GAME Genome Annotation Markup Elements

GAME was designed and developed by Suzanna E. Lewis and Erwin Frise at the University of California Berkeley. The goal of GAME is to provide an XML DTD and tools for annotating gene sequence features. GAME provides a group of DTDs for molecular biology. These DTDs can be combined to create more expressive DTDs. Annotations are collected features describing related sequences of genomic DNA, transcripts, mRNAs and cDNAs (which are treated as the logical equivalent of mRNAs), and proteins. Each of these molecules has regions along its length ('features') that are described in annotations. The features themselves are a combined summary of the results of both computational and genetic analysis of that DNA, RNA, or amino-acid sequence. Computational analyses are not considered features and are treated as primary data, as are the results of experimental analyses carried out at the bench. In other words, analytical results can be used to identify features, but are not considered features on their own in this context. Thus, each molecule is described in terms ofboth primary analytical results and expert-defined features that are supported by the preceding results. The combination of all these associated fea ture descriptions about the related molecules, from gene to protein, constitutes a statement that is called an 'annotation'. Noticeably, GAME does not actually include a sequence DTD. This is because sequence are treated in a separate DTD-let. So far, there is an XML DTD and an XSL stylesheet for bioxml:game0.2. Although the XSL stylesheet is outdated, it still enables the conversion of game1.001 documents into bioxml:game0.2 documents. This is very useful, since the Drosophila genome, for example, is available only in game1.001 format. Of course, GAME will be even more useful once there is a bioxml:game0.3 parser for bioPerl, bioPython, and bioJava. The current bioxml parser in bioPerl, used for parsing sequence elements, can already import data into bioPerl. The DTD is well commented for use in creating one's own interfaces (see http://www.bioxml.org/Projects/game/).

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