Assessing agreement on classification tasks: the kappa statistic
Computational Linguistics
A corpus-based investigation of definite description use
Computational Linguistics
Anaphora for everyone: pronominal anaphora resoluation without a parser
COLING '96 Proceedings of the 16th conference on Computational linguistics - Volume 1
Overview and utilization of the NCI Thesaurus: Conference Papers
Comparative and Functional Genomics
The Penn Treebank: annotating predicate argument structure
HLT '94 Proceedings of the workshop on Human Language Technology
Domain-specific language models and lexicons for tagging
Journal of Biomedical Informatics
Text Mining for Biology And Biomedicine
Text Mining for Biology And Biomedicine
Guest Editorial: Current issues in biomedical text mining and natural language processing
Journal of Biomedical Informatics
Methodological Review: What can natural language processing do for clinical decision support?
Journal of Biomedical Informatics
Proceedings of the 1st ACM International Health Informatics Symposium
An interface for rapid natural language processing development in UIMA
HLT '11 Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies: Systems Demonstrations
Information extraction from pathology reports in a hospital setting
Proceedings of the 20th ACM international conference on Information and knowledge management
Journal of Biomedical Informatics
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We introduce an extensible and modifiable knowledge representation model to represent cancer disease characteristics in a comparable and consistent fashion. We describe a system, MedTAS/P which automatically instantiates the knowledge representation model from free-text pathology reports. MedTAS/P is based on an open-source framework and its components use natural language processing principles, machine learning and rules to discover and populate elements of the model. To validate the model and measure the accuracy of MedTAS/P, we developed a gold-standard corpus of manually annotated colon cancer pathology reports. MedTAS/P achieves F1-scores of 0.97-1.0 for instantiating classes in the knowledge representation model such as histologies or anatomical sites, and F1-scores of 0.82-0.93 for primary tumors or lymph nodes, which require the extractions of relations. An F1-score of 0.65 is reported for metastatic tumors, a lower score predominantly due to a very small number of instances in the training and test sets.