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0. Title and abstract
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1. Introduction to bioinformatics
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1.1 Bioinformatics?
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1.2 Proteins
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1.2.1 What are proteins?
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1.2.2 Protein sequence databases
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1.2.3 Database redundancy
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1.2.4 Annotation
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1.3 Genes
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1.3.1 What are genes?
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1.3.2 Nucleic acid sequence databases
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2. BIOML fundamentals
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2.1 Introduction
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2.2 Logical layout–trees, branches and leaves
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2.3 Logical layout using nested statements
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3. Elements and tags
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3.1 Introduction
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3.2 Gene-specific elements
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3.2.1 Summary
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3.2.2 A simple <gene> example
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3.3 Protein-specific elements
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3.3.1 Summary
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3.3.2 Simple <protein> examples
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3.4 General elements and tags
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3.4.1 General purpose elements
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3.4.2 Organism-identifying elements
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3.4.3 Location elements
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3.4.4 Literature references
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3.4.5 Database reference
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3.4.6 URL-based resources
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3.4.7 Binary data
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3.4.8 Forms
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3.4.9 Global attributes and entities
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4. Extending BIOML
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4.1 Extension mechanisms
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4.2 BIOML extension entities
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Appendix A. Reference material
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Appendix B. Glossary
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Appendix C. Document Type Definition
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