| Download categories |
| Language |
| DTD |
| Browser |
| Code |
| HTML examples |
| Proteome Template Library |
| Other Biological XML sites |
| Bioinformatics file formats |
| BioPerl XML |
|
WDVL: XML (Web Developers Virtual Library) |
| BlastXML DTD |
| Oasis SGML/XML News |
|
BioPerl discussion group (This group has an XML thread) |
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 protected by copyright and it may be copied freely. The complete source code for 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 use the code for a purpose outside of the its license, please contact us.
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.
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Documents |
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The BIOML Language Feb. 20, 1999 |
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 March 24, 1999 release of the language. It includes the following improvements:
- improved DTD compatibility with Internet Explorer 5's XML parser;
- simplified entity constructions (they are really up to the browser anyway);
- conversion from UTF-8 to the more broadly supported iso-8859-1 character set; and
- addition of a "RootURL" attribute for the BIOML element.
| Document Type Definition |
bioml.dtd
July 31, 1999 |
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 protected by copyright and may be freely copied for any purpose.
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BioBrow |
1. BioBrow v. 1.3
build 1.9 July 31, 1999 2. The browser code. 3. Firewall hints. |
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:
- click on this item;
- save the file "bbinstall.exe" to a temporary directory – remember what directory you place it in;
- once the file has been saved, open that directory and double click on "bbinstall.exe"; and then
- double click on "setup.exe".
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 Examples |
| Human insulin |
| Tumor necrosis factor alpha |
| FAS antigen |
| 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 as 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 view both the HTML source that you are reading and BIOML home page for the BIOML browser, inside of lt;script> tags.
| Proteome template library 1.0 |
| via FTP |
| via HTML |
The Proteome Template Library (PTL) is part of an ongoing R&D effort by Proteometrics. The goal of the project is to bring sequence and biological information together in a structure that will be intuitive to people trained either in biology or computer science. It currently contains approximately 4900 proteome entries (i.e., it represents 4900 species) amounting to 152 MBytes of BIOML content.
This library consists of all of the sequence information currently stored in the Protein Identification Resource (PIR) and the Protein Data Base (PDB), represented using BIOML. Extensive use of HTML resources is included in this library.
The library is arranged around biological organism taxonomy, using the US National Center for Biologics Information taxonomy information as a guide. The choice of which taxa to represent was made based on the number of organisms that would be included within that taxon, rather than strictly following the taxonomic hierarchy.
In proteomes with more that twenty known sequences, the proteins are arranged into a series of functional or tissue-type subsets in order to organization to a visual interface. Some proteins may properly fall within more than one of these subsets: for clarity, an individual protein is listed only once in a proteome representation.
PTL was designed to be viewed with the BIOML Browser, available above. However, Internet Explorer (version 5) has the capability of reading XML content and displaying it in a readable form. This display is mainly of interest to people who like to read XML files: biologists are much better off with the real BIOML Browser software. Internet Explorer cannot read some of the larger proteome files because of its own internal limitations (e.g. human, mouse, rat, thale kress or rice).
| Contacts | The BIOML Team |
BIOML was designed and written by the BIOML core team at Proteometrics, LLC (New York, NY, USA) and Proteometrics Canada Ltd (Winnipeg, MB, Canada). David States (Washington University in St. Louis) and Paul Gordon (Institute for Marine Bioscience, NRCC, Halifax) have contributed to the DTD language definition. If you have any comments or suggestions about the language, please email us directly.
A moderated version of all comments and susgestion will be posted to a BIOML discussion board, currently under preparation. If you do not wish your correspondence to appear in the discussion board, please indicate this clearly in your email.
