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106 5 Survey of Ontologies in Bioinformatics

MML

The Medical Markup Language provides the XML-based standard for medi-

cal data exchange/storage (Guo et al. 2003).

MotifML motifml.org

MotifML is a language for representing the computationally predicted DNA

motifs (often in the regulatory region such as promoters) generated by the

Gibbs motif sampler, AlignACE, BioProspector, and CONSENSUS. MotifML

was created by the authors of this book and two collaborators (Sui Huang

and Jerzy Letkowski). MotifML uses the Web Ontology Language (OWL) to

specify the data structure of a MotifML document. MotifML is supported by

Java-based visualization tools such as MotifML viewers.

NeuroML http://www.neuroml.org/main.html

The Neural Open Markup Language is an XML language for describing mod-

els, methods, and literature for neuroscience. NeuroML uses XSD to specify

the syntactic requirements for the model descriptions (Goddard et al. 2001).

ProML

The Protein Markup Language is for specifying protein sequences, struc-

tures, and families using an open XML standard. ProML allows machine-

readable representations of key protein features (Hanisch et al. 2002).

TML

Taxonomic Markup Language is mainly an XML format for representing the

topology of a phylogeny, but also includes a representation for statistical

metadata (e.g., branch length, retention index, and consistency index) de-

scribing the phylogeny (Gilmour 2000). It is notable that for TML, the hier-

archical nature of a phylogeny is readily represented by XML.

5.3 Macromolecular Sequence Databases

The rapid expansion of nucleotide sequence data available in public data-

bases is revolutionizing biomedical research. Sequence databases such as

GenBank have a variety of uses, including the discovery of novel genes,

identification of homologous genes, analysis of alternative splicing, chromo-

somal localization of genes, and detection of polymorphisms (Pandey and

Lewitter 1999). Macromolecular sequence databases are classified according

to whether they deal with nucleotide sequences or protein sequences.