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Literature-based Resurrection of Neglected Medical Discoveries

Don R. Swanson
2011 Journal of Biomedical Discovery and Collaboration  
The context of literature-based discovery In our previous work on literature-based discovery, the case in which the A and C literatures were disjoint --i.e. had no articles in common --has been of central  ...  Just how much can be estimated from the scope of the Medical Subject Heading (MeSH) schedules.  ... 
doi:10.5210/disco.v6i0.3515 pmid:21509725 pmcid:PMC3097086 fatcat:dw3hppsflzeahesfbgf3fgzzu4

BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation

Anthony ML Liekens, Jeroen De Knijf, Walter Daelemans, Bart Goethals, Peter De Rijk, Jurgen Del-Favero
2011 Genome Biology  
We present BioGraph, a data integration and data mining platform for the exploration and discovery of biomedical information.  ...  The platform offers prioritizations of putative disease genes, supported by functional hypotheses.  ...  Acknowledgements This work was supported by the GOA project 'BioGraph: Text mining on heterogeneous databases: An application to optimized discovery of disease relevant genetic variants' of the University  ... 
doi:10.1186/gb-2011-12-6-r57 pmid:21696594 pmcid:PMC3218845 fatcat:zrc6r2d6djep3bmuu7ghq5swlu

An interactive system for finding complementary literatures: a stimulus to scientific discovery

Don R. Swanson, Neil R. Smalheiser
1997 Artificial Intelligence  
Information developed in one area of research may be of value in another without anyone becoming aware of the fact.  ...  We describe and evaluate interactive software and database search strategies that facilitate the discovery of previously unknown cross specialty information of scientific interest.  ...  The 1996 Metathesaurus is a synthesis of 38 different source vocabularies (one of which is Medical Subject Headings (MeSH)).  ... 
doi:10.1016/s0004-3702(97)00008-8 fatcat:f5tnuxr2pndrxdjz6pp4opiwxu

Literature mining in support of drug discovery

P. Agarwal, D. B. Searls
2008 Briefings in Bioinformatics  
While attention in this arena has tended to focus on integration of primary data from omics and other large platform technologies contributing to drug discovery and development, the scientific literature  ...  The drug discovery enterprise provides strong drivers for data integration.  ...  Acknowledgements The authors would like to thank Vinod Kumar, Liwen Liu, Tom White, Dilip Rajagopalan, William Reisdorf, Karen Kabnick and Ron Liu for their contributions.  ... 
doi:10.1093/bib/bbn035 pmid:18820304 fatcat:kwdvc766yvgnnnslnupz2r7qky

Reflective Random Indexing and indirect inference: A scalable method for discovery of implicit connections

Trevor Cohen, Roger Schvaneveldt, Dominic Widdows
2010 Journal of Biomedical Informatics  
The discovery of implicit connections between terms that do not occur together in any scientific document underlies the model of literature-based knowledge discovery first proposed by Swanson.  ...  RRI is shown to lead to more clearly related indirect connections and to outperform existing RI implementations in the prediction of future direct co-occurrence in the MEDLINE corpus.  ...  We would like to thank Tom Landauer for providing the TASA corpus, and to acknowledge Google Inc. for their support of author DW's ongoing research on the subject.  ... 
doi:10.1016/j.jbi.2009.09.003 pmid:19761870 fatcat:vzlnntofhfc6tbvbwwcusgld2y

Text-based discovery in biomedicine: the architecture of the DAD-system

M Weeber, H Klein, A R Aronson, J G Mork, L T de Jong-van den Berg, R Vos
2000 Proceedings. AMIA Symposium  
As scientific publications are a condensation of this knowledge, literature-based discovery tools may help the individual scientist to explore new useful domains.  ...  We describe the general architecture and illustrate its operation by a simulation of a well-known text-based discovery: The favorable effects of fish oil on patients suffering from Raynaud's disease [1  ...  Using text one discipline may be usefulfor the other without rewords, Medical Subject Headings (MeSH), and many searchers knowing it.  ... 
pmid:11080015 pmcid:PMC2243779 fatcat:5ctiddditvgs3duyqdxmikd3nq

Scientometric analysis and knowledge mapping of literature-based discovery (1986-2020) [article]

Andrej Kastrin, Dimitar Hristovski
2020 arXiv   pre-print
Literature-based discovery (LBD) aims to discover valuable latent relationships between disparate sets of literatures.  ...  The United States plays a leading role in LBD research with the University of Chicago as the dominant institution.  ...  Availability of data and material The data set discussed in this paper has been deposited in the public repository Zenodo ( and is freely available to the research  ... 
arXiv:2006.08486v1 fatcat:fhtplszgcrft3j6prvvtdbuw6u

Outlier Detection in Cross-Context Link Discovery for Creative Literature Mining

I. Petric, B. Cestnik, N. Lavrac, T. Urbancic
2010 Computer journal  
This paper investigates the role of outliers in literature-based knowledge discovery.  ...  The proposed approach contributes to cross-context link discovery by proving the utility of outlier detection for finding bisociative links in the process of autism literature exploration, as well as by  ...  ACKNOWLEDGEMENT The authors acknowledge helpful discussions with Blaž Fortuna (main developer of OntoGen), Marta Macedoni-Lukšič (medical expert on autism) and the partners of the BISON consortium.  ... 
doi:10.1093/comjnl/bxq074 fatcat:tkfrx66xenbxfpupkcq2i75b6q

Context-driven automatic subgraph creation for literature-based discovery

Delroy Cameron, Ramakanth Kavuluru, Thomas C. Rindflesch, Amit P. Sheth, Krishnaprasad Thirunarayan, Olivier Bodenreider
2015 Journal of Biomedical Informatics  
Literature-based discovery (LBD) is characterized by uncovering hidden associations in non-interacting scientific literature.  ...  Subject Heading (MeSH) descriptors.  ...  Conflict of interest: None. Acknowledgement This research was supported in part by the Intramural Research Program of the US National Institutes of Health, National Library of Medicine.  ... 
doi:10.1016/j.jbi.2015.01.014 pmid:25661592 pmcid:PMC4888806 fatcat:hiladpi4jjhr7e72rtyrzyqtl4

Using Literature Based Discovery to Gain Insights Into the Metabolomic Processes of Cardiac Arrest

Sam Henry, D. Shanaka Wijesinghe, Aidan Myers, Bridget T. McInnes
2021 Frontiers in Research Metrics and Analytics  
Observed changes in metabolite levels are indicative of changes in these pathways, and provide valuable insights toward the cause, progression, and treatment of diseases.  ...  These insights lead to our proposal (for the first time) of LCAT as a druggable target; the effects of which are supported by in vivo studies which were brought forth by this work.  ...  Medical Subject Headings). It includes over 100 knowledge sources and classification systems encoded with different semantic and syntactic structures.  ... 
doi:10.3389/frma.2021.644728 pmid:34250435 pmcid:PMC8267364 fatcat:5y6v6e7afrcxxmvrgnmt4wtzem

Adopting Literature-based Discovery on Rehabilitation Therapy Repositioning for Stroke [article]

Guilin Meng, Yong Huang, Qi Yu, Ying Ding, David Wild, Yanxin Zhao, Min Song, Xueyuan Liu
2018 bioRxiv   pre-print
One informatics translational approach, called ABC model in Literature-based Discovery, was used to mine an existing rehabilitation candidate which is most likely to be repositioned for stroke.  ...  The results seem to be promoted in clinical knowledge discovery.  ...  ABC model has played a number of 266 roles in the direction of drug discovery and repositioning.  ... 
doi:10.1101/422154 fatcat:nfi4unyy4bgivdnnnfxhpexd4u

Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects

Andreas Lardos, Ahmad Aghaebrahimian, Anna Koroleva, Julia Sidorova, Evelyn Wolfram, Maria Anisimova, Manuel Gil
2022 Frontiers in Bioinformatics  
Literature-based discovery (LBD) mines existing literature in order to generate new hypotheses by finding links between previously disconnected pieces of knowledge.  ...  Most of the 91 natural product-related discoveries in our sample of reported use cases of LBD were addressed at a computer science audience.  ...  Terms and relations in different LBD systems can be represented as n-grams, Unified Medical Language System (UMLS) concepts (Rindflesch and Fiszman, 2003; Kilicoglu et al., 2020) , Medical Subject Heading  ... 
doi:10.3389/fbinf.2022.827207 fatcat:dduof4mwrza5lcqzwqtq2fuz44

Discovery as Regulation

Diego Zambrano
2020 Michigan law review  
The core insight of the project is that in the private-enforcement context—where Congress deliberately employs private litigants as the main method of statutory enforcement—there is a surprisingly strong  ...  This approach has a vast array of implications for the scope of discovery as well as the debate over costs.  ...  the role that discovery has grown to play in complex litigation and private-enforcement cases. 93 My goal in this Section is to very briefly explain the conventional view of discovery, which is based  ... 
doi:10.36644/mlr.119.1.discovery fatcat:hdichybx7jgqfml66p7kd6voci

The Brain is a Social Network

Claudio Tomazzoli, Silvia Francesca Storti, Ilaria Boscolo Galazzo, Matteo Cristani, Gloria Menegaz
2017 International Workshop on Knowledge Discovery on the Web  
domain such as brain connectivity.  ...  This approach is mainly grounded upon the correct usage of three basic graph-theoretic measures: degree centrality, closeness centrality and betweeness centrality.  ...  Conclusions In this paper we investigated the application of a model of Semantic Social Network analysis, based on topic centrality, to the description of the brain functional connectivity evoked by di  ... 
dblp:conf/kdweb/TomazzoliSGCM17 fatcat:k2c5w6vcszhmna5czn3x4gnux4

Exploration of Shared Themes Between Food Security and Internet of Things Research Through Literature-Based Discovery

Cristian Mejia, Yuya Kajikawa
2021 Frontiers in Research Metrics and Analytics  
This paper applied a literature-based discovery methodology utilizing citation networks and text mining in order to extract and represent shared terminologies found in disjoint academic literature on food  ...  The topic of food security includes research on improvements in nutrition, sustainable agriculture, and a plurality of other social challenges, while the Internet of Things refers to a collection of technologies  ...  Medline Subject Heading (MESH) (Baker, 2010) .  ... 
doi:10.3389/frma.2021.652285 pmid:34056514 pmcid:PMC8159171 fatcat:wrisbsg3ebbcfk6fstdhtmzf7a
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