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
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.
1. BioBrow v. 1.1
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.
Tumor necrosis factor alpha
Bacteriophage phi-X174 virus
¶ 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):
¶ 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.