Cover Pages: BIOpolymer Markup Language (BIOML)

[January 22, 2002] BIOML was designed by the BIOML core team at Proteometrics, LLC and Proteometrics Canada Ltd. It is 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."

"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..."

[Description 2000] The BIOpolymer Markup Language (BIOML) is "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. 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." BIOML was designed and written by Ron Beavis, with help from David Fenyö (ProteoMetrics, LLC) and Brian Chait (Rockefeller University). David States (Washington University) has assisted in the editing of the DTD language definition.

References:

BIOML Home Page
The Biopolymer Markup Language: BIOML. Working Draft Proposal.
BIOML XML DTD. The XML DTD supplies 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. This DTD is not protected by copyright and may be freely copied for any purpose." [cache]
BIOML DTD - March 24, 1999. Author: Ronald Beavis.
[January 22, 2002] "An XML Application for Genomic Data Interoperation." By Kei-Hoi Cheung, Yang Liu, Anuj Kumar, Michael Snyder, Mark Gerstein, and Perry Miller. Pages 97-103 (with 12 references) in Proceedings Second Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001). Bethesda, MD, USA, 4-6 November 2001. Los Alamitos, CA: IEEE Computer Society, 2001. "As the Extensible Markup Language (XML) becomes a popular or standard language for exchanging data over the Internet/Web, there are a growing number of genome Web sites that make their data available in XML format. Publishing genomic data in XML format alone would not be that useful if there is a lack of development of software applications that could take advantage of the XML technology to process these XML-formatted data. This paper illustrates the usefulness of XML in representing and interoperating genomic data between two different data sources (Snyder's laboratory at Yale and SGD at Stanford). In particular, we compare the locations of transposon insertions in the yeast DNA sequences that have been identified by BLAST searches with the chromosomal locations of the yeast open reading frames (ORFs) stored in SGD. Such a comparison allows us to characterize the transposon insertions by indicating whether they fall into any ORFs (which may potentially encode proteins that possess essential biological functions). To implement this XML-based interoperation, we used NCBIs 'blastall' (which gives an XML output option) and SGD's yeast nucleotide sequence dataset to establish a local blast server. Also, we converted the SGD's ORF location data file (which is available in tab-delimited formal) into an XML document based on the BIOML (BIOpolymer Markup Language) standard..."
See also: bio.perl.org
See also: Biological XML Developers Kit (Bio-XDK) - "This distribution is intended to help researchers investigate and implement XML technologies..."
Related topics:


SEARCH \| ABOUT \| INDEX \| NEWS \| CORE STANDARDS \| TECHNOLOGY REPORTS \| EVENTS \| LIBRARY