Abstract
Investigators in bioinformatics are often confronted with the difficult task of connecting ideas, which are found scattered around the literature, using robust keyword searches. It is often customary to identify only a few keywords in a research article to facilitate search algorithms, which is usually completed in absence of a general approach that would serve to index all possible keywords of an article’s characteristic attributes. Based on only a hand-full of keywords, articles are therefore prioritized by search algorithms that point investigators to seeming subsets of their knowledge. In addition, many articles escape algorithm search strategies due to the fact that their keywords were vague, or have become unfashionable terms. In this case, the article, as well as its source of knowledge, may be lost to the community. Owing to the growing size of the literature, we introduce a text mining method and tool, (BeagleTM), for knowledge harvesting from papers in a literature corpus without the use of article meta-data. Unlike other text mining tools that only highlight found keywords in articles, our method allows users to visually ascertain which keywords have been featured in studies together with others in peer-reviewed work. Drawing from an arbitrarily-sized corpus, BeagleTM creates visual networks describing interrelationships between user-defined terms to facilitate the discovery of connected or parallel studies. We report the effectiveness of BeagleTM by illustrating its ability to connect the keywords from types of PTMs (post-translational modifications), stress-factors, and disorders together according to their relationships. These relationships facilitate the discovery of connected studies, which is often challenging to determine due to the frequently unrelated keywords that were tied to relevant articles containing this type of information.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Splendiani, A., Donato, M., Drăghici, S.: Ontologies for bioinformatics. In: Springer Handbook of Bio-/Neuroinformatics, pp. 441–461. Springer, Heidelberg (2014)
Schouten, K., Frasincar, F., Dekker, R., Riezebos, M.: Heracles: a framework for developing and evaluating text mining algorithms. Expert Syst. Appl. 127, 68–84 (2019)
Allahyari, M., Pouriyeh, S., Assefi, M., Safaei, S., Trippe, E.D., Gutierrez, J.B., Kochut, K.: A brief survey of text mining: classification, clustering and extraction techniques. arXiv preprint arXiv:1707.02919 (2017)
Sharma, S., Srivastava, S.K.: Review on text mining algorithms. Int. J. Comput. Appl. 134(8), 39–43 (2016)
Lamurias, A., Couto, F.M.: Text mining for bioinformatics using biomedical literature. In: Encyclopedia of Bioinformatics and Computational Biology, vol. 1 (2019)
Paynter, R., Bañez, L.L., Berliner, E., Erinoff, E., Lege-Matsuura, J., Potter, S., Uhl, S.: EPC methods: an exploration of the use of text-mining software in systematic reviews (2016)
Maynard, D., Roberts, I., Greenwood, M.A., Rout, D., Bontcheva, K.: A framework for real-time semantic social media analysis. Web Seman.: Sci. Serv. Agents World Wide Web 44, 75-88 (2017)
Feinerer, I.: Introduction to the tm package text mining in R (2017)
Williams, G.J., et al.: Rattle: a data mining GUI for R. R J. 1(2), 45–55 (2009)
Müller, H.-M., Van Auken, K.M., Li, Y., Sternberg, P.: Textpresso central: a customizable platform for searching, text mining, viewing, and curating biomedical literature. BMC Bioinform. 19(1), 94 (2018)
Wei, C.-H., Kao, H.-Y., Lu, Z.: PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res. 44, gkt441 (2013)
Kim, S., Kwon, D., Shin, S.-Y., Wilbur, W.J.: PIE the search: searching PubMed literature for protein interaction information. Bioinformatics 28(4), 597–598 (2011)
Kim, S., Yeganova, L., Wilbur, W.J.: Meshable: searching pubmed abstracts by utilizing mesh and mesh-derived topical terms. Bioinformatics 32(19), 3044–3046 (2016)
Papadopoulou, P., Lytras, M., Marouli, C.: Bioinformatics as applied to medicine: challenges faced moving from big data to smart data to wise data. In: Applying Big Data Analytics in Bioinformatics and Medicine, pp. 1–25. IGI Global (2018)
Ncbi, R.C.: Database resources of the national center for biotechnology information. Nucleic Acids Res. 45(D1), D12 (2017)
Marcelli, S., Corbo, M., Iannuzzi, F., Negri, L., Blandini, F., Nisticò, R., Feligioni, M.: The involvement of post-translational modifications in Alzheimer’s disease. Curr. Alzheimer Res. 15, 313–335 (2017)
Hunnicut, J., Liu, Y., Richardson, A., Salmon, A.B.: MsrA overexpression targeted to the mitochondria, but not cytosol, preserves insulin sensitivity in diet-induced obese mice. PloS One 10(10), e0139844 (2015)
Schult, D.A., Swart, P.: Exploring network structure, dynamics, and function using networkX. In: Proceedings of the 7th Python in Science Conferences (SciPy 2008), vol. 2008, pp. 11–16 (2008)
Bonham-Carter, O., Pedersen, J., Bastola, D.: A content and structural assessment of oxidative motifs across a diverse set of life forms. Comput. Biol. Med. 53, 179–189 (2014)
Bonham-Carter, O., Pedersen, J., Najjar, L., Bastola, D.: Modeling the effects of microgravity on oxidation in mitochondria: a protein damage assessment across a diverse set of life forms. In: IEEE Data Mining Workshop (ICDMW), pp. 250–257. IEEE (2013)
Thygesen, C., Boll, I., Finsen, B., Modzel, M., Larsen, M.R.: Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev. Proteomics 15(3), 245–258 (2018)
Li, Y., Chigurupati, S., Holloway, H.W., Mughal, M., Tweedie, D., Bruestle, D.A., Mattson, M.P., Wang, Y., Harvey, B.K., Ray, B., et al.: Exendin-4 ameliorates motor neuron degeneration in cellular and animal models of amyotrophic lateral sclerosis. PLoS One 7(2), e32008 (2012)
Milani, P., Ambrosi, G., Gammoh, O., Blandini, F., Cereda, C.: SOD1 and DJ-1 converge at Nrf2 pathway: a clue for antioxidant therapeutic potential in neurodegeneration. Oxidative Med. Cell. Longevity 2013 (2013)
Collins, J.A., Moots, R.J., Clegg, P.D., Milner, P.I.: Resveratrol and n-acetylcysteine influence redox balance in equine articular chondrocytes under acidic and very low oxygen conditions. Free Radical Biol. Med. 86, 57–64 (2015)
Bastard, A., Coelho, C., Briandet, R., Canette, A., Gougeon, R., Alexandre, H., Guzzo, J., Weidmann, S.: Effect of biofilm formation by Oenococcus oeni on malolactic fermentation and the release of aromatic compounds in wine. Front. Microbiol. 7, 613 (2016)
Millan, M.J.: The epigenetic dimension of Alzheimer’s disease: causal, consequence, or curiosity? Dialogues Clin. Neurosci. 16(3), 373 (2014)
Ansari, A., Rahman, M., Saha, S.K., Saikot, F.K., Deep, A., Kim, K.-H., et al.: Function of the SIRT3 mitochondrial deacetylase in cellular physiology, cancer, and neurodegenerative disease. Aging Cell 16(1), 4–16 (2017)
Ferrer, I.: Early involvement of the cerebral cortex in Parkinson’s disease: convergence of multiple metabolic defects. Progress Neurobiol. 88(2), 89–103 (2009)
Stetz, G., Tse, A., Verkhivker, G.M.: Dissecting structure-encoded determinants of allosteric cross-talk between post-translational modification sites in the Hsp90 chaperones. Sci. Rep. 8(1), 6899 (2018)
Bonham-Carter, O., Thapa, I., Bastola, D.: Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms. In: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 774–781. ACM (2014)
Acknowledgment
I would like to thank Janyl Jumadinova for her help in proofing this manuscript.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this paper
Cite this paper
Bonham-Carter, O. (2020). BeagleTM: An Adaptable Text Mining Method for Relationship Discovery in Literature. In: Arai, K., Kapoor, S., Bhatia, R. (eds) Advances in Information and Communication. FICC 2020. Advances in Intelligent Systems and Computing, vol 1130. Springer, Cham. https://doi.org/10.1007/978-3-030-39442-4_19
Download citation
DOI: https://doi.org/10.1007/978-3-030-39442-4_19
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-39441-7
Online ISBN: 978-3-030-39442-4
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)