Erik M van Mulligen

Summary

Affiliation: Erasmus MC
Country: The Netherlands

Publications

  1. doi request reprint The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships
    Erik M van Mulligen
    Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Biomed Inform 45:879-84. 2012
  2. pmc Training multidisciplinary biomedical informatics students: three years of experience
    Erik M van Mulligen
    Deartment of Medical Informatics, Erasmus University Medical Center Rotterdam, PO Box 1738, 3000 DR, Rotterdam, The Netherlands
    J Am Med Inform Assoc 15:246-54. 2008
  3. ncbi request reprint Contextual annotation of web pages for interactive browsing
    Erik van Mulligen
    Dept of Medical Informatics, Erasmus University Medical Center Rotterdam, PO Box 1738, 3000 DR Rotterdam, The Netherlands
    Stud Health Technol Inform 107:94-8. 2004
  4. pmc Using rule-based natural language processing to improve disease normalization in biomedical text
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Am Med Inform Assoc 20:876-81. 2013
  5. pmc Extraction of chemical-induced diseases using prior knowledge and textual information
    Ewoud Pons
    Department of Medical Informatics Department of Radiology, Erasmus University Medical Center, 3000 DR Rotterdam, PO Box 2040, The Netherlands
    Database (Oxford) 2016:. 2016
  6. pmc Knowledge-based extraction of adverse drug events from biomedical text
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, P, O, Box 2040, 3000, CA, Rotterdam, The Netherlands
    BMC Bioinformatics 15:64. 2014
  7. pmc Training text chunkers on a silver standard corpus: can silver replace gold?
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, P, O, Box 2040, 3000 CA Rotterdam, The Netherlands
    BMC Bioinformatics 13:17. 2012
  8. doi request reprint Evaluation of a multinational, multilingual vaccine debate on Twitter
    Benedikt F H Becker
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands Electronic address
    Vaccine 34:6166-6171. 2016
  9. doi request reprint Using an ensemble system to improve concept extraction from clinical records
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Biomed Inform 45:423-8. 2012
  10. pmc Thesaurus-based disambiguation of gene symbols
    Bob J A Schijvenaars
    Department of Medical Informatics, Erasmus University Medical Center Rotterdam, P O Box 1738, 3000 DR Rotterdam, The Netherlands
    BMC Bioinformatics 6:149. 2005

Collaborators

Detail Information

Publications19

  1. doi request reprint The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships
    Erik M van Mulligen
    Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Biomed Inform 45:879-84. 2012
    ..These annotated relationships will be used to train and evaluate text-mining software to capture these relationships in texts...
  2. pmc Training multidisciplinary biomedical informatics students: three years of experience
    Erik M van Mulligen
    Deartment of Medical Informatics, Erasmus University Medical Center Rotterdam, PO Box 1738, 3000 DR, Rotterdam, The Netherlands
    J Am Med Inform Assoc 15:246-54. 2008
    ....
  3. ncbi request reprint Contextual annotation of web pages for interactive browsing
    Erik van Mulligen
    Dept of Medical Informatics, Erasmus University Medical Center Rotterdam, PO Box 1738, 3000 DR Rotterdam, The Netherlands
    Stud Health Technol Inform 107:94-8. 2004
    ..The new approach merges the searching and browsing into one combined "read-and-search" mode and alleviates the shift users are normally forced to between searching and reading...
  4. pmc Using rule-based natural language processing to improve disease normalization in biomedical text
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Am Med Inform Assoc 20:876-81. 2013
    ..Popular concept normalization tools in the biomedical field are dictionary-based. In this study we investigate the usefulness of natural language processing (NLP) as an adjunct to dictionary-based concept normalization...
  5. pmc Extraction of chemical-induced diseases using prior knowledge and textual information
    Ewoud Pons
    Department of Medical Informatics Department of Radiology, Erasmus University Medical Center, 3000 DR Rotterdam, PO Box 2040, The Netherlands
    Database (Oxford) 2016:. 2016
    ..Several post-challenge modifications of the systems resulted in substantially improvedF-scores (0.828 for DNER and 0.602 for CID). RELigator is available as a web service athttp://biosemantics.org/index.php/software/religator. ..
  6. pmc Knowledge-based extraction of adverse drug events from biomedical text
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, P, O, Box 2040, 3000, CA, Rotterdam, The Netherlands
    BMC Bioinformatics 15:64. 2014
    ..The performance of the system was evaluated on the ADE corpus, consisting of 1644 abstracts with manually annotated adverse drug events. Fifty abstracts were used for training, the remaining abstracts were used for testing...
  7. pmc Training text chunkers on a silver standard corpus: can silver replace gold?
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, P, O, Box 2040, 3000 CA Rotterdam, The Netherlands
    BMC Bioinformatics 13:17. 2012
    ..We explored two use scenarios: one in which chunkers are trained on an SSC in a new domain for which a GSC is not available, and one in which chunkers are trained on an available, although small GSC but supplemented with an SSC...
  8. doi request reprint Evaluation of a multinational, multilingual vaccine debate on Twitter
    Benedikt F H Becker
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands Electronic address
    Vaccine 34:6166-6171. 2016
    ..This research further explores the value of monitoring social media to understand public sentiment about an international vaccination programme...
  9. doi request reprint Using an ensemble system to improve concept extraction from clinical records
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Biomed Inform 45:423-8. 2012
    ..The ensemble-based approach is straightforward and allows the balancing of precision versus recall of the combined system. The ensemble system is freely available and can easily be extended, integrated in other systems, and retrained...
  10. pmc Thesaurus-based disambiguation of gene symbols
    Bob J A Schijvenaars
    Department of Medical Informatics, Erasmus University Medical Center Rotterdam, P O Box 1738, 3000 DR Rotterdam, The Netherlands
    BMC Bioinformatics 6:149. 2005
    ..Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck...
  11. pmc Rewriting and suppressing UMLS terms for improved biomedical term identification
    Kristina M Hettne
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Biomed Semantics 1:5. 2010
    ..The 50 most frequently found terms together with a sample of 100 randomly selected terms were evaluated for every rule...
  12. ncbi request reprint Databases for knowledge discovery. Examples from biomedicine and health care
    Jan H van Bemmel
    Department of Medical Informatics, Erasmus University and Erasmus MC Rotterdam, Dr Molewaterplein 50, P O Box 1738, 3000 DR Rotterdam, The Netherlands
    Int J Med Inform 75:257-67. 2006
    ..The examples that we shall offer are representative for using computers in scientific research in general, but in medical and health informatics in particular...
  13. doi request reprint Comparing and combining chunkers of biomedical text
    Ning Kang
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Biomed Inform 44:354-60. 2011
    ..The combination of chunker results by a simple voting scheme can further improve performance and allows for different precision-recall settings...
  14. pmc Novel protein-protein interactions inferred from literature context
    Herman H H B M van Haagen
    Biosemantics Association, Department of Human Genetics, Leiden University Medical Center, Leiden, and Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    PLoS ONE 4:e7894. 2009
    ..Our framework can be used for prioritizing potential interaction partners, hitherto undiscovered, for follow-up studies and to aid the generation of accurate protein interaction maps...
  15. pmc A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC
    Jan A Kors
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Am Med Inform Assoc 22:948-56. 2015
    ..To create a multilingual gold-standard corpus for biomedical concept recognition...
  16. pmc Evaluating Social Media Networks in Medicines Safety Surveillance: Two Case Studies
    Preciosa M Coloma
    Department of Medical Informatics, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
    Drug Saf 38:921-30. 2015
    ..There is growing interest in whether social media can capture patient-generated information relevant for medicines safety surveillance that cannot be found in traditional sources...
  17. doi request reprint A novel feature-based approach to extract drug-drug interactions from biomedical text
    Quoc Chinh Bui
    Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Informatics Institute, University of Amsterdam, The Netherlands, Complexity Institute, Nanyang Technological University, Singapore and ITMO University, St Petersburg, Russian Federation
    Bioinformatics 30:3365-71. 2014
    ..As most newly discovered DDIs are made available through scientific publications, automatic DDI extraction is highly relevant...
  18. pmc Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining
    Kristina M Hettne
    Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
    J Cheminform 2:3. 2010
    ..ChemSpider is a chemical database that has undergone extensive manual curation aimed at establishing valid chemical name-to-structure relationships...
  19. ncbi request reprint Ligand-based approach to in silico pharmacology: nuclear receptor profiling
    Jordi Mestres
    Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d Investigació Mèdica and Universitat Pompeu Fabra, Dr Aiguader 80, 08003 Barcelona, Catalonia, Spain
    J Chem Inf Model 46:2725-36. 2006
    ..Overall, the present findings suggest that ligand-based approaches to protein family profiling appear as a promising means toward the establishment of novel tools for in silico pharmacology...