BIOML Proposal, 19990220
BIOML Home Page The Biopolymer Markup Language—BIOML
Working Draft Proposal

Table of Contents

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

Appendix A. Reference material
Appendix B. Glossary
Appendix C. Document Type Definition

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