Research Topics
Species | Martijn J SchuemieSummaryAffiliation: Erasmus MC Country: The Netherlands Publications
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Publications
Distribution of information in biomedical abstracts and full-text publicationsM J Schuemie
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, P O Box 1738, 3000 DR, Rotterdam, The Netherlands
Bioinformatics 20:2597-604. 2004..Only 30% of the gene symbols in the abstract are accompanied by their corresponding names, and a further 8% of the gene names are found in the full text. In the full text, only 18% of the gene symbols are accompanied by their gene names...- Structuring and extracting knowledge for the support of hypothesis generation in molecular biologyMarco Roos
Informatics Institute, University of Amsterdam, Amsterdam, 1098 SJ, The Netherlands
BMC Bioinformatics 10:S9. 2009..While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes... - Word sense disambiguation in the biomedical domain: an overviewMartijn J Schuemie
Biosemantics Group, Medical Informatics Department, Erasmus Medical Center, Dr Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
J Comput Biol 12:554-65. 2005..WSD algorithms should preferably be able to take into account both known and unknown senses of a word. Without WSD, automatic metaanalysis of large corpora of text will be error prone... - Methods for drug safety signal detection in longitudinal observational databases: LGPS and LEOPARDMartijn J Schuemie
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
Pharmacoepidemiol Drug Saf 20:292-9. 2011..Here a sequential set of methods for detecting and filtering drug safety signals in longitudinal databases is presented... - Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identificationMartijn J Schuemie
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, P O Box 1738, 3000 DR, Rotterdam, The Netherlands
J Biomed Inform 40:316-24. 2007..Application of 23 spelling variation rules to the combined dictionaries further increased recall. However, many rules appeared to have no effect and some appear to have a detrimental effect on precision... - GeneE: gene and protein query expansion with disambiguationMartijn J Schuemie
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, P O Box 2040, 3000 CA, Rotterdam, The Netherlands
Bioinformatics 26:147-8. 2010..The query expansion algorithm is also available as a web service. AVAILABILITY: http://biosemantics.org/geneE.. - Jane: suggesting journals, finding expertsMartijn J Schuemie
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
Bioinformatics 24:727-8. 2008..g. the title and abstract of a manuscript), can suggest journals and experts who have published similar articles. AVAILABILITY: http://biosemantics.org/jane... - Mapping the domain of medical informaticsM J Schuemie
Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Dr Molewaterplein 50, 3015GE Rotterdam, The Netherlands
Methods Inf Med 48:76-83. 2009..The domain of medical informatics (MI) is not well defined. It covers a wide range of research topics. Our objective is to characterize the field of MI by means of the scientific literature in this domain... - EU-ADR healthcare database network vs. spontaneous reporting system database: preliminary comparison of signal detectionGianluca Trifiro
Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
Stud Health Technol Inform 166:25-30. 2011..The methodology for signal detection in EU-ADR is still under development and testing phase... - Literature-based concept profiles for gene annotation: the issue of weightingRob Jelier
Erasmus University Medical Centre, Department of Medical Informatics, P O Box 2040, 3000 CA Rotterdam, The Netherlands
Int J Med Inform 77:354-62. 2008..Various schemes have been proposed to determine these weights, but no comparative studies of the different approaches are available. Here we compare several weighting approaches in a large scale classification experiment... - Novel protein-protein interactions inferred from literature contextHerman 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... - Thesaurus-based disambiguation of gene symbolsBob 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... - Anni 2.0: a multipurpose text-mining tool for the life sciencesRob Jelier
Department of Medical Informatics, Erasmus MC University Medical Center, Dr, Molewaterplein, Rotterdam, 3015 GE, The Netherlands
Genome Biol 9:R96. 2008..In this article we illustrate Anni's usability by applying the tool to two use cases: interpretation of a set of differentially expressed genes, and literature-based knowledge discovery... - A dictionary to identify small molecules and drugs in free textKristina M Hettne
Department of Health Risk Analysis and Toxicology, Maastricht University, Maastricht, The Netherlands
Bioinformatics 25:2983-91. 2009..Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers... - An inventory of publications on electronic medical records revisitedP W Moorman
Department of Medical Informatics, Erasmus MC, 3015 GE Rotterdam, The Netherlands
Methods Inf Med 48:454-8. 2009..In this short review we provide an update of our earlier inventories of publications indexed in MedLine with the MeSH term 'Medical Records Systems, Computerized'... - Rewriting and suppressing UMLS terms for improved biomedical term identificationKristina M Hettne
Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
J Biomed Semantics 1:5. 2010..abstract:.. - Combining electronic healthcare databases in Europe to allow for large-scale drug safety monitoring: the EU-ADR ProjectPreciosa M Coloma
Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
Pharmacoepidemiol Drug Saf 20:1-11. 2011..In this proof-of-concept paper we describe the framework, process, and preliminary results of combining data from European electronic healthcare record (EHR) databases for large-scale monitoring of drug safety...