skip to main content
survey

A Systematic Review on Literature-based Discovery: General Overview, Methodology, & Statistical Analysis

Published: 10 December 2019 Publication History

Abstract

The vast nature of scientific publications brings out the importance of Literature-Based Discovery (LBD) research that is highly beneficial to accelerate knowledge acquisition and the research development process. LBD is a knowledge discovery workflow that automatically detects significant, implicit knowledge associations hidden in fragmented knowledge areas by analysing existing scientific literature. Therefore, the LBD output not only assists in formulating scientifically sensible, novel research hypotheses but also encourages the development of cross-disciplinary research. In this systematic review, we provide an in-depth analysis of the computational techniques used in the LBD process using a novel, up-to-date, and detailed classification. Moreover, we also summarise the key milestones of the discipline through a timeline of topics. To provide a general overview of the discipline, the review outlines LBD validation checks, major LBD tools, application areas, domains, and generalisability of LBD methodologies. We also outline the insights gathered through our statistical analysis that capture the trends in LBD literature. To conclude, we discuss the prevailing research deficiencies in the discipline by highlighting the challenges and opportunities of future LBD research.

References

[1]
Caroline B. Ahlers, Dimitar Hristovski, Halil Kilicoglu, and Thomas C. Rindflesch. 2007. Using the literature-based discovery paradigm to investigate drug mechanisms. In Proceedings of the AMIA Symposium, Vol. 2007. American Medical Informatics Association, 6.
[2]
Ali Ahmed. 2016. Literature-based discovery: Critical analysis and future directions. Int. J. Comput. Sci. Netw. Sec. 16, 7 (2016), 11.
[3]
Christos Andronis, Anuj Sharma, Vassilis Virvilis, Spyros Deftereos, and Aris Persidis. 2011. Literature mining, ontologies and information visualization for drug repurposing. Brief. Bioinform. 12, 4 (2011), 357--368.
[4]
Alan R. Aronson. 2001. Effective mapping of biomedical text to the UMLS metathesaurus: The MetaMap program. In Proceedings of the AMIA Symposium. American Medical Informatics Association, 17.
[5]
Hiteshwar Kumar Azad and Akshay Deepak. 2017. Query expansion techniques for information retrieval: A survey. arXiv preprint arXiv:1708.00247 (2017).
[6]
Seung Han Baek, Dahee Lee, Minjoo Kim, Jong Ho Lee, and Min Song. 2017. Enriching plausible new hypothesis generation in . PloS One 12, 7 (2017), e0180539.
[7]
Nancy C. Baker and Bradley M. Hemminger. 2010. Mining connections between chemicals, proteins, and diseases extracted from Medline annotations. J. Biomed. Inform. 43, 4 (2010), 510--519.
[8]
Ritwik Banerjee, Yejin Choi, Gaurav Piyush, Ameya Naik, and I. Ramakrishnan. 2014. Automated suggestion of tests for identifying likelihood of adverse drug events. In Proceedings of the IEEE International Conference on Healthcare Informatics. Citeseer, 170--176.
[9]
Tanja Bekhuis. 2006. Conceptual biology, hypothesis discovery, and text mining: Swanson’s legacy. Biomed. Dig. Lib. 3, 1 (2006), 2.
[10]
Margherita Berardi, Michele Lapi, Pietro Leo, and Corrado Loglisci. 2005. Mining generalized association rules on biomedical literature. In Proceedings of the International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems. Springer, 500--509.
[11]
Sanmitra Bhattacharya and Padmini Srinivasan. 2012. A semantic approach to involve Twitter in LBD efforts. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW’12). IEEE, 248--253.
[12]
Halil Bisgin, Zhichao Liu, Hong Fang, Xiaowei Xu, and Weida Tong. 2011. Mining FDA drug labels using an unsupervised learning technique-topic modeling. BMC Bioinform., Vol. 12. BioMed Central, S11.
[13]
Olivier Bodenreider. 2004. The unified medical language system (UMLS): Integrating biomedical terminology. Nucl. Acids Res. 32, suppl_1 (2004), D267--D270.
[14]
Peter Bruza, Richard Cole, Dawei Song, and Zeeniya Bari. 2006. Towards operational abduction from a cognitive perspective. Logic J. IGPL 14, 2 (2006), 161--177.
[15]
Peter Bruza, Dawei Song, and Robert McArthur. 2004. Abduction in semantic space: Towards a logic of discovery. Logic J. IGPL 12, 2 (2004), 97--109.
[16]
Michael J. Cairelli, Marcelo Fiszman, Han Zhang, and Thomas C. Rindflesch. 2015. Networks of neuroinjury semantic predications to identify biomarkers for mild traumatic brain injury. J. Biomed. Seman. 6, 1 (2015), 25.
[17]
Michael J. Cairelli, Christopher M. Miller, Marcelo Fiszman, T. Elizabeth Workman, and Thomas C. Rindflesch. 2013. Semantic MEDLINE for discovery browsing: Using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. In Proceedings of the AMIA Symposium, Vol. 2013. American Medical Informatics Association, 164.
[18]
Delroy Cameron, Olivier Bodenreider, Hima Yalamanchili, Tu Danh, Sreeram Vallabhaneni, Krishnaprasad Thirunarayan, Amit P. Sheth, and Thomas C. Rindflesch. 2013. A graph-based recovery and decomposition of Swanson’s hypothesis using semantic predications. J. Biomed. Inform. 46, 2 (2013), 238--251.
[19]
Delroy Cameron, Ramakanth Kavuluru, Thomas C. Rindflesch, Amit P. Sheth, Krishnaprasad Thirunarayan, and Olivier Bodenreider. 2015. Context-driven automatic subgraph creation for literature-based discovery. J. Biomed. Inform. 54 (2015), 141--157.
[20]
Chris Cheadle, Hongbao Cao, Andrey Kalinin, and Jaqui Hodgkinson. 2017. Advanced literature analysis in a Big Data world. Ann. New York Acad. Sci. 1387, 1 (2017), 25--33.
[21]
Sabrina Cherdioui and Fatiha Boubekeur. 2013. Information retrieval techniques for knowledge discovery in biomedical literature. In Proceedings of the 11th International Symposium on Programming and Systems (ISPS’13). IEEE, 137--142.
[22]
Warren A. Cheung, B. F. Francis Ouellette, and Wyeth W. Wasserman. 2012. Inferring novel gene-disease associations using medical subject heading over-representation profiles. Genome Med. 4, 9 (2012), 75.
[23]
Warren A. Cheung, B. F. Francis Ouellette, and Wyeth W. Wasserman. 2012. Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). BMC Bioinform. 13, 1 (2012), 249.
[24]
Trevor Cohen, Roger Schvaneveldt, and Dominic Widdows. 2010. Reflective random indexing and indirect inference: A scalable method for discovery of implicit connections. J. Biomed. Inform. 43, 2 (2010), 240--256.
[25]
Trevor Cohen and Roger W. Schvaneveldt. 2010. The trajectory of scientific discovery: Concept co-occurrence and converging semantic distance. In Proceedings of the World Congress on Medical and Health (Medical) Informatics (MedInfo’10). 661--665.
[26]
Trevor Cohen, Roger W. Schvaneveldt, and Thomas C. Rindflesch. 2009. Predication-based semantic indexing: Permutations as a means to encode predications in semantic space. In Proceedings of the AMIA Symposium, Vol. 2009. American Medical Informatics Association, 114.
[27]
Trevor Cohen, G. Kerr Whitfield, Roger W. Schvaneveldt, Kavitha Mukund, and Thomas Rindflesch. 2010. EpiphaNet: An interactive tool to support biomedical discoveries. J. Biomed. Discov. Collab. 5 (2010), 21.
[28]
Trevor Cohen, Dominic Widdows, and Thomas Rindflesch. 2014. Expansion-by-analogy: A vector symbolic approach to semantic search. In Proceedings of the International Symposium on Quantum Interaction. Springer, 54--66.
[29]
Trevor Cohen, Dominic Widdows, Roger Schvaneveldt, and Thomas C. Rindflesch. 2011. Finding schizophrenia’s Prozac emergent relational similarity in predication space. In Proceedings of the International Symposium on Quantum Interaction. Springer, 48--59.
[30]
Trevor Cohen, Dominic Widdows, Roger W. Schvaneveldt, Peter Davies, and Thomas C. Rindflesch. 2012. Discovering discovery patterns with predication-based semantic indexing. J. Biomed. Inform. 45, 6 (2012), 1049--1065.
[31]
Trevor Cohen, Dominic Widdows, Roger W. Schvaneveldt, and Thomas C. Rindflesch. 2010. Logical leaps and quantum connectives: Forging paths through predication space. In Proceedings of the AAAI Fall Symposium Series.
[32]
Trevor Cohen, Dominic Widdows, Clifford Stephan, Ralph Zinner, Jeri Kim, Thomas Rindflesch, and Peter Davies. 2014. Predicting high-throughput screening results with scalable literature-based discovery methods. CPT: Pharmacom. Syst. Pharmacol. 3, 10 (2014), 1--9.
[33]
Richard J. Cole and Peter D. Bruza. 2005. A bare bones approach to literature-based discovery: An analysis of the Raynaud’s/Fish-oil and migraine-magnesium discoveries in semantic space. In Proceedings of the International Conference on Discovery Science. Springer, 84--98.
[34]
Ronan Collobert and Jason Weston. 2008. A unified architecture for natural language processing: Deep neural networks with multitask learning. In Proceedings of the 25th International Conference on Machine Learning. ACM, 160--167.
[35]
Gamal Crichton, Yufan Guo, Sampo Pyysalo, and Anna Korhonen. 2018. Neural networks for link prediction in realistic biomedical graphs: A multi-dimensional evaluation of graph embedding-based approaches. BMC Bioinform. 19, 1 (2018), 176.
[36]
Roy Davies. 1989. The creation of new knowledge by information retrieval and classification. J. Document. 45, 4 (1989), 273--301.
[37]
C. C. der Eijk, E. M. Van Mulligen, and J. den Berg. 2002. Finding complementary scientific concepts using a conceptual associative spatial graph. In Proceedings of the 6th World Multi-Conference on Systemics, Cybernetics and Informatics, Vol. XIII, Proceedings: Concepts and Applications of Systemics, Cybernetics and Informatics III.
[38]
Ying Ding, Min Song, Jia Han, Qi Yu, Erjia Yan, Lili Lin, and Tamy Chambers. 2013. Entitymetrics: Measuring the impact of entities. PloS One 8, 8 (2013), e71416.
[39]
Weiwei Dong, Yixuan Liu, Weijie Zhu, Quan Mou, Jinliang Wang, and Yi Hu. 2014. Simulation of Swanson’s literature-based discovery: Anandamide treatment inhibits growth of gastric cancer cells in vitro and in silico. PloS One 9, 6 (2014), e100436.
[40]
Alberto Faro, Daniela Giordano, and Concetto Spampinato. 2011. Combining literature text mining with microarray data: Advances for system biology modeling. Brief. Bioinform. 13, 1 (2011), 61--82.
[41]
Raoul Frijters, Marianne Van Vugt, Ruben Smeets, René Van Schaik, Jacob De Vlieg, and Wynand Alkema. 2010. Literature mining for the discovery of hidden connections between drugs, genes and diseases. PLoS Comput. Biol. 6, 9 (2010), e1000943.
[42]
Matteo Gabetta, Cristiana Larizza, and Riccardo Bellazzi. 2013. A unified medical language system (UMLS) based system for literature-based discovery in medicine. Stud. Health Technol. Inform. 192 (2013), 412--416.
[43]
Murat C. Ganiz, William M. Pottenger, and Christopher D. Janneck. 2005. Recent advances in literature based discovery. Technical report. Lehih University; 2005. LU-CSE-05-027.
[44]
Hongjie Gao, Yinghui Wang, Jinzhe Tao, Zhaihua Liu, Jinghua Li, Tong Yu, Qi Yu, Ye Tian, and Huamin Zhang. 2015. Cordyceps Sinensis may have a dual effect on diabetic retinopathy. In Proceedings of the 7th International Conference on Information Technology in Medicine and Education (ITME’15). IEEE, 63--67.
[45]
J. Caleb Goodwin, Trevor Cohen, and Thomas Rindflesch. 2012. Discovery by scent: Discovery browsing system based on the information foraging theory. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW’12). IEEE, 232--239.
[46]
Vishrawas Gopalakrishnan, Kishlay Jha, Guangxu Xun, Hung Q. Ngo, and Aidong Zhang. 2017. Towards self-learning based hypotheses generation in biomedical text domain. Bioinformatics 34, 12 (2017), 2103--2115.
[47]
Michael Gordon, Robert K. Lindsay, and Weiguo Fan. 2002. Literature-based discovery on the World Wide Web. ACM Trans. Int. Technol. 2, 4 (2002), 261--275.
[48]
Michael D. Gordon and Susan Dumais. 1998. Using latent semantic indexing for literature based discovery. J. Amer. Soc. Inform. Sci. 49, 8 (1998), 674--685.
[49]
Michael D. Gordon and Robert K. Lindsay. 1996. Toward discovery support systems: A replication, re-examination, and extension of Swanson’s work on literature-based discovery of a connection between Raynaud’s and fish oil. J. Amer. Soc. Inform. Sci. 47, 2 (1996), 116--128.
[50]
Donatella Gubiani, Elsa Fabbretti, Bojan Cestnik, Nada Lavrač, and Tanja Urbančič. 2017. Outlier based literature exploration for cross-domain linking of Alzheimer’s disease and gut microbiota. Exp. Syst. Applic. 85 (2017), 386--396.
[51]
Fatih Mehmet Gulec, Tahir Bicakci, Ebru Akcapinar Sezer, Hayri Sever, and Vijay V. Raghavan. 2010. Analyzing the effectiveness of pruning and grouping methods used in literature-based discovery tools. In Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology, Vol. 3. IEEE, 304--308.
[52]
Weisen Guo and Steven B. Kraines. 2009. Discovering relationship associations in life sciences using ontology and inference. In Proceedings of the International Conference on Knowledge Discovery and Information Retrieval. 10--17.
[53]
Weisen Guo and Steven B. Kraines. 2009. Extracting relationship associations from semantic graphs in life sciences. In Proceedings of the International Joint Conference on Knowledge Discovery, Knowledge Engineering, and Knowledge Management. Springer, 53--67.
[54]
David A. Hanauer, Mohammed Saeed, Kai Zheng, Qiaozhu Mei, Kerby Shedden, Alan R. Aronson, and Naren Ramakrishnan. 2014. Applying MetaMap to Medline for identifying novel associations in a large clinical dataset: A feasibility analysis. J. Amer. Med. Inform. Assoc. 21, 5 (2014), 925--937.
[55]
Tatsunori B. Hashimoto, David Alvarez-Melis, and Tommi S. Jaakkola. 2015. Word, graph, and manifold embedding from Markov processes. arXiv preprint arXiv:1509.05808 (2015).
[56]
Sam Henry and Bridget T. McInnes. 2017. Literature based discovery: Models, methods, and trends. J. Biomed. Inform. 74 (2017), 20--32.
[57]
Julian P. T. Higgins and Sally Green (Eds.). 2008. Cochrane Handbook for Systematic Reviews of Interventions. Version 5.0.0 (updated February 2008), The Cochrane Collaboration, 2008.
[58]
M. Shahriar Hossain, Joseph Gresock, Yvette Edmonds, Richard Helm, Malcolm Potts, and Naren Ramakrishnan. 2012. Connecting the dots between abstracts. PloS One 7, 1 (2012), e29509.
[59]
Dimitar Hristovski, Carol Friedman, Thomas C. Rindflesch, and Borut Peterlin. 2006. Exploiting semantic relations for literature-based discovery. In Proceedings of the AMIA Symposium, Vol. 2006. American Medical Informatics Association, 349.
[60]
Dimitar Hristovski, Andrej Kastrin, Dejan Dinevski, Anita Burgun, Lovro Žiberna, and Thomas C. Rindflesch. 2016. Using literature-based discovery to explain adverse drug effects. J. Med. Syst. 40, 8 (2016), 185.
[61]
D. Hristovski, A. Kastrin, D. Dinevski, and T. C. Rindflesch. 2015. Towards implementing semantic literature-based discovery with a graph database. In Proceedings of the7th International Conference on Advances in Databases, Knowledge, and Data Applications. 180--184.
[62]
Dimitar Hristovski, Andrej Kastrin, Dejan Dinevski, and Thomas C. Rindflesch. 2015. Constructing a graph database for semantic literature-based discovery. Stud. Health Technol. Inform. 216 (2015), 1094--1094.
[63]
Dimitar Hristovski, Andrej Kastrin, Borut Peterlin, and Thomas C. Rindflesch. 2010. Combining semantic relations and DNA microarray data for novel hypotheses generation. In Linking Literature, Information, and Knowledge for Biology. Springer, 53--61.
[64]
Dimitar Hristovski, Andrej Kastrin, and Thomas C. Rindflesch. 2015. Semantics-based cross-domain collaboration recommendation in the life sciences: Preliminary results. In Proceedings of the IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM’15). IEEE, 805--806.
[65]
Dimitar Hristovski, Andrej Kastrin, and Thomas C. Rindflesch. 2016. Implementing semantics-based cross-domain collaboration recommendation in biomedicine with a graph database. In Proceedings of theInternational Conference on Advances in Databases, Knowledge, and Data Applications (DBKDA’16). 104.
[66]
Dimitar Hristovski, Borut Peterlin, Joyce A. Mitchell, and Susanne M. Humphrey. 2005. Using literature-based discovery to identify disease candidate genes. Int. J. Med. Inform. 74, 2--4 (2005), 289--298.
[67]
Dimitar Hristovski, Borut Peterlin, Joyce A. Mitchell, Susanne M. Humphrey, L. Sitbon, and I. Turner. 2003. Improving literature based discovery support by genetic knowledge integration. Stud. Health. Technol. Inform. 95 (2003).
[68]
Dimitar Hristovski, Janez Stare, Borut Peterlin, and Saso Dzeroski. 2001. Supporting discovery in medicine by association rule mining in Medline and UMLS. Stud. Health Technol. Inform. 2 (2001), 1344--1348.
[69]
Xiaohua Hu, Guangrong Li, Illhoi Yoo, Xiaodan Zhang, and Xuheng Xu. 2005. A semantic-based approach for mining undiscovered public knowledge from biomedical literature. In Proceedings of the IEEE International Conference on Granular Computing, Vol. 1. IEEE, 22--27.
[70]
Xiaohua Hu, Xiaodan Zhang, Illhoi Yoo, Xiaofeng Wang, and Jiali Feng. 2010. Mining hidden connections among biomedical concepts from disjoint biomedical literature sets through semantic-based association rule. Int. J. Intell. Syst. 25, 2 (2010), 207--223.
[71]
Xiaohua Hu, Xiaodan Zhang, Illhoi Yoo, and Yanqing Zhang. 2006. A semantic approach for mining hidden links from complementary and non-interactive biomedical literature. In Proceedings of the SIAM International Conference on Data Mining. SIAM, 200--209.
[72]
Yanhui Hu, Lisa M. Hines, Haifeng Weng, Dongmei Zuo, Miguel Rivera, Andrea Richardson, and Joshua LaBaer. 2003. Analysis of genomic and proteomic data using advanced literature mining. J. Proteome Res. 2, 4 (2003), 405--412.
[73]
Shuiqing Huang, Lin He, Bo Yang, and Ming Zhang. 2012. A compound correlation model for disjoint literature-based knowledge discovery. In Aslib Proc., Vol. 64. Emerald Group Publishing Limited, 423--436.
[74]
W. Huang and Y. Nakamori. 2004. Fuzzy predicting new association rules from current scientific literature. In Proceedings of the IEEE Annual Meeting of the Fuzzy Information, 2004. Processing NAFIPS’04., Vol. 1. IEEE, 450--455.
[75]
Wei Huang, Yoshiteru Nakamori, Shouyang Wang, and Tieju Ma. 2005. Mining medline for new possible relations of concepts. In Proceedings of the International Conference on Computational and Information Science. Springer, 794--799.
[76]
Wei Huang, Yoshiteru Nakamori, Shouyang Wang, and Tieju Ma. 2005. Mining scientific literature to predict new relationships. Intell. Data Anal. 9, 2 (2005), 219--234.
[77]
Yan Huang, Li Wang, and Lin-sen Zan. 2016. ARN: Analysis and prediction by adipogenic professional database. BMC Syst. Biol. 10, 1 (2016), 57.
[78]
Junguk Hur, Kelli Sullivan, Adam Schuyler, Yu Hong, Manjusha Pande, David States, H. Jagadish, and Eva Feldman. 2010. Literature-based discovery of diabetes-and ROS-related targets. BMC Med. Genom. 3, 1 (2010), 49.
[79]
Ali Z. Ijaz, Min Song, and Doheon Lee. 2010. MKEM: A multi-level knowledge emergence model for mining undiscovered public knowledge. In BMC Bioinform., Vol. 11. BioMed Central, S3.
[80]
Ander Iruetaguena, J. J. Garcia Adeva, Juan Manuel Pikatza, Unai Segundo, David Buenestado, and Raúl Barrena. 2013. Automatic retrieval of current evidence to support update of bibliography in clinical guidelines. Exp. Syst. Applic. 40, 6 (2013), 2081--2091.
[81]
Vitavin Ittipanuvat, Katsuhide Fujita, Yuya Kajikawa, Junichiro Mori, and Ichiro Sakata. 2012. Finding linkage between technology and social issues: A literature based discovery approach. In Proceedings of the Conference on Technology Management for Emerging Technologies (PICMET’12). IEEE, 2310--2321.
[82]
Vitavin Ittipanuvat, Katsuhide Fujita, Ichiro Sakata, and Yuya Kajikawa. 2014. Finding linkage between technology and social issue: A literature-based discovery approach. J. Eng. Technol. Manag. 32 (2014), 160--184.
[83]
Rob Jelier, Martijn J. Schuemie, Antoine Veldhoven, Lambert C. J. Dorssers, Guido Jenster, and Jan A. Kors. 2008. Anni 2.0: A multipurpose text-mining tool for the life sciences. Genome Biol. 9, 6 (2008), R96.
[84]
Kishlay Jha and Wei Jin. 2016. Mining hidden knowledge from the counterterrorism dataset using graph-based approach. In Proceedings of the International Conference on Applications of Natural Language to Information Systems. Springer, 310--317.
[85]
Kishlay Jha and Wei Jin. 2016. Mining novel knowledge from biomedical literature using statistical measures and domain knowledge. In Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM, 317--326.
[86]
Matjaž Juršič, Bojan Cestnik, Tanja Urbančič, and Nada Lavrač. 2012. Cross-domain literature mining: Finding bridging concepts with CrossBee. In Proceedings of the 3rd International Conference on Computational Creativity. 33--40.
[87]
Matjaž Juršič, Bojan Cestnik, Tanja Urbančič, and Nada Lavrač. 2013. HCI empowered literature mining for cross-domain knowledge discovery. In Human-computer Interaction and Knowledge Discovery in Complex, Unstructured, Big Data. Springer, 124--135.
[88]
Andrej Kastrin and Dimitar Hristovski. 2008. A fast document classification algorithm for gene symbol disambiguation in the BITOLA literature-based discovery support system. In Proceedings of the AMIA Symposium, Vol. 2008. American Medical Informatics Association, 358.
[89]
Andrej Kastrin, Borut Peterlin, and Dimitar Hristovski. 2010. Chi-square-based scoring function for categorization of MEDLINE citations. Meth. Inform. Med. 49, 04 (2010), 371--378.
[90]
Andrej Kastrin, Thomas C. Rindflesch, and Dimitar Hristovski. 2014. Link prediction in a MeSH co-occurrence network: Preliminary results. Stud. Health Technol. Inform. 205 (2014), 579--583.
[91]
Andrej Kastrin, Thomas C. Rindflesch, and Dimitar Hristovski. 2014. Link prediction on the semantic MEDLINE network. In Proceedings of the International Conference on Discovery Science. Springer, 135--143.
[92]
Andrej Kastrin, Thomas C. Rindflesch, and Dimitar Hristovski. 2016. Link prediction on a network of co-occurring MeSH terms: Towards literature-based discovery. Meth. Inform. Med. 55, 4 (2016), 340--346.
[93]
Nathan Kibwami and Apollo Tutesigensi. 2014. Using the literature based discovery research method in a context of builtenvironment research. In Proceedings of the 30th ARCOM Conference, Vol. 1. ARCOM, 227--236.
[94]
Hyunjin Kim and Sanghyun Park. 2016. Discovering disease-associated drugs using web crawl data. In Proceedings of the 31st ACM Symposium on Applied Computing. ACM, 9--14.
[95]
Yong Hwan Kim, Seung Han Beak, Andreas Charidimou, and Min Song. 2016. Discovering new genes in the pathways of common sporadic neurodegenerative diseases: A bioinformatics approach. J. Alzh. Dis. 51, 1 (2016), 293--312.
[96]
George J. Klir and Bo Yuan. 1996. Fuzzy sets and fuzzy logic: Theory and applications. Poss. Theor. vs Probab. Theor. 32, 2 (1996).
[97]
Anna Korhonen, Yufan Guo, Simon Baker, Meliha Yetisgen-Yildiz, Ulla Stenius, Masashi Narita, and Pietro Liò. 2014. Improving literature-based discovery with advanced text mining. In Proceedings of the International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics. Springer, 89--98.
[98]
Ronald N. Kostoff. 2007. Validating discovery in literature-based discovery. J. Biomed. Inform. 40, 4 (2007), 448--450. Public Health Informatics.
[99]
Ronald N. Kostoff. 2008. Literature-related discovery (LRD): Potential treatments for cataracts. Technol. Forec. Soc. Change 75, 2 (2008), 215--225.
[100]
Ronald N. Kostoff. 2011. Literature-related discovery: Potential treatments and preventatives for SARS. Technol. Forec. Soc. Change 78, 7 (2011), 1164--1173.
[101]
Ronald N. Kostoff. 2014. Literature-related discovery: Common factors for Parkinson’s Disease and Crohn’s Disease. Scientometrics 100, 3 (2014), 623--657.
[102]
Ronald N. Kostoff, Joel A. Block, Jeffrey L. Solka, Michael B. Briggs, Robert L. Rushenberg, Jesse A. Stump, Dustin Johnson, Terence J. Lyons, and Jeffrey R. Wyatt. 2007. Literature-related Discovery: A Review. Technical Report. Office of Naval Research, Arlington, VA.
[103]
Ronald N. Kostoff, Joel A. Block, Jeffrey L. Solka, Michael B. Briggs, Robert L. Rushenberg, Jesse A. Stump, Dustin Johnson, Terence J. Lyons, and Jeffrey R. Wyatt. 2009. Literature-related discovery. Ann. Rev. Inform. Sci. Technol. 43, 1 (2009), 1--71.
[104]
Ronald N. Kostoff, Joel A. Block, Jesse A. Stump, and Dustin Johnson. 2008. Literature-related discovery (LRD): Potential treatments for Raynaud’s Phenomenon. Technol. Forec. Soc. Change 75, 2 (2008), 203--214.
[105]
Ronald N. Kostoff, Joel A. Block, Jesse A. Stump, and Kirstin M. Pfeil. 2004. Information content in Medline record fields. Int. J. Med. Inform. 73, 6 (2004), 515--527.
[106]
Ronald N. Kostoff and Michael B. Briggs. 2008. Literature-related discovery (LRD): Potential treatments for Parkinson’s disease. Technol. Forec. Soc. Change 75, 2 (2008), 226--238.
[107]
Ronald N. Kostoff, Michael B. Briggs, and Terence J. Lyons. 2008. Literature-related discovery (LRD): Potential treatments for multiple sclerosis. Technol. Forec. Soc. Change 75, 2 (2008), 239--255.
[108]
Ronald N. Kostoff, Michael B. Briggs, Jeffrey L. Solka, and Robert L. Rushenberg. 2008. Literature-related discovery (LRD): Methodology. Technol. Forec. Soc. Change 75, 2 (2008), 186--202.
[109]
Ronald N. Kostoff and Clifford G. Y. Lau. 2013. Combined biological and health effects of electromagnetic fields and other agents in the published literature. Technol. Forec. Soc. Change 80, 7 (2013), 1331--1349.
[110]
Ronald N. Kostoff and Uptal Patel. 2015. Literature-related discovery and innovation: Chronic kidney disease. Technol. Forec. Soc. Change 91 (2015), 341--351.
[111]
Ronald N. Kostoff, Jeffrey L. Solka, Robert L. Rushenberg, and Jeffrey A. Wyatt. 2008. Literature-related discovery (LRD): Water purification. Technol. Forec. Soc. Change 75, 2 (2008), 256--275.
[112]
Cartik R. Kothari and P. R. Payne. 2015. A metadata based knowledge discovery methodology for seeding translational research. Stud. Health Technol. Inform. 216 (2015), 1071--1071.
[113]
Steven B. Kraines, Weisen Guo, Daisuke Hoshiyama, Takaki Makino, Haruo Mizutani, Yoshihiro Okuda, Yo Shidahara, and Toshihisa Takagi. 2013. Literature-based knowledge discovery from relationship associations based on a DL ontology created from MeSH. Proceedings of the International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management. 87.
[114]
Steven B. Kraines, Weisen Guo, Daisuke Hoshiyama, Haruo Mizutani, and Toshihisa Takagi. 2010. Generating literature-based knowledge discoveries in life sciences using relationship associations. In Proceedings of the International Conference on Knowledge Discovery and Information Retrieval (KDIR’10). 35--44.
[115]
Samuel K. Kwofie, Aleksandar Radovanovic, Vijayaraghava S. Sundararajan, Monique Maqungo, Alan Christoffels, and Vladimir B. Bajic. 2011. Dragon exploratory system on hepatitis C virus (DESHCV). Infect., Genet. Evol. 11, 4 (2011), 734--739.
[116]
Dahee Lee, Won Chul Kim, Andreas Charidimou, and Min Song. 2015. A bird’s-eye view of Alzheimer’s disease research: Reflecting different perspectives of indexers, authors, or citers in mapping the field. J. Alzh. Dis. 45, 4 (2015), 1207--1222.
[117]
Eftychia Lekka, Spyros N. Deftereos, Aris Persidis, Andreas Persidis, and Christos Andronis. 2011. Literature analysis for systematic drug repurposing: A case study from Biovista. Drug Disc. Today: Therap. Strat. 8, 3--4 (2011), 103--108.
[118]
Jake Lever, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin R. Jones, Martin Krzywinski, and Steven J. M. Jones. 2017. A collaborative filtering-based approach to biomedical knowledge discovery. Bioinformatics 34, 4 (2017), 652--659.
[119]
Omer Levy and Yoav Goldberg. 2014. Linguistic regularities in sparse and explicit word representations. In Proceedings of the 18th Conference on Computational Natural Language Learning. 171--180.
[120]
Chen Li, Maria Liakata, and Dietrich Rebholz-Schuhmann. 2013. Biological network extraction from scientific literature: State of the art and challenges. Brief. Bioinform. 15, 5 (2013), 856--877.
[121]
Rui Liang, Lei Wang, and Gang Wang. 2013. New insight into genes in association with asthma: Literature-based mining and network centrality analysis. Chinese Med. J. 126, 13 (2013), 2472--2479.
[122]
Robert K. Lindsay and Michael D. Gordon. 1999. Literature-based discovery by lexical statistics. J. Amer. Soc. Inform. Sci. 50, 7 (1999), 574--587.
[123]
Corrado Loglisci and Michelangelo Ceci. 2011. Discovering temporal bisociations for linking concepts over time. In Proceedings of the Joint European Conference on Machine Learning and Knowledge Discovery in Databases. Springer, 358--373.
[124]
Wesley D. Maciel, Alessandra C. Faria-Campos, Marcos A. Gonçalves, and Sérgio V. A. Campos. 2011. Can the vector space model be used to identify biological entity activities? In BMC Genomics, Vol. 12. BioMed Central, S1.
[125]
Diana Maclean and Margo Seltzer. 2011. Mining the web for medical hypotheses: A proof-of-concept system. In Proceedings of the International Conference on Health Informatics. 303--308.
[126]
Scott A. Malec, Peng Wei, Hua Xu, Elmer V. Bernstam, Sahiti Myneni, and Trevor Cohen. 2016. Literature-based discovery of confounding in observational clinical data. In Proceedings of the AMIA Symposium, Vol. 2016. American Medical Informatics Association, 1920.
[127]
Erwin Marsi, Pinar Øzturk, Elias Aamot, Gleb Valerjevich Sizov, and Murat Van Ardelan. 2014. Towards text mining in climate science: Extraction of quantitative variables and their relations. In Proceedings of the Fourth Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing. Reykjavik, 2014.
[128]
Ales Maver, Dimitar Hristovski, Thomas C. Rindflesch, and Borut Peterlin. 2013. Integration of data from omic studies with the literature-based discovery towards identification of novel treatments for neovascularization in diabetic retinopathy. BioMed Research International (24 Nov. 2013).
[129]
M. Heidi McClure. 2012. Preliminary experiments on literature based discovery using the semantic vectors package. In Proceedings on the International Conference on Artificial Intelligence (ICAI’12). The Steering Committee of the World Congress in Computer Science, Computer Engineering, and Applied Computing (WorldComp), 1.
[130]
Sarnoff Mednick. 1962. The associative basis of the creative process. Psychol. Rev. 69, 3 (1962), 220.
[131]
Tomas Mikolov, Ilya Sutskever, Kai Chen, Greg S. Corrado, and Jeff Dean. 2013. Distributed representations of words and phrases and their compositionality. In Proceedings of the Advances in Neural Information Processing Systems Conference. 3111--3119.
[132]
Christopher M. Miller, Thomas C. Rindflesch, Marcelo Fiszman, Dimitar Hristovski, Dongwook Shin, Graciela Rosemblat, Han Zhang, and Kingman P. Strohl. 2012. A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men. Sleep 35, 2 (2012), 279--285.
[133]
Andriy Mnih and Geoffrey E. Hinton. 2009. A scalable hierarchical distributed language model. In Proceedings of the Advances in Neural Information Processing Systems Conference. 1081--1088.
[134]
Martin G. Moehrle. 2005. What is TRIZ? From conceptual basics to a framework for research. Creat. Innov. Manag. 14, 1 (2005), 3--13.
[135]
Justin Mower, Devika Subramanian, Ning Shang, and Trevor Cohen. 2016. Classification-by-analogy: Using vector representations of implicit relationships to identify plausibly causal drug/side-effect relationships. In Proceedings of the AMIA Symposium, Vol. 2016. American Medical Informatics Association, 1940.
[136]
Hiroko Nakamura, Shingo Ii, Hidenori Chida, Ken Friedl, Shinji Suzuki, Junichiro Mori, and Yuya Kajikawa. 2014. Shedding light on a neglected area: A new approach to knowledge creation. Sustain. Sci. 9, 2 (2014), 193--204.
[137]
Arzucan Özgür, Zuoshuang Xiang, Dragomir R. Radev, and Yongqun He. 2010. Literature-based discovery of IFN- and vaccine-mediated gene interaction networks. BioMed Res. Int. 2010 (2010).
[138]
Arzucan Özgür, Zuoshuang Xiang, Dragomir R. Radev, and Yongqun He. 2011. Mining of vaccine-associated IFN- gene interaction networks using the vaccine ontology. J. Biomed. Sem., Vol. 2. BioMed Central, S8.
[139]
Sunghong Park, Dong-gi Lee, and Hyunjung Shin. 2017. Network mirroring for drug repositioning. BMC Med. Inform. Dec. Mak. 17, 1 (2017), 55.
[140]
Yufang Peng, Gary Bonifield, and Neil R. Smalheiser. 2017. Gaps within the biomedical literature: Initial characterization and assessment of strategies for discovery. Front. Res. Met. Anal. 2 (2017), 3.
[141]
Andreas Persidis, Spyros Deftereos, and Aris Persidis. 2004. Systems literature analysis. Pharmacogenomics 5, 7 (2004), 943--947.
[142]
Ingrid Petrič, Bojan Cestnik, Nada Lavrač, and Tanja Urbančič. 2012. Outlier detection in cross-context link discovery for creative literature mining. Comput. J. 55, 1 (2012), 47--61.
[143]
Ingrid Petric, Balázs Ligeti, Balazs Gyorffy, and Sándor Pongor. 2014. Biomedical hypothesis generation by text mining and gene prioritization. Prot. Pept. Lett. 21, 8 (2014), 847--857.
[144]
Ingrid Petriĕ, Tanja Urbanĕiĕ, Bojan Cestnik, and Marta Macedoni-Lukšiĕ. 2009. Literature mining method RaJoLink for uncovering relations between biomedical concepts. J. Biomed. Inform. 42, 2 (2009), 219--227.
[145]
Peter Pirolli. 2007. Information Foraging Theory: Adaptive Interaction with Information. Oxford University Press.
[146]
Wanda Pratt and Meliha Yetisgen-Yildiz. 2003. LitLinker: Capturing connections across the biomedical literature. In Proceedings of the 2nd International Conference on Knowledge Capture. ACM, 105--112.
[147]
Judita Preiss. 2014. Seeking informativeness in literature based discovery. In Proceedings of the Workshop on Biomedical Natural Language Processing (BioNLP’14). 112--117.
[148]
Judita Preiss and Mark Stevenson. 2016. The effect of word sense disambiguation accuracy on literature based discovery. BMC Med. Inform. Dec. Mak. 16, 1 (2016), 57.
[149]
Judita Preiss and Mark Stevenson. 2017. Quantifying and filtering knowledge generated by literature based discovery. BMC Bioinform. 18, 7 (2017), 249.
[150]
Judita Preiss, Mark Stevenson, and Robert Gaizauskas. 2015. Exploring relation types for literature-based discovery. J. Amer. Med. Inform. Assoc. 22, 5 (2015), 987--992.
[151]
Murali K. Pusala, Ryan G. Benton, Vijay V. Raghavan, and Raju N. Gottumukkala. 2017. Supervised approach to rank predicted links using interestingness measures. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM’17). IEEE, 1085--1092.
[152]
Ji Qi and Yukio Ohsawa. 2016. Matrix-like visualization based on topic modeling for discovering connections between disjoint disciplines. Intell. Decis. Technol. 10, 3 (2016), 273--283.
[153]
Qing Qian, Na Hong, and Xinying An. 2012. Structuring the Chinese disjointed literature-based knowledge discovery system: The key technologies to success. J. Inform. Sci. 38, 6 (2012), 532--539.
[154]
N. M. Ramadan, H. Halvorson, A. Vande-Linde, Steven R. Levine, J. A. Helpern, and K. M. A. Welch. 1989. Low brain magnesium in migraine. Headache: J. Head Face Pain 29, 7 (1989), 416--419.
[155]
Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Dingcheng Li, Rashmi Prasad, and Hongfang Liu. 2015. A new method for prioritizing drug repositioning candidates extracted by literature-based discovery. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM’15). IEEE, 669--674.
[156]
Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Liwei Wang, Rashmi Prasad, and Hongfang Liu. 2016. Prioritizing adverse drug reaction and drug repositioning candidates generated by literature-based discovery. In Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM, 289--296.
[157]
Majid Rastegar-Mojarad and Rashmi Prasad. 2015. Toward a complete database of drug repurposing candidates extracted from social media, biomedical literature, and genetic data. In Proceedings of the International Conference on Healthcare Informatics (ICHI’15). IEEE, 494--494.
[158]
Thomas C. Rindflesch and Marcelo Fiszman. 2003. The interaction of domain knowledge and linguistic structure in natural language processing: Interpreting hypernymic propositions in biomedical text. J. Biomed. Inform. 36, 6 (2003), 462--477.
[159]
Sujoy Roy, Daqing Yun, Behrouz Madahian, Michael W. Berry, Lih-Yuan Deng, Daniel Goldowitz, and Ramin Homayouni. 2017. Navigating the functional landscape of transcription factors via non-negative Tensor factorization analysis of MeDline abstracts. Front. Bioeng. Biotechnol. 5 (2017), 48.
[160]
Shengtian Sang, Zhihao Yang, Zongyao Li, and Hongfei Lin. 2015. Supervised learning based hypothesis generation from biomedical literature. BioMed Res. Int. 2015 (2015).
[161]
Shengtian Sang, Zhihao Yang, Lei Wang, Xiaoxia Liu, Hongfei Lin, and Jian Wang. 2018. SemaTyP: A knowledge graph based literature mining method for drug discovery. BMC Bioinform. 19, 1 (2018), 193.
[162]
Jennifer Schroeder, Jennifer Xu, Hsinchun Chen, and Michael Chau. 2007. Automated criminal link analysis based on domain knowledge. J. Amer. Soc. Inform. Sci. Technol. 58, 6 (2007), 842--855.
[163]
Yakub Sebastian, Eu-Gene Siew, and Sylvester Olubolu Orimaye. 2015. Predicting future links between disjoint research areas using heterogeneous bibliographic information network. In Proceedings of the Pacific-Asia Conference on Knowledge Discovery and Data Mining. Springer, 610--621.
[164]
Yakub Sebastian, Eu-Gene Siew, and Sylvester O. Orimaye. 2017. Emerging approaches in literature-based discovery: Techniques and performance review. Knowl. Eng. Rev. 32 (2017).
[165]
Yakub Sebastian, Eu-Gene Siew, and Sylvester Olubolu Orimaye. 2017. Learning the heterogeneous bibliographic information network for literature-based discovery. Knowl.-based Syst. 115 (2017), 66--79.
[166]
Kazuhiro Seki and Javed Mostafa. 2007. Literature-based discovery by an enhanced information retrieval model. In Proceedings of the International Conference on Discovery Science. Springer, 185--196.
[167]
Kazuhiro Seki and Javed Mostafa. 2009. Discovering implicit associations among critical biological entities. Int. J. Data Mining Bioinform. 3, 2 (2009), 105--123.
[168]
Ning Shang, Hua Xu, Thomas C. Rindflesch, and Trevor Cohen. 2014. Identifying plausible adverse drug reactions using knowledge extracted from the literature. J. Biomed. Inform. 52 (2014), 293--310.
[169]
Naoki Shibata, Yuya Kajikawa, Yoshiyuki Takeda, and Katsumori Matsushima. 2009. Comparative study on methods of detecting research fronts using different types of citation. J. Amer. Soc. Inform. Sci. Technol. 60, 3 (2009), 571--580.
[170]
Neil R. Smalheiser. 2005. The Arrowsmith project: 2005 status report. In Proceedings of the International Conference on Discovery Science. Springer, 26--43.
[171]
Neil R. Smalheiser. 2012. Literature-based discovery: Beyond the ABCs. J. Amer. Soc. Inform. Sci. Technol. 63, 2 (2012), 218--224.
[172]
Neil R. Smalheiser. 2017. Rediscovering Don Swanson: The past, present and future of literature-based discovery. J. Data Inform. Sci. 2, 4 (2017), 43--64.
[173]
Neil R. Smalheiser, Vetle I. Torvik, Amanda Bischoff-Grethe, Lauren B. Burhans, Michael Gabriel, Ramin Homayouni, Alireza Kashef, Maryann E. Martone, Guy A. Perkins, Diana L. Price, Andrew C. Talk, and Ruth West. 2006. Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators. J. Biomed. Discov. Collab. 1, 1 (2006), 8.
[174]
Neil R. Smalheiser, Vetle I. Torvik, and Wei Zhou. 2009. Arrowsmith two-node search interface: A tutorial on finding meaningful links between two disparate sets of articles in MEDLINE. Comput. Meth. Prog. Biomed. 94, 2 (2009), 190--197.
[175]
Min Song, Go Eun Heo, and Ying Ding. 2015. SemPathFinder: Semantic path analysis for discovering publicly unknown knowledge. J. Informet. 9, 4 (2015), 686--703.
[176]
E. L. Spinak, S. Launy, and B. Grillo. 1999. Detection of unknown public knowledge through the semantic mapping by disciplines in large databases. In Proceedings of the International Society for Scientometrics and Informetrics. 457--467.
[177]
Ramakrishnan Srikant and Rakesh Agrawal. 1995. Mining generalized association rules. In Proc. of the 21st Int'l Conference on Very Large Databases, Zurich, Switzerland, September 1995.
[178]
Mythily Srinivasan, Corinne Blackburn, Mohamed Mohamed, A. V. Sivagami, and Janice Blum. 2015. Literature--Based Discovery of Salivary Biomarkers for Type 2 Diabetes Mellitus. Biomark Insights 10 (2015), 39--45.
[179]
Padmini Srinivasan. 2004. Text mining: Generating hypotheses from MEDLINE. J. Amer. Soc. Inform. Sci. Technol. 55, 5 (2004), 396--413.
[180]
Padmini Srinivasan and Bisharah Libbus. 2004. Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 20, suppl_1 (2004), i290--i296.
[181]
Johannes Stegmann and Guenter Grohmann. 2003. Hypothesis generation guided by co-word clustering. Scientometrics 56, 1 (2003), 111--135.
[182]
Friedrich Steimann. 1997. Fuzzy set theory in medicine. Artific. Intell. Med. 11, 1 (1997), 1--7.
[183]
J. Su and C. Zhou. 2009. Literature-based multidiscipline knowledge discovery: A new application of bibliometrics. In Proceedings of the 12th International Conference on Scientometrics and Informetrics (ISSI’09) (1 2009), 165--172.
[184]
Don R. Swanson and Neil R. Smalheiser. 1999. Implicit text linkages between Medline records: Using arrowsmith as an aid to scientific discovery. Library Trends 48, 1 (1999), 48--59.
[185]
Don R. Swanson. 1986. Fish oil, Raynaud’s syndrome, and undiscovered public knowledge. Persp. Biol. Med. 30, 1 (1986), 7--18.
[186]
Don R. Swanson. 1988. Migraine and magnesium: Eleven neglected connections. Persp. Biol. Med. 31, 4 (1988), 526--557.
[187]
Don R. Swanson. 2001. ASIST award of merit acceptance speech: On the fragmentation of knowledge, the connection explosion, and assembling other people’s ideas. Bull. Amer. Soc. Inform. Sci. Technol. 27, 3 (2001), 12--14.
[188]
Don R. Swanson and Neil R. Smalheiser. 1996. Undiscovered public knowledge: A ten-year update. In Proceedings of the Conference on Knowledge Discovery and Data Mining (KDD’96). 295--298.
[189]
Don R. Swanson and Neil R. Smalheiser. 1997. An interactive system for finding complementary literatures: A stimulus to scientific discovery. Artific. Intell. 91, 2 (1997), 183--203.
[190]
Don R. Swanson, Neil R. Smalheiser, and Abraham Bookstein. 2001. Information discovery from complementary literatures: Categorizing viruses as potential weapons. J. Amer. Soc. Inform. Sci. Technol. 52, 10 (2001), 797--812.
[191]
Don R. Swanson, Neil R. Smalheiser, and Vetle I. Torvik. 2006. Ranking indirect connections in literature-based discovery: The role of medical subject headings. J. Amer. Soc. Inform. Sci. Technol. 57, 11 (2006), 1427--1439.
[192]
Michael Symonds, Peter Bruza, and Laurianne Sitbon. 2014. The efficiency of corpus-based distributional models for literature-based discovery on large data sets. In Proceedings of the 2nd Australasian Web Conference, Vol. 155. Australian Computer Society, Inc., 49--57.
[193]
Michael Symonds, Peter Bruza, Guido Zuccon, Bevan Koopman, Laurianne Sitbon, and Ian Turner. 2014. Automatic query expansion: A structural linguistic perspective. J. Assoc. Inform. Sci. Technol. 65, 8 (2014), 1577--1596.
[194]
Supphachai Thaicharoen, Tom Altman, Katheleen Gardiner, and Krzysztof J. Cios. 2009. Discovering relational knowledge from two disjoint sets of literatures using inductive logic programming. In Proceedings of the IEEE Symposium on Computational Intelligence and Data Mining (CIDM’09). IEEE, 283--290.
[195]
Vetle I. Torvik and Neil R. Smalheiser. 2007. A quantitative model for linking two disparate sets of articles in MEDLINE. Bioinformatics 23, 13 (2007), 1658--1665.
[196]
Guy Tsafnat, Dennis Jasch, Agam Misra, Miew Keen Choong, Frank P-Y Lin, and Enrico Coiera. 2014. Gene--disease association with literature based enrichment. J. Biomed. Inform. 49 (2014), 221--226.
[197]
Howard Turtle and W. Bruce Croft. 1991. Evaluation of an inference network-based retrieval model. ACM Trans. Inform. Syst. 9, 3 (1991), 187--222.
[198]
Tanja Urbančič, Ingrid Petrič, Bojan Cestnik, and Marta Macedoni-Lukšič. 2007. Literature mining: Towards better understanding of autism. In Proceedings of the Conference on Artificial Intelligence in Medicine in Europe. Springer, 217--226.
[199]
C. Christiaan van der Eijk, Erik M. van Mulligen, Jan A. Kors, Barend Mons, and Jan van den Berg. 2004. Constructing an associative concept space for literature-based discovery. J. Amer. Soc. Inform. Sci. Technol. 55, 5 (2004), 436--444.
[200]
Jose M. Vicente-Gomila. 2014. The contribution of syntactic-semantic approach to the search for complementary literatures for scientific or technical discovery. Scientometrics 100, 3 (2014), 659--673.
[201]
María-Esther Vidal, Louiqa Raschid, Natalia Márquez, Jean Carlo Rivera, and Edna Ruckhaus. 2010. BioNav: An ontology-based framework to discover semantic links in the cloud of linked data. In Proceedings of the Extended Semantic Web Conference. Springer, 441--445.
[202]
María-Esther Vidal, Jean-Carlo Rivera, Luis-Daniel Ibáñez, Louiqa Raschid, Guillermo Palma, Héctor Rodriguez, and Edna Ruckhaus. 2014. An authority-flow based ranking approach to discover potential novel associations between linked data. Semantic Web 5, 1 (2014), 23--46.
[203]
Wytze J. Vlietstra, Ronald Zielman, Robin M. van Dongen, Erik A. Schultes, Floris Wiesman, Rein Vos, Erik M. van Mulligen, and Jan A. Kors. 2017. Automated extraction of potential migraine biomarkers using a semantic graph. J. Biomed. Inform. 71 (2017), 178--189.
[204]
Rein Vos, Sil Aarts, Erik van Mulligen, Job Metsemakers, Martin P. van Boxtel, Frans Verhey, and Marjan van den Akker. 2013. Finding potentially new multimorbidity patterns of psychiatric and somatic diseases: Exploring the use of literature-based discovery in primary care research. J. Amer. Med. Inform. Assoc. 21, 1 (2013), 139--145.
[205]
Marc Weeber, Henny Klein, Alan R. Aronson, James G. Mork, L. T. De Jong-van Den Berg, and Rein Vos. 2000. Text-based discovery in biomedicine: The architecture of the DAD-system. In Proceedings of the AMIA Symposium. American Medical Informatics Association, 903.
[206]
Marc Weeber, Henny Klein, Lolkje T. W. De Jong-Van Den Berg, and Rein Vos. 2001. Using concepts in literature-based discovery: Simulating Swanson’s Raynaud-fish oil and migraine-magnesium discoveries. J. Amer. Soc. Inform. Sci. Technol. 52, 7 (2001), 548--557.
[207]
Marc Weeber, Jan A. Kors, and Barend Mons. 2005. Online tools to support literature-based discovery in the life sciences. Brief. Bioinform. 6, 3 (2005), 277--286.
[208]
Frâncila Weidt and Rodrigo Silva. 2016. Systematic literature review in computer science-a practical guide. Relatór. Técnic. DCC/UFJF 1 (2016).
[209]
Bartlomiej Wilkowski, Marcelo Fiszman, Christopher Miller, Dimitar Hristovski, Sivaram Arabandi, Graciela Rosemblat, and T. Rindflesch. 2011. Discovery browsing with semantic predications and graph theory. In Proceedings of the AMIA Symposium.
[210]
Bartłomiej Wilkowski, Marcelo Fiszman, Christopher M. Miller, Dimitar Hristovski, Sivaram Arabandi, Graciela Rosemblat, and Thomas C. Rindflesch. 2011. Graph-based methods for discovery browsing with semantic predications. In Proceedings of the AMIA Symposium, Vol. 2011. American Medical Informatics Association, 1514.
[211]
T. Elizabeth Workman, Marcelo Fiszman, Michael J. Cairelli, Diane Nahl, and Thomas C. Rindflesch. 2016. Spark, an application based on serendipitous knowledge discovery. J. Biomed. Inform. 60 (2016), 23--37.
[212]
T. Elizabeth Workman, Marcelo Fiszman, Thomas C. Rindflesch, and Diane Nahl. 2014. Framing serendipitous information-seeking behavior for facilitating literature-based discovery: A proposed model. J. Assoc. Inform. Sci. Technol. 65, 3 (2014), 501--512.
[213]
Jonathan D. Wren. 2004. Extending the mutual information measure to rank inferred literature relationships. BMC Bioinform. 5, 1 (2004), 145.
[214]
Jonathan D. Wren, Raffi Bekeredjian, Jelena A. Stewart, Ralph V. Shohet, and Harold R. Garner. 2004. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 20, 3 (2004), 389--398.
[215]
Guangxu Xun, Kishlay Jha, Vishrawas Gopalakrishnan, Yaliang Li, and Aidong Zhang. 2017. Generating medical hypotheses based on evolutionary medical concepts. In Proceedings of the IEEE International Conference on Data Mining (ICDM’17), Vol. 2017. 535--544.
[216]
Hsih-Te Yang, Jiun-Huang Ju, Yue-Ting Wong, Ilya Shmulevich, and Jung-Hsien Chiang. 2017. Literature-based discovery of new candidates for drug repurposing. Brief. Bioinform. 18, 3 (2017), 488--497.
[217]
Liu Yao, Zhou Yang, Sui Zhifang, and Wang Zhenguo. 2008. Research on non-interactive literature-based knowledge discovery. In Proceedings of the International Conference on Computer Science and Software Engineering, Vol. 1. IEEE, 747--752.
[218]
Chunlei Ye, Fuhai Leng, and Xin Guo. 2010. Clustering algorithm in literature-based discovery. In Proceedings of the 7th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD’10), Vol. 4. IEEE, 1625--1629.
[219]
Meliha Yetisgen-Yildiz. 2006. Litlinker: A system for searching potential discoveries in biomedical literature. In Proceedings of the ACM SIGIR Conference. 6--11.
[220]
Meliha Yetisgen-Yildiz and Wanda Pratt. 2006. Using statistical and knowledge-based approaches for literature-based discovery. J. Biomed. Inform. 39, 6 (2006), 600--611.
[221]
Meliha Yetisgen-Yildiz and Wanda Pratt. 2009. A new evaluation methodology for literature-based discovery systems. J. Biomed. Inform. 42, 4 (2009), 633--643.
[222]
Yuanbo Zhan, Shuang Zhou, Ying Li, Sen Mu, Ruijie Zhang, Xuejing Song, Feng Lin, Ruimin Zhang, and Bin Zhang. 2017. Using the BITOLA system to identify candidate molecules in the interaction between oral lichen planus and depression. Behav. Brain Res. 320 (2017), 136--142.
[223]
Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. Pakhomov, and Genevieve B. Melton. 2014. Exploiting literature-derived knowledge and semantics to identify potential prostate cancer drugs. Cancer Inform. 13 (2014), CIN--S13889.
[224]
Enxiang Zhou, N. A. Hui, Min Shu, Baiping Wu, and Jianlin Zhou. 2015. Systematic analysis of the p53-related microRNAs in breast cancer revealing their essential roles in the cell cycle. Oncol. Lett. 10, 6 (2015), 3488--3494.

Cited By

View all
  • (2024)Revolutionizing Learning Landscapes: Unleashing the Potential of AI in the Realm of Academic ResearchArtificial Intelligence: A Multidisciplinary Approach towards Teaching and Learning10.2174/9789815305180124010014(242-264)Online publication date: 18-Nov-2024
  • (2024)Enhancing Biomedical Knowledge Discovery for Diseases: An Open-Source Framework Applied on Rett Syndrome and Alzheimer’s DiseaseIEEE Access10.1109/ACCESS.2024.350971412(180652-180673)Online publication date: 2024
  • (2024)Towards a science exocortexDigital Discovery10.1039/D4DD00178HOnline publication date: 2024
  • Show More Cited By

Recommendations

Comments

Information & Contributors

Information

Published In

cover image ACM Computing Surveys
ACM Computing Surveys  Volume 52, Issue 6
November 2020
806 pages
ISSN:0360-0300
EISSN:1557-7341
DOI:10.1145/3368196
  • Editor:
  • Sartaj Sahni
Issue’s Table of Contents
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 10 December 2019
Accepted: 01 October 2019
Revised: 01 July 2019
Received: 01 February 2019
Published in CSUR Volume 52, Issue 6

Permissions

Request permissions for this article.

Check for updates

Author Tags

  1. LBD
  2. Literature-based discovery
  3. hypotheses generation
  4. knowledge discovery
  5. literature mining
  6. systematic review
  7. text mining

Qualifiers

  • Survey
  • Research
  • Refereed

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • Downloads (Last 12 months)169
  • Downloads (Last 6 weeks)6
Reflects downloads up to 01 Mar 2025

Other Metrics

Citations

Cited By

View all
  • (2024)Revolutionizing Learning Landscapes: Unleashing the Potential of AI in the Realm of Academic ResearchArtificial Intelligence: A Multidisciplinary Approach towards Teaching and Learning10.2174/9789815305180124010014(242-264)Online publication date: 18-Nov-2024
  • (2024)Enhancing Biomedical Knowledge Discovery for Diseases: An Open-Source Framework Applied on Rett Syndrome and Alzheimer’s DiseaseIEEE Access10.1109/ACCESS.2024.350971412(180652-180673)Online publication date: 2024
  • (2024)Towards a science exocortexDigital Discovery10.1039/D4DD00178HOnline publication date: 2024
  • (2024)NLP Applications—Biomedical LiteratureNatural Language Processing in Biomedicine10.1007/978-3-031-55865-8_13(351-395)Online publication date: 9-Jun-2024
  • (2023)Dynamics of link formation in networks structured on the basis of predictive termsRussian Technological Journal10.32362/2500-316X-2023-11-3-17-2911:3(17-29)Online publication date: 2-Jun-2023
  • (2023)Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer modelsBMC Bioinformatics10.1186/s12859-023-05539-y24:1Online publication date: 1-Nov-2023
  • (2023)Low-Latency Dimensional Expansion and Anomaly Detection Empowered Secure IoT NetworkIEEE Transactions on Network and Service Management10.1109/TNSM.2023.324679820:3(3865-3879)Online publication date: 1-Sep-2023
  • (2023)Interpretable Clinical Trial Search using Pubmed Citation Network2023 IEEE International Conference on Digital Health (ICDH)10.1109/ICDH60066.2023.00056(328-338)Online publication date: Jul-2023
  • (2023)Analysis of research dynamics in sport management using topic modellingManaging Sport and Leisure10.1080/23750472.2023.2200449(1-22)Online publication date: 15-Apr-2023
  • (2023)Graph embedding-based link prediction for literature-based discovery in Alzheimer’s DiseaseJournal of Biomedical Informatics10.1016/j.jbi.2023.104464145:COnline publication date: 1-Sep-2023
  • Show More Cited By

View Options

Login options

Full Access

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

HTML Format

View this article in HTML Format.

HTML Format

Figures

Tables

Media

Share

Share

Share this Publication link

Share on social media