Zhiyong Lu

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  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 39:D38-51. 2011
  9. 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
  10. 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

Collaborators

Detail Information

Publications27

  1. 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
    ....
  2. 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
    ....
  3. 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
    ....
  4. 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
    ....
  5. 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...
  6. 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...
  7. 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...
  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 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...
  9. 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...
  10. 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...
  11. 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...
  12. 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/. ..
  13. 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...
  14. 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...
  15. 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/..
  16. 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/..
  17. 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...
  18. 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...
  19. 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...
  20. 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
    ....
  21. 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...
  22. 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...
  23. 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
    ....
  24. 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
    ....
  25. doi request reprint 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/ ..
  26. 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)...
  27. 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...