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Motivation: As the number of clinical reports in the peer-reviewed medical literature keeps growing, there is an increasing need for online search tools to find and analyze publications on patients with similar clinical characteristics. This problem is especially critical and challenging for rare diseases, where publications of large series are scarce. Through an applied example, we illustrate how to automatically identify new relevant cases and semantically annotate the relevant literature about patient case reports to capture the phenotype of a rare disease named cerebrotendinous xanthomatosis.Results: Our results confirm that it is possible to automatically identify new relevant case reports with a high precision and to annotate them with a satisfactory quality (74% F-measure). Automated annotation with an emphasis to entirely describe all phenotypic abnormalities found in a disease may facilitate curation efforts by supplying phenotype retrieval and assessment of their frequency.Availability and Supplementary information: http://www.usc.es/keam/Phenotype Annotation/.Database URL: http://www.usc.es/keam/PhenotypeAnnotation/