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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].