Zhiyong Lu

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Evaluation of Query Expansion Using MeSH in PubMed
    Zhiyong Lu
    National Center for Biotechnology Information, NCBI, National Library of Medicine, Bethesda, MD, 20894 USA, E mail
    Inf Retr Boston 12:69-80. 2009
  2. pmc The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    BMC Bioinformatics 12:S3. 2011
  3. pmc OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
    Lawrence Hunter
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    BMC Bioinformatics 9:78. 2008
  4. pmc Semantic role labeling for protein transport predicates
    Steven Bethard
    Computer Science Department, University of Colorado at Boulder, Boulder, CO, USA
    BMC Bioinformatics 9:277. 2008
  5. pmc Evaluating relevance ranking strategies for MEDLINE retrieval
    Zhiyong Lu
    NCBI NLM NIH, 8600 Rockville Pike, Bethesda, MD 20852, USA
    J Am Med Inform Assoc 16:32-6. 2009
  6. pmc Improving accuracy for identifying related PubMed queries by an integrated approach
    Zhiyong Lu
    National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Biomed Inform 42:831-8. 2009
  7. pmc Identifying related journals through log analysis
    Zhiyong Lu
    National Center for Biotechnology Information NCBI, 8600 Rockville Pike, Bethesda, MD 20852, USA
    Bioinformatics 25:3038-9. 2009
  8. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D13-25. 2012
  9. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
  10. pmc Extraction of data deposition statements from the literature: a method for automatically tracking research results
    Aurélie Névéol
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
    Bioinformatics 27:3306-12. 2011

Detail Information

Publications49

  1. pmc Evaluation of Query Expansion Using MeSH in PubMed
    Zhiyong Lu
    National Center for Biotechnology Information, NCBI, National Library of Medicine, Bethesda, MD, 20894 USA, E mail
    Inf Retr Boston 12:69-80. 2009
    ..Experimental results suggest that query expansion using MeSH in PubMed can generally improve retrieval performance, but the improvement may not affect end PubMed users in realistic situations...
  2. pmc The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    BMC Bioinformatics 12:S3. 2011
    ....
  3. pmc OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
    Lawrence Hunter
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    BMC Bioinformatics 9:78. 2008
    ....
  4. pmc Semantic role labeling for protein transport predicates
    Steven Bethard
    Computer Science Department, University of Colorado at Boulder, Boulder, CO, USA
    BMC Bioinformatics 9:277. 2008
    ....
  5. pmc Evaluating relevance ranking strategies for MEDLINE retrieval
    Zhiyong Lu
    NCBI NLM NIH, 8600 Rockville Pike, Bethesda, MD 20852, USA
    J Am Med Inform Assoc 16:32-6. 2009
    ....
  6. pmc Improving accuracy for identifying related PubMed queries by an integrated approach
    Zhiyong Lu
    National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Biomed Inform 42:831-8. 2009
    ..The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments...
  7. pmc Identifying related journals through log analysis
    Zhiyong Lu
    National Center for Biotechnology Information NCBI, 8600 Rockville Pike, Bethesda, MD 20852, USA
    Bioinformatics 25:3038-9. 2009
    ..To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data...
  8. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D13-25. 2012
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  9. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  10. pmc Extraction of data deposition statements from the literature: a method for automatically tracking research results
    Aurélie Névéol
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
    Bioinformatics 27:3306-12. 2011
    ..For this reason, it is important to be able to identify instances of data production and deposition for potential re-use. Herein, we report on the automatic identification of data deposition statements in research articles...
  11. pmc Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction
    Aurélie Névéol
    National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Biomed Inform 44:310-8. 2011
    ..Our experience suggests using an automatic tool to assist large-scale manual annotation projects. This helps speed-up the annotation time and improve annotation consistency while maintaining high quality of the final annotations...
  12. pmc BioC interoperability track overview
    Donald C Comeau
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R O C, Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695 7617, USA, WBI, Institute for Computer Science, Humboldt Universitat zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charite Universitatsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R O C, Germany
    Database (Oxford) 2014:. 2014
    ..The ease of use, broad support and rapidly growing number of tools demonstrate the need for and value of the BioC format. Database URL: http://bioc.sourceforge.net/...
  13. pmc DNorm: disease name normalization with pairwise learning to rank
    Robert Leaman
    National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, MD 20894, USA and Department of Biomedical Informatics, Arizona State University, 13212 East Shea Blvd, Scottsdale, AZ 85259, USA
    Bioinformatics 29:2909-17. 2013
    ....
  14. pmc tmVar: a text mining approach for extracting sequence variants in biomedical literature
    Chih Hsuan Wei
    National Center for Biotechnology Information NCBI, National Library of Medicine NLM, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 29:1433-9. 2013
    ..As such, new automatic approaches are greatly needed for extracting different kinds of mutations with high accuracy...
  15. pmc PubTator: a web-based text mining tool for assisting biocuration
    Chih Hsuan Wei
    National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:W518-22. 2013
    ..PubTator is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/. ..
  16. pmc Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information
    Sun Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Database (Oxford) 2012:bas042. 2012
    ..Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team...
  17. pmc SR4GN: a species recognition software tool for gene normalization
    Chih Hsuan Wei
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
    PLoS ONE 7:e38460. 2012
    ..Finally, SR4GN is implemented as a standalone software tool, thus making it convenient and robust for use in many text-mining applications. SR4GN can be downloaded at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/downloads/SR4GN...
  18. pmc Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
    Chih Hsuan Wei
    National Center for Biotechnology Information, Bethesda, MD 20894, USA
    Database (Oxford) 2016:. 2016
    ..Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/...
  19. pmc BioC: a minimalist approach to interoperability for biomedical text processing
    Donald C Comeau
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, Harvard Medical School, Harvard University, Boston, MA 02115 USA, Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA, Structural and Computational Biology Group, Spanish National Cancer Research Centre, Madrid E 28029, Spain, Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, National ICT Australia NICTA, Victoria Research Laboratory, The University of Melbourne, Parkville VIC 3010, Australia and Department of Biology, North Carolina State University, Raleigh, NC 27695, USA
    Database (Oxford) 2013:bat064. 2013
    ..We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net/ ..
  20. pmc Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts
    Chih Hsuan Wei
    National Center for Biotechnology Information NCBI, National Library of Medicine NLM, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Database (Oxford) 2012:bas041. 2012
    ..These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/..
  21. pmc Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE
    Aurélie Névéol
    National Center for Biotechnology Information, US National Library of Medicine, Bethesda, MD 20894, USA
    Database (Oxford) 2012:bas026. 2012
    ..Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/..
  22. pmc Click-words: learning to predict document keywords from a user perspective
    Rezarta Islamaj Doğan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 26:2767-75. 2010
    ..Although they often overlap, click-words differ significantly from other document keywords...
  23. pmc Systematic identification of pharmacogenomics information from clinical trials
    Jiao Li
    National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Biomed Inform 45:870-8. 2012
    ..This work has practical implications in enriching our existing knowledge on PGx gene-drug-disease relationships as well as suggesting crosslinks between ClinicalTrials.gov and other PGx knowledge bases...
  24. pmc Automatic identification and normalization of dosage forms in drug monographs
    Jiao Li
    National Library of Medicine, Bethesda, MD 20894, USA
    BMC Med Inform Decis Mak 12:9. 2012
    ..Each day, millions of health consumers seek drug-related information on the Web. Despite some efforts in linking related resources, drug information is largely scattered in a wide variety of websites of different quality and credibility...
  25. pmc PubMed and beyond: a survey of web tools for searching biomedical literature
    Zhiyong Lu
    National Center for Biotechnology Information NCBI, National Library of Medicine, Bethesda, MD 20894, USA
    Database (Oxford) 2011:baq036. 2011
    ..Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search...
  26. pmc A context-blocks model for identifying clinical relationships in patient records
    Rezarta Islamaj Doğan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    BMC Bioinformatics 12:S3. 2011
    ....
  27. pmc Finding query suggestions for PubMed
    Zhiyong Lu
    National Library of Medicine, Bethesda, MD, 20894, USA
    AMIA Annu Symp Proc 2009:396-400. 2009
    ..Automatic assessment using clickthrough data show that each day, the new feature is used consistently between 6% and 10% of the time when it is shown, suggesting that it has quickly become a popular new feature in PubMed...
  28. pmc Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing
    John D Burger
    The MITRE Corporation, Bedford, MA 01730, USA, Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and The University of Maryland, Baltimore County, Baltimore MD 21250, USA
    Database (Oxford) 2014:. 2014
    ..These techniques were applied to extract gene- mutation relations from biomedical abstracts with the goal of supporting production scale capture of gene-mutation-disease findings as an open source resource for personalized medicine...
  29. pmc Challenges in clinical natural language processing for automated disorder normalization
    Robert Leaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States Electronic address
    J Biomed Inform 57:28-37. 2015
    ..In this work, we aim to identify the cause for this performance difference and introduce general solutions...
  30. pmc Beyond accuracy: creating interoperable and scalable text-mining web services
    Chih Hsuan Wei
    National Center for Biotechnology Information NCBI, National Library of Medicine NLM, Bethesda, MD 20894, USA
    Bioinformatics 32:1907-10. 2016
    ..To maximize scalability, we have preprocessed all PubMed articles, and use a computer cluster for processing large requests of arbitrary text...
  31. pmc Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature
    Ayush Singhal
    National Center for Biotechnology Information NCBI, National Library of Medicine NLM, National Institutes of Health, Bethesda, MD, USA
    J Am Med Inform Assoc 23:766-72. 2016
    ..The aim of this work is to design a tool that automates the extraction of disease-related mutations from biomedical text to advance database curation for the support of precision medicine...
  32. pmc Mining chemical patents with an ensemble of open systems
    Robert Leaman
    National Center for Biotechnology Information NCBI, 8600 Rockville Pike, Bethesda, MD, USA
    Database (Oxford) 2016:. 2016
    ..Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/. ..
  33. ncbi request reprint Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health
    Michael Simmons
    National Center for Biotechnology Information NCBI, National Library of Medicine NLM, 8600 Rockville Pike, Bldg 38A, 10N1003A, Bethesda, MD, 20894, USA
    Adv Exp Med Biol 939:139-166. 2016
    ..Text mining is an indispensable tool for translating genotype-phenotype data into effective clinical care that will undoubtedly play an important role in the eventual realization of precision medicine...
  34. pmc GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains
    Chih Hsuan Wei
    National Center for Biotechnology Information NCBI, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biomed Res Int 2015:918710. 2015
    ..The GNormPlus source code and its annotated corpus are freely available, and the results of applying GNormPlus to the entire PubMed are freely accessible through our web-based tool PubTator. ..
  35. pmc Identifying named entities from PubMed for enriching semantic categories
    Sun Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA
    BMC Bioinformatics 16:57. 2015
    ..However, the standard terminology in such collections suffers from low usage in biomedical literature, e.g. only 13% of UMLS terms appear in MEDLINE...
  36. pmc Automatic extraction of drug indications from FDA drug labels
    Ritu Khare
    National Center for Biotechnology Information NCBI, NIH, Bethesda, MD 20894
    AMIA Annu Symp Proc 2014:787-94. 2014
    ..Given its performance, we conclude that our end-to-end approach has the potential to significantly reduce human annotation costs. ..
  37. pmc LabeledIn: cataloging labeled indications for human drugs
    Ritu Khare
    National Center for Biotechnology Information NCBI, U S National Institutes of Health, 8600 Rockville Pike, Bethesda, USA Electronic address
    J Biomed Inform 52:448-56. 2014
    ..Future work includes expanding our coverage to more drugs and integration with other resources. The LabeledIn dataset and the annotation guidelines are available at http://ftp.ncbi.nlm.nih.gov/pub/lu/LabeledIn/. ..
  38. pmc NCBI disease corpus: a resource for disease name recognition and concept normalization
    Rezarta Islamaj Dogan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Biomed Inform 47:1-10. 2014
    ..The NCBI disease corpus, guidelines and other associated resources are available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/. ..
  39. pmc Predicting clicks of PubMed articles
    Yuqing Mao
    National Center for Biotechnology Information NCBI, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    AMIA Annu Symp Proc 2013:947-56. 2013
    ..This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed. ..
  40. pmc Extracting Rx information from clinical narrative
    James G Mork
    US National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    J Am Med Inform Assoc 17:536-9. 2010
    ....
  41. pmc A New Method for Computational Drug Repositioning Using Drug Pairwise Similarity
    Jiao Li
    National Center for Biotechnology Information NCBI, National Institutes of Health NIH Bethesda, USA
    Proceedings (IEEE Int Conf Bioinformatics Biomed) 2012:1-4. 2012
    ..Our results indicate that combining chemical structure and drug target information results in better prediction performance and that the proposed approach successfully captures the implicit information between drug targets...
  42. pmc Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges
    Ayush Singhal
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Database (Oxford) 2016:. 2016
    ....
  43. pmc Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine
    Ayush Singhal
    National Center for Biotechnology Information NCBI, National Library of Medicine NLM, National Institutes of Health NIH, Bethesda, Maryland, United States of America
    PLoS Comput Biol 12:e1005017. 2016
    ..We conclude that our process represents an important and broadly applicable improvement to the state of the art for curation of disease-gene-variant relationships...
  44. pmc TaggerOne: joint named entity recognition and normalization with semi-Markov Models
    Robert Leaman
    National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 32:2839-46. 2016
    ..NER and normalization systems are also typically used in a serial pipeline, causing cascading errors and limiting the ability of the NER system to directly exploit the lexical information provided by the normalization...
  45. pmc Crowdsourcing and mining crowd data
    Robert Leaman
    National Center for Biotechnology Information NCBI, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Pac Symp Biocomput . 2015
    ..The following sections are included: Introduction, Session articles, Acknowledgements and References...
  46. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
    ..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  47. pmc Accessing biomedical literature in the current information landscape
    Ritu Khare
    National Center for Biotechnology Information, U S National Library of Medicine, NIH, Blg 38 A, Rm 1003B, 8600 Rockville Pike, Bethesda, MD, 20894, USA
    Methods Mol Biol 1159:11-31. 2014
    ..Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy...
  48. pmc The gene normalization task in BioCreative III
    Zhiyong Lu
    National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
    BMC Bioinformatics 12:S2. 2011
    ..We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k)...