Contents -- Acknowledgments -- 1 Introduction -- 1.1 What Is Biomedical Text Mining? -- 1.2 Example: The BRCA1 Pathway -- 1.3 Challenges in Biomedical Text Mining -- 2 Fundamental Concepts in Biomedical Text Analysis -- 2.1 Biomedical Text Sources -- 2.2 Natural Language Concepts -- 2.3 Challenges in Natural Language Processing -- 2.4 Natural Language Processing Tasks -- 2.5 Biomedical Vocabularies and Ontologies -- 2.6 Summary -- 3 Information Retrieval -- 3.1 Example: The BRCA1 Pathway (Revisited) -- 3.2 Indexing, Keywords, and Boolean Queries -- 3.3 Similarity Queries and the Vector Model -- 3.4 Beyond Cosine-Based Similarity -- 3.5 Text Categorization -- 3.6 Summary -- 4 Information Extraction -- 4.1 Named-Entity Recognition -- 4.2 Normalization of Named Entities -- 4.3 Relation Extraction -- 4.4 Summary -- 5 Evaluation -- 5.1 Performance Evaluation in Text Retrieval and Extraction -- 5.2 Evaluation Measures -- 5.3 Shared Evaluation Tasks -- 5.4 Summary -- 6 Putting It All Together: Current Applications and Future Directions -- 6.1 Recognizing and Linking Bioentities -- 6.2 Supporting Database Curation -- 6.3 Text as Data: A Gateway to Discovery and Prediction -- 6.4 Future Directions -- References -- Index.