104 5 Survey of Ontologies in Bioinformatics
versity of Auckland and affiliated research groups. The purpose of CellML
is to store and exchange computer-based biological models. CellML allows
scientists to share models even if they are using different model-building
software. It also enables them to reuse components from one model in an-
other, thus accelerating model building. CellML includes information about
model structure (how the parts of a model are organizationally related to one
another), mathematics (equations describing the underlying biological pro-
cesses), and metadata (additional information about the model that allows
scientists to search for specific models or model components in a database or
other repository).
CellML is intended to support the definition of models of cellular and sub-
cellular processes. This markup language facilitates the reuse of models and
parts of models by employing a component-based architecture. Models are
split into logical subparts called components that are connected together to
form a model.
CellML separates the specification of the underlying mathematics of a mod-
el from a particular implementation of the model’s solution. This makes a
model independent of a particular operating system or programming lan-
guage, and allows modelers to easily integrate parts of other peoples’ mod-
els into their own models. CellML also allows the generation of equations
for publishing from the same definition upon which the solution method is
based, removing inconsistencies between the model and associated results in
academic papers, and allowing others to reliably reproduce these.RNAML www-lbit.iro.umontreal.ca/rnaml
RNAML provides a standard syntax that allows for the storage and exchange
of information about RNA sequence as well as secondary and tertiary struc-
tures. The syntax permits the description of higher-level information about
the data, including, but not restricted to, base pairs, base triples, and pseu-
doknots (Waugh et al. 2002).
Because of the hierarchical nature of XML, RNAML is a valuable method
for structuring the knowledge related to RNA molecules into a nested-struc-
tured text document. For example, in RNAML, a “molecule” is an element
consisting of the following three lower-level elements: identity (which con-
tains two nested elements, name and taxonomy), sequence (which contains
three nested elements, numbering-system, seq-data, and seq-annotation), and
structure (which contains one nested element, model). To ensure compatibil-
ity with other existing standards of RNA nomenclature, RNAML uses in-
cluding formats such as the International Union of Pure and Applied Chem-