Martin Krallinger

Summary

Country: Spain

Publications

  1. pmc Overview of the BioCreative III Workshop
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S1. 2011
  2. pmc BioCreative III interactive task: an overview
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S4. 2011
  3. pmc Corpus refactoring: a feasibility study
    Helen L Johnson
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 2:4. 2007
  4. pmc PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    Nucleic Acids Res 37:W160-5. 2009
  5. pmc Extraction of human kinase mutations from literature, databases and genotyping studies
    Martin Krallinger
    Spanish National Cancer Research Centre, Madrid, Spain
    BMC Bioinformatics 10:S1. 2009
  6. ncbi request reprint Text mining and protein annotations: the construction and use of protein description sentences
    Martin Krallinger
    Dep Struct Comp Biology Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro, 3, E 28029 Madrid, Spain
    Genome Inform 17:121-30. 2006
  7. 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
  8. pmc Linking genes to literature: text mining, information extraction, and retrieval applications for biology
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S8. 2008
  9. pmc How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience
    Martin Krallinger
    Structural and Computational Biology Group, Spanish National Cancer Research Centre CNIO, Spain
    Database (Oxford) 2012:bas017. 2012
  10. ncbi request reprint An Overview of BioCreative II.5
    Florian Leitner
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
    IEEE/ACM Trans Comput Biol Bioinform 7:385-99. 2010

Detail Information

Publications24

  1. pmc Overview of the BioCreative III Workshop
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S1. 2011
    ..This special issue contains overview papers for the three tasks of BioCreative III...
  2. pmc BioCreative III interactive task: an overview
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S4. 2011
    ..To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested...
  3. pmc Corpus refactoring: a feasibility study
    Helen L Johnson
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 2:4. 2007
    ..We tracked the total time expended and the success rates of the automated steps...
  4. pmc PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish National Cancer Center CNIO, Melchor Fernandez Almagro 3, Madrid, 28029, Spain
    Nucleic Acids Res 37:W160-5. 2009
    ..PLAN2L does not require registration and is freely accessible at http://zope.bioinfo.cnio.es/plan2l...
  5. pmc Extraction of human kinase mutations from literature, databases and genotyping studies
    Martin Krallinger
    Spanish National Cancer Research Centre, Madrid, Spain
    BMC Bioinformatics 10:S1. 2009
    ..Previously published mutation extraction approaches did not sufficiently distinguish between two fundamentally different variation origin categories, namely natural occurring and induced mutations generated through in vitro experiments...
  6. ncbi request reprint Text mining and protein annotations: the construction and use of protein description sentences
    Martin Krallinger
    Dep Struct Comp Biology Spanish National Cancer Centre CNIO, Melchor Fernandez Almagro, 3, E 28029 Madrid, Spain
    Genome Inform 17:121-30. 2006
    ..The steps used for the corpus construction and its features are presented. Moreover, some of the potential applications of the Prodisen corpus for biomedical text mining purposes are explored and the obtained results are presented...
  7. 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
    ....
  8. pmc Linking genes to literature: text mining, information extraction, and retrieval applications for biology
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S8. 2008
    ..Additional descriptions of some of the systems discussed here are available on the internet http://zope.bioinfo.cnio.es/bionlp_tools/...
  9. pmc How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience
    Martin Krallinger
    Structural and Computational Biology Group, Spanish National Cancer Research Centre CNIO, Spain
    Database (Oxford) 2012:bas017. 2012
    ..Special emphasis is given to protein-protein interaction data and PSI-MI terms referring to interaction detection methods...
  10. ncbi request reprint An Overview of BioCreative II.5
    Florian Leitner
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
    IEEE/ACM Trans Comput Biol Bioinform 7:385-99. 2010
    ..42 and AUC iP/R was 0.29. Ensemble systems improved performance for the interacting protein task...
  11. pmc Overview of the protein-protein interaction annotation extraction task of BioCreative II
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S4. 2008
    ..Text-mining systems have been implemented to extract binary protein interactions from articles, but a comprehensive comparison between the different techniques as well as with manual curation was missing...
  12. pmc Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S1. 2008
    ....
  13. pmc FragKB: structural and literature annotation resource of conserved peptide fragments and residues
    Ashish V Tendulkar
    Structural Biology and Biocomputing Programme, Spanish National Cancer Center, Madrid, Spain
    PLoS ONE 5:e9679. 2010
    ..Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining...
  14. doi request reprint Creating reference datasets for systems biology applications using text mining
    Martin Krallinger
    Structural Biology and Biocomputing Group, Spanish National Cancer Research Centre, Madrid, Spain
    Ann N Y Acad Sci 1158:14-28. 2009
    ....
  15. pmc Introducing meta-services for biomedical information extraction
    Florian Leitner
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S6. 2008
    ..This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations...
  16. 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/ ..
  17. pmc Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology
    Ana M Rojas
    Centro Nacional de Investigaciones Oncologicas, Structural Biology and Biocomputing Programme, Madrid, Spain
    PLoS ONE 7:e31813. 2012
    ..Combining integrated bio-computational approaches and single gene experimental follow-ups could be key to exploring the still hidden regions of the human spindle system...
  18. doi request reprint Analysis of biological processes and diseases using text mining approaches
    Martin Krallinger
    Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
    Methods Mol Biol 593:341-82. 2010
    ..Future trends in text mining emphasize the importance of community efforts such as the BioCreative challenge for the development and integration of multiple systems into a common platform provided by the BioCreative Metaserver...
  19. pmc Evaluation of BioCreAtIvE assessment of task 2
    Christian Blaschke
    Bioalma SL, Ronda de Poniente 4 2nd floor, Tres Cantos, E 28760, Madrid, Spain
    BMC Bioinformatics 6:S16. 2005
    ..In order to make text mining tools useable in real world scenarios, for instance to assist database curators during annotation of protein function, comparisons and evaluations of different approaches on full text articles are needed...
  20. pmc Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining
    Jose M G Izarzugaza
    Structural Computational Biology Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre Madrid, Spain
    Front Physiol 3:323. 2012
    ..Finally, we will discuss how text mining approaches constitute a powerful tool for the interpretation of the consequences of mutations in the context of disease genome analysis with particular focus on cancer...
  21. pmc Text-mining and information-retrieval services for molecular biology
    Martin Krallinger
    National Center of Biotechnology, CNB CSIC, Cantoblanco, E 28049 Madrid, Spain
    Genome Biol 6:224. 2005
    ..A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators...
  22. pmc A sentence sliding window approach to extract protein annotations from biomedical articles
    Martin Krallinger
    Protein Design Group, National Center of Biotechnology, CNB CSIC, Cantoblanco, E 28049 Madrid, Spain
    BMC Bioinformatics 6:S19. 2005
    ....
  23. ncbi request reprint Text-mining approaches in molecular biology and biomedicine
    Martin Krallinger
    Protein Design Group, National Center of Biotechnology CNB CSIC, Cantoblanco, E 28049 Madrid, Spain
    Drug Discov Today 10:439-45. 2005
    ..Finally, we will consider the recent evolution of this field and the efforts for community-based evaluations...
  24. ncbi request reprint Text mining for metabolic pathways, signaling cascades, and protein networks
    Robert Hoffmann
    National Center for Biotechnology, CNB CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
    Sci STKE 2005:pe21. 2005
    ..The next challenge is the generation of comprehensive information regarding the general function of signaling pathways and protein interaction networks...