Introduction
¶ This page is devoted to a new XML language, designed to be used for the annotation of biopolymer sequence information. BIOML allows the full specification of all experimental information known about molecular entities composed of biopolymers, for example, proteins and genes. There is currently no general method of annotating biopolymer sequences, in their biological context. The goal of BIOML is to provide an extensible framework for this annotation and to provide a common vehicle for exchanging this information between scientists using the World Wide Web.
¶ BIOML was designed to be a freely available standard. Therefore, the Document Type Definition (DTD) is not copyright and it may be copied freely. The source code for most of the Proteometrics BIOML browser is also available below. The language definition draft document is copyright, but any non-commerical use is allowed. If you would like to ask any questions about a particular use of the language or documents, or you would like to see more code on the site, please contact the individuals listed below.
¶ 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.
Documents
The BIOML
Language
Feb. 20, 1999
Language definition
¶ This entry will take you to the document that defines the BIOML Language. It is meant for the interested technical reader who would like to understand the structure of the language so that they can write fluent BIOML. A simplified tutorial version of the language is currently in preparation and it will be released soon. The current document replaces the Jan. 20 1999 release of the language. It includes the following improvements:

1. an improved mechanism for extending key attributes and elements;
2. addition of the xml:space attribute to selected elements;
3. removal of the <query> element as redundant (use <file> instead);
4. an improved set of content models for selected elements;
5. several errors in the DTD were corrected on Mar. 6, 1999, which did not require any changes to the document, other than "Appendix C" and "bioml.dtd"; and
6. several more errors in the DTD were corrected on Mar. 24, 1999, which did not require any changes to the document, other than "Appendix C" and "bioml.dtd".

These changes were made based on comments from users and some redesign work by the core team. The documentation explaining the improved extension mechanism (Chapter 4) will be of interest to anyone interested in customizing the language for their own uses.
Dcoument Type Definition
bioml.dtd
Mar. 24, 1999
Data Type Definitions
¶ The "bioml.dtd" file is the technical definition of the core elements and attributes of BIOML. This definition describes the minimum set of elements necessary for BIOML, which can be extended to fit the needs of a particular application, using the extension mechanism outlined in the current XML definition.
Note: This DTD is not copyright and may be freely copied.
BioBrow
1. BioBrow v. 1.1
build 0.4
Feb. 27, 1999
2. The browser code.
3. Firewall hints.
BioBrow – The BIOML Browser
¶ This item allows you to download the current version of BioBrow, the BIOML browser for Windows 95, 98 and NT.
To setup the new version of the program, follow these directions:

1. click on this item;
2. save the file "biotest.exe" to a temporary directory – remember what directory you place it in;
3. once the file has been saved, open that directory and double click on "biotest.exe";
4. close all running copies of BioBrow; and
5. double click on "setup.exe".

After setup is finished, you will be asked to reboot your computer (setup installs the most recent, Y2K compatible version of Windows controls). Select "Yes" and then wait for the reboot to occur. Then double click on the "BioBrow" file in the "BiomlBrowser" directory and open the file "Readme.bml" for some instructions.
¶ BioBrow comes with a network installer, so you can upgrade your version of BioBrow to the most recent one without having to come back to this page. BIOML has sufficient functionality that you can create interlinked sets of BIOML documents, in the same way that you can interlink HTML documents. It can also be embedded into HTML documents – this page has an embedded BIOML document in it. If you look at this page with BioBrow, you will be able to see the BIOML portion, in addition to the HTML that can be read by conventional Web Browsers.
BIOML Examples
Human insulin
Tumor necrosis factor alpha
FAS antigen
Bacteriophage phi-X174 virus
Examples
¶ The links on the left will retrieve some selected examples of BIOML files. After you have read the language documentation, you can use these files to learn the general syntax of the language, when it is applied to real biological objects. Novice XML programmers may wish to download BioBrow rather than reading the text files, because the browser makes the hierarchical nature of the data model much clearer.
¶ This page is itself an example of BIOML. If you select the "View" menu on your HTML browser and then select "View page source", you can see both the HTML source that you are reading, but at the end of the page you will also find the BIOML home page for the BIOML browser, inside of <script> tags.
¶ You can also retrieve BIOML translations of PIR (Protein Identification Resource) or SWISSPROT files. Just enter the PIR or SWISSPROT identifier (e.g., human insulin is INS_HUMAN in SWISSPROT, but it is IPHU for PIR):
Contacts
Ron Beavis
David Fenyö
The Authors
¶ BIOML was designed and written by the BIOML core team:

* Ron Beavis, designer;
* David Fenyö, critic; and
* Brian Chait, tester.

David States (Washington University in St. Louis) and Paul Gordon (Institute for Marine Bioscience, NRCC, Halifax) have assisted in the creation of the current version the DTD language definition. If you have any comments or suggestions about the language, please contact Ron Beavis directly. If you have any questions about using the language commercially, please contact David Fenyö.