5.2 Ontology Languages in Bioinformatics 101
Figure 5.5 The BSML representation for the SWISS-PROT entry P04637.BioML http://www.rdcormia.com/COIN78/files/XML_Finals/
BIOML/Pages/BIOML.htm
The Biopolymer Markup Language provides an extensible framework for an-
notating experimental information about molecular entities, such as proteins
and genes. Many examples of BioML documents were shown in chapter 1.
The four chemical letters of DNA, G, C, A, and T, have their normal mean-
ings as individual nucleotides (case-insensitive). White space (e.g., spaces,
tabs, carriage returns) are ignored by the parser, and can be freely added to
aid the flow and readability of the file. The parser also ignores any character
that cannot be a nucleotide residue, allowing the author to include numbers
and other symbols that make reading the file easier. The kinds of element for
DNA, RNA, and protein in BioML are presented in table 5.1.
The BioML ontology can also be used to refer to public database entries.
For example, one can refer to the GenBank entry for the DNA sequence en-
coding the humanδ-aminolevulinate dehydratase as follows:
A notable feature of BioML is that it allows for the inclusion of nontextual
data, such as binary data (Fenyo 1999). Also, BioML possesses a mechanism