views of the MITRE Corporation or Georgia Institute of Technology.
- Ahlskog, J. E. (2005). The Parkinson’s Disease treatment book: Partnering with your doctor to get the most from your medications (1st ed.). USA: Oxford University Press.Google Scholar
- Annese, V., Valvano, M. R., Palmieri, O., Latiano, A., Bossa, F., & Andriulli, A. (2006). Multidrug resistance 1 gene in inflammatory bowel disease: A meta-analysis. World Journal of Gastroenterology, 12(23), 3636–3644.Google Scholar
- Baumgart, D. C. (2009). The diagnosis and treatment of Crohn’s Disease and ulcerative colitis. Deutsches Arzteblatt International, 106(8), 123–133.Google Scholar
- Cadwallader, J. N. (Editor), Altorjay, I. (Contributor), Ammous, A. (Contributor), Ayadi, S. (Contributor), Bedioui, H. (Contributor). (2008). Crohn’s Disease: Etiology, pathogenesis and interventions (1st ed). Nova Science Publishers.Google Scholar
- Cao, M., & Gao, X. (2005). Combining contents and citations for scientific document classification. In AI 2005: Advances in artificial intelligence (pp. 143–152). Berlin: Springer.Google Scholar
- Couto, T., Cristo, M., Gonçalves, M., Calado, P., Ziviani, N., de Moura, E. S., et al. (2006). A comparative study of citations and links in document classification. In Proceedings of the 6th ACM/IEEE-CS joint conference on digital libraries, pp. 75–84.Google Scholar
- Forte, A., De Sanctis, R., Leonetti, G., Manfredelli, S., Urbano, V., & Bezzi, M. (2008). Dietary chemoprevention of colorectal cancer. Annali Italiani Di Chirurgia, 79(4), 261–267.Google Scholar
- Janssens, F. (2007). Clustering of scientific fields by integrating text mining and bibliometrics. Doctoral dissertation. Faculty of Engineering, Katholieke Universiteit Leuven, Belgium.Google Scholar
- Janssens, F., Quoc, V. T., Glänzel, W., & De Moor, B. (2006). Integration of textual content and link information for accurate clustering of science fields. In InSCit2006, Current research in information sciences and technologies: Multidisciplinary approaches to global information systems. I., pp. 615–619.Google Scholar
- Karypis, G. (2010). CLUTO—A clustering toolkit. http://www.cs.umn.edu/~cluto.
- Kostoff, R. N. (2010). Literature-related discovery: Common factors for Parkinson’s Disease and Crohn’s Disease. DTIC Technical Report Number ADA525269. (http://www.dtic.mil/) Defense Technical Information Center. Fort Belvoir, VA.
- Kostoff, R. N., Block, J. A., Solka, J. A., Briggs, M. B., Rushenberg, R. L., Stump, J. A., et al. (2009). Literature-related discovery. ARIST, 43, 241–285.Google Scholar
- Lang, A. E. (2007). Parkinsonism. In: L. Goldman & D. Ausiello (eds.), Cecil textbook of medicine (23rd ed, Chap. 433). Philadelphia, PA: Saunders Elsevier.Google Scholar
- Latella, G., Sferra, R., Vetuschi, A., Zanninelli, G., D’Angelo, A., Catitti, V., et al. (2008). Prevention of colonic fibrosis by Boswellia and Scutellaria extracts in rats with colitis induced by 2,4,5-trinitrobenzene sulphonic acid. European Journal of Clinical Investigation, 38(6), 410–420.CrossRefGoogle Scholar
- Liu, X. H., Yu, S., Janssens, F., Glanzel, W., Moreau, Y., & De Moor, B. (2010). Weighted hybrid clustering by combining text mining and bibliometrics on a large-scale journal database. Journal of the American Society for Information Science and Technology, 61(6), 1105–1119.Google Scholar
- Maresca, M., Yahi, N., Younes-Sakr, L., Boyron, M., Caporiccio, B., & Fantini, J. (2008). Both direct and indirect effects account for the pro-inflammatory activity of enteropathogenic mycotoxins on the human intestinal epithelium: Stimulation of interleukin-8 secretion, potentiation of interleukin-1 beta effect and increase in the transepithelial passage of commensal bacteria. Toxicology and Applied Pharmacology, 228(1), 84–92.CrossRefGoogle Scholar
- McBrewster, J., Miller, F. P., Vandome, A. F. (Eds.). (2009). Crohn´s Disease: Treatment of Crohns disease, biological therapy for inflammatory bowel disease, Mycobacterium avium subspecies paratuberculosis, Ulcerative colitis, Capsule endoscopy. Alphascript Publishing.Google Scholar
- Miller, C. M., Rindflesch, T. C., Fiszman, M., Hristovski, D., Shin, D., Rosemblat, G., et al. (2012). A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men. Sleep, 35(2), 279–285.Google Scholar
- Search (2010). Search Technology, Inc., 6025 The Corners Parkway, Suite 202, Norcross, GA 30092, http://www.thevantagepoint.com. 2010.
- Sen, S. K., & Gan, S. K. (1983). A mathematical extension of the idea of bibliographic coupling and its applications. Annals of Library Science and Documentation, 30(2), 78–82.Google Scholar
- Smalheiser, N. R. (2005). The arrowsmith project: 2005 status report. Discovery Science, Proceedings Book Series: Lecture Notes in Computer Science, 3735, 26–43.Google Scholar
- Swanson, D. R. (1987). Two medical literatures that are logically but not bibliographically connected. Journal of the American Society for Information Science, 38(4), 228–233.Google Scholar
- Swanson, D. R. (1988). Migraine and magnesium: Eleven neglected connections. Perspectives in Biology and Medicine, 31, 526–557.Google Scholar
- Swanson, D. R. (1990). Somatomedin C and arginine; implicit connections between mutually-isolated literatures. Perspectives in Biology and Medicine, 33, 157–186.Google Scholar
- Wilkins, T., Jarvis, K., & Patel, J. (2011). Diagnosis and management of Crohn’s disease. American Family Physician, 84(12), 1365–1375.Google Scholar
- Zhu, S., Yu, K., Chi, Y., & Gong, Y. (2007). Combining content and link for classification using matrix factorization. In Proceedings of the 30th annual international ACM SIGIR conference on research and development in information retrieval, pp. 487–494.Google Scholar