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102 5 Survey of Ontologies in Bioinformatics

DNA RNA Protein

<dna> <rna> <protein>

<promoter> <rdomain> <subunit>

<gene> <ra> <homolog>

<exon> <rmod> <peptide>

<intron> <rvariant> <domain>

<ddomain> <rstart> <aa>

<da> <rstop> <amod>

<dmod> <avariant>

<dvariant> <aconflict>

<dstart>

<dstop>

Table 5.1 The elements for DNA, RNA, and protein in BioML

that accepts information conforming to other standard formats, such as the

Protein Data Bank (PDB) format.

SBML http://www.sbw-sbml.org

The Systems Biology Markup Language is an XML-based language for stor-

ing biochemical models (Hucka et al. 2003). Formally defined using the Uni-

fied Modeling Language (UML) (UML 2004), SBML contains structures for

representing compartments, species, and reactions, as well as optional unit

definitions, such as parameters and rules (constraints). SBML is still under

active development at the California Institute of Technology.

SBML level-1 is aimed at providing a basic representation of biochemical

reaction networks. A model in SBML consists of the following components

(Hucka et al. 2003):

1. Compartment: a container of finite volume for well-stirred substances
   where reactions take place


2. Species: a chemical substance or entity that takes part in a reaction


3. Reaction: a statement describing some transformation


4. Parameter: a quantity that has a symbolic name


5. Unit definition: a name for a unit used in the expression of quantities in a
   model