Martin Krallinger

Summary

Country: Spain

Publications

  1. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi 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 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

Publications23

  1. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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...
  6. ncbi 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
    ....
  7. ncbi 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/...
  8. ncbi 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...
  9. ncbi 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 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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...
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi 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...
  20. ncbi 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...
  21. ncbi 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
    ....
  22. ncbi 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...
  23. ncbi 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...