Purpose： The late Don R. Swanson was well appreciated during his lifetime as Dean of the Graduate Library School at University of Chicago, as winner of the American Society for Information Science Award of Merit for ...Purpose： The late Don R. Swanson was well appreciated during his lifetime as Dean of the Graduate Library School at University of Chicago, as winner of the American Society for Information Science Award of Merit for 2000, and as author of many seminal articles. In this informal essay, I will give my personal perspective on Don＇s contributions to science, and outline some current and future directions in literature-based discovery that are rooted in concepts that he developed.Design/methodology/approach： Personal recollections and literature review. Findings： The Swanson A-B-C model of literature-based discovery has been successfully used by laboratory investigators analyzing their findings and hypotheses. It continues to be a fertile area of research in a wide range of application areas including text mining, drug repurposing, studies of scientific innovation, knowledge discovery in databases, and bioinformatics. Recently, additional modes of discovery that do not follow the A-B-C model have also been proposed and explored （e.g. so-called storytelling, gaps, analogies, link prediction, negative consensus, outliers, and revival of neglected or discarded research questions）. Research limitations： This paper reflects the opinions of the author and is not a comprehensive nor technically based review of literature-based discovery. Practical implications： The general scientific public is still not aware of the availability of tools for literature-based discovery. Our Arrowsmith project site maintains a suite of discovery tools that are free and open to the public （http：//arrowsmith.psych.uic.edu）, as does BITOLA which is maintained by Dmitar Hristovski （http：// http：//ibmi.mf.uni-lj.si/bitola）, and Epiphanet which is maintained by Trevor Cohen （http：//epiphanet.uth.tme.edu/）. Bringing user-friendly tools to the public should be a high priority, since even more than advancing basic research in informatics, it is vital that we ensure that scientists actually use discovery tools and that these are actually able to help them make experimental discoveries in the lab and in the clinic. Originality/value： This paper discusses problems and issues which were inherent in Don＇s thoughts during his life, including those which have not yet been fully taken up and studied systematically.展开更多
Inflammatory bowel disease(IBD)incidence has been increasing steadily,most dramatically in the Western developed countries.Treatment often includes lifelong immunosuppressive therapy and surgery.There is a critical ne...Inflammatory bowel disease(IBD)incidence has been increasing steadily,most dramatically in the Western developed countries.Treatment often includes lifelong immunosuppressive therapy and surgery.There is a critical need to reduce the burden of IBD and to discover medical therapies with better efficacy and fewer potential side-effects.Repurposing of treatments originally studied in other diseases with similar pathogenesis is less costly and time intensive than de novo drug discovery.This study used a treatment repurposing methodology,the literature-related discovery and innovation(LRDI)text mining system,to identify potential treatments(developed for non-IBD diseases)with sufficient promise for extrapolation to treatment of IBD.By searching for desirable patterns of twenty key biomarkers relevant to IBD(e.g.,inflammation,reactive oxygen species,autophagy,barrier function),the LRDI-based query retrieved approximately 9500 records from Medline.The most recent 350 records were further analyzed for proof-of-concept.Approximately 18%(64/350)met the criteria for discovery(not previously studied in IBD human or animal models)and relevance for application to IBD treatment.Many of the treatments were compounds derived from herbal remedies,and the majority of treatments were being studied in cancer,diabetes,and central nervous system disease,such as depression and dementia.As further validation of the search strategy,the query identified ten treatments that have just recently begun testing in IBD models in the last three years.Literature-related discovery and innovation text mining contains a unique search strategy with tremendous potential to identify treatments for repurposing.A more comprehensive query with additional key biomarkers would have retrieved many thousands more records,further increasing the yield of IBD treatment repurposing discovery.展开更多
Based on the analysis of the existing ranking terminology or subject relevancy of documents methods through an intermediary collection as a catalyst(designated as Group B collection) for the purpose of of non-interact...Based on the analysis of the existing ranking terminology or subject relevancy of documents methods through an intermediary collection as a catalyst(designated as Group B collection) for the purpose of of non-interactive literature-based discovery, this article proposes a bi-directional document occurrence frequency based ranking method according to the 'concurrence theory' and the degree and extent of the subject relevancy. This method explores and further refines the ranking method that is based on the occurrence frequency of the usage of certain terminologies and documents and injects a new insightful perspective of the concurrence of appropriate terminologies/documents in the 'low occurrence frequency component' of three non-interactive document collections. A preliminary experiment was conducted to analyze and to test the significance and viability of our newly designed operational method.展开更多
基金supported by NIH grants R01LM010817 and P01AG039347
文摘Purpose： The late Don R. Swanson was well appreciated during his lifetime as Dean of the Graduate Library School at University of Chicago, as winner of the American Society for Information Science Award of Merit for 2000, and as author of many seminal articles. In this informal essay, I will give my personal perspective on Don＇s contributions to science, and outline some current and future directions in literature-based discovery that are rooted in concepts that he developed.Design/methodology/approach： Personal recollections and literature review. Findings： The Swanson A-B-C model of literature-based discovery has been successfully used by laboratory investigators analyzing their findings and hypotheses. It continues to be a fertile area of research in a wide range of application areas including text mining, drug repurposing, studies of scientific innovation, knowledge discovery in databases, and bioinformatics. Recently, additional modes of discovery that do not follow the A-B-C model have also been proposed and explored （e.g. so-called storytelling, gaps, analogies, link prediction, negative consensus, outliers, and revival of neglected or discarded research questions）. Research limitations： This paper reflects the opinions of the author and is not a comprehensive nor technically based review of literature-based discovery. Practical implications： The general scientific public is still not aware of the availability of tools for literature-based discovery. Our Arrowsmith project site maintains a suite of discovery tools that are free and open to the public （http：//arrowsmith.psych.uic.edu）, as does BITOLA which is maintained by Dmitar Hristovski （http：// http：//ibmi.mf.uni-lj.si/bitola）, and Epiphanet which is maintained by Trevor Cohen （http：//epiphanet.uth.tme.edu/）. Bringing user-friendly tools to the public should be a high priority, since even more than advancing basic research in informatics, it is vital that we ensure that scientists actually use discovery tools and that these are actually able to help them make experimental discoveries in the lab and in the clinic. Originality/value： This paper discusses problems and issues which were inherent in Don＇s thoughts during his life, including those which have not yet been fully taken up and studied systematically.
文摘Inflammatory bowel disease(IBD)incidence has been increasing steadily,most dramatically in the Western developed countries.Treatment often includes lifelong immunosuppressive therapy and surgery.There is a critical need to reduce the burden of IBD and to discover medical therapies with better efficacy and fewer potential side-effects.Repurposing of treatments originally studied in other diseases with similar pathogenesis is less costly and time intensive than de novo drug discovery.This study used a treatment repurposing methodology,the literature-related discovery and innovation(LRDI)text mining system,to identify potential treatments(developed for non-IBD diseases)with sufficient promise for extrapolation to treatment of IBD.By searching for desirable patterns of twenty key biomarkers relevant to IBD(e.g.,inflammation,reactive oxygen species,autophagy,barrier function),the LRDI-based query retrieved approximately 9500 records from Medline.The most recent 350 records were further analyzed for proof-of-concept.Approximately 18%(64/350)met the criteria for discovery(not previously studied in IBD human or animal models)and relevance for application to IBD treatment.Many of the treatments were compounds derived from herbal remedies,and the majority of treatments were being studied in cancer,diabetes,and central nervous system disease,such as depression and dementia.As further validation of the search strategy,the query identified ten treatments that have just recently begun testing in IBD models in the last three years.Literature-related discovery and innovation text mining contains a unique search strategy with tremendous potential to identify treatments for repurposing.A more comprehensive query with additional key biomarkers would have retrieved many thousands more records,further increasing the yield of IBD treatment repurposing discovery.
基金supported by Humanities and Social Science Foundation of Ministry of Education of China(Grant No.07JA870005)
文摘Based on the analysis of the existing ranking terminology or subject relevancy of documents methods through an intermediary collection as a catalyst(designated as Group B collection) for the purpose of of non-interactive literature-based discovery, this article proposes a bi-directional document occurrence frequency based ranking method according to the 'concurrence theory' and the degree and extent of the subject relevancy. This method explores and further refines the ranking method that is based on the occurrence frequency of the usage of certain terminologies and documents and injects a new insightful perspective of the concurrence of appropriate terminologies/documents in the 'low occurrence frequency component' of three non-interactive document collections. A preliminary experiment was conducted to analyze and to test the significance and viability of our newly designed operational method.
