Research Topics
| Martin KrallingerSummaryCountry: Spain Publications
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Detail Information
Publications
Corpus refactoring: a feasibility studyHelen 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...- Linking genes to literature: text mining, information extraction, and retrieval applications for biologyMartin 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/... - Text mining and protein annotations: the construction and use of protein description sentencesMartin 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... - Extraction of human kinase mutations from literature, databases and genotyping studiesMartin 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... - The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full textMartin Krallinger
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
BMC Bioinformatics 12:S3. 2011.... - PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extractionMartin 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... - An Overview of BioCreative II.5Florian 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... - FragKB: structural and literature annotation resource of conserved peptide fragments and residuesAshish 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... - Evaluation of text-mining systems for biology: overview of the Second BioCreative community challengeMartin Krallinger
Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
Genome Biol 9:S1. 2008.... - Overview of the protein-protein interaction annotation extraction task of BioCreative IIMartin 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... - How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experienceMartin 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... - Introducing meta-services for biomedical information extractionFlorian 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... - Creating reference datasets for systems biology applications using text miningMartin Krallinger
Structural Biology and Biocomputing Group, Spanish National Cancer Research Centre, Madrid, Spain
Ann N Y Acad Sci 1158:14-28. 2009.... - Analysis of biological processes and diseases using text mining approachesMartin 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... - Evaluation of BioCreAtIvE assessment of task 2Christian 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... - Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biologyAna 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... - Text-mining and information-retrieval services for molecular biologyMartin 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... - A sentence sliding window approach to extract protein annotations from biomedical articlesMartin Krallinger
Protein Design Group, National Center of Biotechnology, CNB CSIC, Cantoblanco, E 28049 Madrid, Spain
BMC Bioinformatics 6:S19. 2005.... - Text-mining approaches in molecular biology and biomedicineMartin 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... - Text mining for metabolic pathways, signaling cascades, and protein networksRobert 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...