5.2 Ontology Languages in Bioinformatics 105
istry (IUPAC) lettering and PDB ATOM records. If RNAML needs to depict
multiple interacting RNA molecules, the interactions of RNA molecules are
presented as character data in aninteractionelement.
AGAVE http://www.animorphics.net/lifesci.html
The Architecture for Genomic Annotation, Visualization and Exchange is an
XML language created by DoubleTwist, Inc., for representing genomic an-
notation data. AGAVE uses XML Schema (XSD) for describing the syntactic
structure of the data. A bioperl script can be used to convert data in the Euro-
pean Molecular Biology Laboratory (EMBL) or Genome Annotation Markup
Elements (GAME) format into the AGAVE format. The XML EMBL (XEMBL)
project of EBI is building a service tool that employs Common Object Re-
quest Broker Architecture (CORBA) servers to access EMBL data. The data
can then be distributed in XML format via a number of mechanisms (Wang
et al. 2002).
CML http://www.xml-cml.org
The Chemical Markup Language was discussed in chapter 1. The purpose of
CML is to manage chemical information (e.g., atomic, molecular, crystallo-
graphic information). CML is supported by tools such as the popular Jumbo
browser. CMLCore retains most of the chemical functionality of CML 1.0,
and extends it by adding handlers for chemical substances, extended bond-
ing models, and names (Murray-Rust and Rzepa 2003).
CytometryML
The Cytometry Markup Language is designed for the representation and ex-
change of cytometry data. CytometryML provides an open, standard XML
format, which may replace the Flow Cytometry Standard (Leif et al. 2003).
GAME http://www.fruitfly.org/comparative
GAME is an XML language for curation of DNA, RNA, or protein sequences.
GAME uses an XML DTD to specify the syntactic structure of the content of
a GAME document. GAME is extensively used within the FlyBase/Berkeley
DrosophilaGenome Project (BDGP). For example, genomic regions for Rho-
dopsin 1 (ninaE), Rhodopsin 2 (Rh2), Rhodopsin 3 (Rh3), Rhodopsin 4 (Rh4),
apterous (ap), even-skipped (eve), fushi-tarazu (ftz) and twist (twi) have
been annotated in GAME format (Bergman et al. 2002; GAME 2002) in four
Drosophilaspecies (D. erecta,D. pseudoobscura,D. willistoni,andD. littoralis)
covering over 500 kb of theD. melanogastergenome.