Cover Pages: Genome Annotation Markup Elements (GAME)

[July 27, 2000] "The goals of GAME, at least in the perspective of the bioxml community, are to provide an xml dtd and tools for annotating biosequence 'features'. bioxml:game is part of bioxml's overall goals of providing a group of 'dtd-lets' for molecular biology. These dtd-let's will be able to be combined to create more expressive dtds. You'll notice that bioxml:game doesn't actually contain a seq dtd. This is because seq is treated in a seperate dtd-let. So it is the goal of bioxml to use a stripped down GAME as the basis for the bioxml seq-features dtd-let. . . So far we have an xml dtd and an xsl stylesheet for bioxml:game0.2. The stylesheet is -- outdated and -- provided to convert game1.001 documents into **bioxml:game0.2** documents. This is very useful since the drosophila genome is available in game1.001 format at ftp://ftp.fruitfly.org/pub/gadfly/. Of course it'll be even more useful once we have a bioxml-game:game0.3 parser for bioperl, biopython and biojava. Hopefully soon. Currently, there is a bioxml parser in bioperl for parsing in seq elements, so you may be able to get this data into bioperl already. I think the dtd is well-commented enough to make sense of most of it, but of course there will be questions. Drop a line by the bioxml mailing list - bioxml-dev@bioxml.org - with questions or comments or if you want to follow the development. . ."

From the early annotated DTD: "GAME Genome Annotation Markup Elements. Document Type Definition DTD - June. 5,1999 - Version 1.0, by Suzanna E. Lewis and Erwin Frise, University of California Berkeley. Annotations are a summarization of all the collected features discerned and described on related sequences of genomic DNA, transcripts, mRNAs (and cDNAs which are treated as their logical equivalent), and proteins. Each of these molecules has regions along their linear length described by annotators as 'features'. The features themselves are a combined summary of both computational and genetic analysis of that DNA, RNA, or AA sequence. Computational analyses are not considered 'features' and are treated as primary data, as are any experimental analyses carried out at the bench. In other words, analytical results may be used to identify features, but are not considered features on their own in this context. Thus, each molecule is described both in terms of primary analytical results and in terms of expert defined features that are supported by the preceding results. The combination of all these associated feature descriptions on the related molecules (from genomic to protein) constitute a statement that is called an annotation. . ."

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