Skip to main content

Table 1 Commonly used XML formats and their features

From: XML schemas for common bioinformatic data types and their application in workflow systems

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
  1. 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].
\