Some time ago, I developed a prototype schema for a new XML-based feature table format. This grew out of an earlier effort to write the XML Schema grammer for the GAME elements, but turned into something significantly different. The philosophy of XFF is to define a format for a `minimalistic' feature table -- in some ways, what GFF is to other flatfile feature formats. But since this is XML, we can then use this as a skeleton to hang other, application-specific, information off. However much detail gets added, it should still be possible for a naive XFF-processing application to extract at least the basic information (location, strand, type, etc.). This means it can be used in a very wide range of applications, ranging from `drawing coloured boxes' type data presentation up to very semantically rich communication and storage. It also differs from a lot of other formats in being fully hierarchical. So, for example, you can group some exon features together within a gene feature. This model comes unashamedly from BioJava, where we've had some good experiences with hierarchical features. Anyway, I've been finding the format very useful for some internal projects, so I've decided to write it up to see if there's any public interest. You can browse a proposal at: http://www.biojava.org/thomasd/XFF/ There are still a few open issues, especially relating to feature ids and idrefs, but this should give a good general idea of what the format is about. I've got some BioJava code for reading and writing XFF -- this is currently a bit tangled up with other things, but I'll try to get it out in the open in the next few days. Is anyone interested in this format? If so, I'd like to get some discussion going with regards to getting a more formal standard defined. In this case, it would be good to move everything over to bioxml.org, so long as people there are interested. Let me know what you think, Thomas. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
