BIOML Proposal, 19990220
The Biopolymer Markup Language - BIOML
Working Draft Proposal
This version: January 10, 1999
Designer Ronald Beavis
Additional contributions
  • David Fenyö, Proteometrics, LLC, New York, NY, USA
  • Brian T. Chait, Rockefeller University, New York, NY, USA
  • David J. States, Washington University in St. Louis, USA
  • Paul Gordon, Institute for Marine Biosciences, NRCC, Halifax, NS, Canada

Abstract This proposal outlines the specification of a new XML application, designed to be used for the annotation of biopolymer sequence information. BIOML would allow the full specification of all experimental information known about molecular entities composed of biopolymers, such as proteins and genes. There is currently no generalized method of annotating biopolymer sequences. The goal of BIOML is to provide an extensible framework for this annotation and to provide a common vehicle for exchanging this information between biological scientists using the World Wide Web.
The idea of BIOML is slightly different from those of other Markup Languages, in that the document that is being described is not truly a document at all. Instead, a BIOML document will describe a physical object, e.g., a particular protein, in such a way that all known experimental information about that object can be associated with the object in a logical and meaningful way. The advantage of using a Markup Language for this task is that the information is necessarily nested at different levels of complexity and it fits in very well with the tree-leaf structure inherent in XML. Additionally, although the primary purpose of BIOML is the transfer of information between machines, the additional style information available when using an XML-based approach will simplify the task of displaying that information on various types of browsing and display software.
This document begins with an outline of the the problem: what types of information must be stored with a biopolymer sequence to make it useful in biological research. The current methods of storing and retrieving biopolymer sequence information using the World Wide Web are then discussed, focussing on the challenges that this interchange poses. The fundamental ideas behind BIOML are then discussed, followed by chapters detailing an initial proposal of the elements, tags and logic required for an implementation of this idea.
Status of this document This document is a working draft proposal, meant only for distribution amoung the editors and authors listed above on this page. This document is NOT a W3C Working Draft. The purpose of this document is to develop the concept and implementation of BIOML to a level at which it may be submitted to W3C for consideration.

Brief Table of Contents Full Table of Contents
1. Introduction to bioinformatics
2. BIOML fundamentals
3. Elements and tags
4. Extending BIOML
Appendix A. Reference material
Appendix B. Glossary
Appendix C. Document Type Definition