Table 1.

Commonly used XML formats and their features

Name	Scope	Pro	Contra
AGAVE	sequence/annotation	XML schema available, stable, format is open and seems to be actively maintained, well documented	XML schema is in BETA status (since Feb. 2003), XML schema defines no namespace, no restriction of sequence data
BioML	sequence/annotation	-	no XML schema available (DTD only), unclear if it is stable and maintained (last modified 1999)
BioSeq	plugin of readseq	-	no XML schema available (DTD can be generated), maintenance and stability unclear, undocumented
BSML	sequence/annotation, sequence alignments	well documented	no XML schema available (DTD only), unclear if it is maintained any longer (last updated 2002)
chadoXML	data base format	-	no XML schema available (DTD can be generated), part of the GMOD XORT software package, undocumented
EMBLxml	sequence data base format	XML schema available	XML schema defines no namespace, no restriction on content elements
GAMEXML	sequence/annotion	used in different OS projects, seem to be stable	no XML schema available (DTD only), maintenance unclear
INSDseq	sequence data base format	lightweight	no XML schema available (DTD only)
MSAML	sequence alignments	-	no XML schema available, project page unreachable (DTD on third party page), maintenance unclear
RNAML	RNA sequence, structure and experimental data	XML schema available, well documented	XML schema defines no namespace, complex and unmanageable, license and maintenance unclear (last modified 2002)
TinySeq	sequence data	stable, active, lightweight	no XML schema available (DTD only), undocumented

The list above contains a summary evaluation of formats with the same scope of application as the HOBIT formats. A more complete list (including detailed features) is available at [57].