The Biopolymer Markup Language—BIOML
Working Draft Proposal
Appendix A. Reference material
This appendix contains a bibliography of reading material that was helpful to
the authors and editors of this proposal.
Bringhurst, Robert The Elements of Typographic Style—2nd Edition:
Hartley & Marks, Vancouver (1996) pp. 350, ISBN 0-88179-132-6.
This book is an invaluable reference for anyone who wants to write anything down on paper and have someone else read it. It is simply a great book and well worth studying.
St. Laurent, Simon XML—A Primer: MIS: Press, Foster City, Ca. (1998)
pp.348, ISBN 1-55828-592-X.
This book is a good introduction to XML. The explanation is particularly clear if the reader has a working knowledge of HTML.
Megginson, David Structuring XML Documents: Prentis Hall PRT, Upper
Saddle River, NJ (1998) pp.420, ISBN 0-13-642299-3.
This book is a technical explanation of the structure and style of good XML. The level of the book is for people interested in writing and extending XML DTDs.
Cooper, Alan About Face—The Essentials of User Interface Design:
Programmer's Press, Foster City, Ca. (1995) pp. 580, ISBN 1-56884-322-4.
The author clearly explains the traps to be wary of when designing a graphic user interface. Learning why something shouldn't be done can be as valuable as learning what actually works.
Alberts, Bruce; Bray, Dennis; Lewis, Julian; Raff, Martin; Roberts, Keith;
Watson, James D. Molecular Biology of The Cell—2nd Edition: Garland
Publishing, Inc., New York, NY (1989) pp. 1288, ISBN 0-8420-3695-6.
A general textbook on cell biology.
Bray, T., Paoli, J. and Sperberg-McQueen, C.M.
Extensible Markup Lanuage (XML) 1.0. (1998)
This document describes the general specifications for an XML. The style of the document makes it difficult for the general user, however anyone interested in designing an XML should try to make their way through it at least once.
Murray-Rust, P., Rzepa, H.S. and Leach, C. CML
- Chemical Markup Language. (1998)
This document describes the specification of an XML specifically written to handle the problem of describing a chemical structure so that it can be rendered properly in a text document.
Spitzner, J.H. Bioinformatic
Sequence Markup Language (BSML). (1997)
This document describes the specification of an XML specifically written to handle the problem of describing a biopolymer structure so that it can be rendered properly in a text document. Anyone interested is advised to read this document before you "make up your mind" about BIOML. Spitzner has used a completely different model for constructing BSML: he has adapted the "as printed on paper" model used by Murray-Rust, et. al in their construction of CML, using many of the same element names for slightly different purposes. This approach is completely different from the model used for BIOML, so appraising the two ideas side by side should give the reader a good view of how a conceptual model affects the development of an XML.