XML schemas - HOBIT
Some Web Services need special grammars for respresenting their data. HOBIT tries to use as much existing grammars as possible, but not all problems are covered.
This is a list of developed XML schemas by HOBIT.
Grammarmaintained byTarget namespace / Description
Hobit Statuscode Henning Mersch
Bielefeld University
Statuscodes for async. WebServices.
See here for detailed description.
Protein and protein set descriptions.
See here for detailed description.
SequenceML BiBiServ-Team
SequenceML deals with all kinds of simple sequence information often used as input for several common bioinformatics tools. It is designed to be used as a replacement for the FASTA format, containing all of FASTA's information content while avoiding that format's aforementioned consistency problems. SequenceML differentiates between nucleic- and aminoacid sequences following the IUPAC standard and also allows the user to add free sequence information based on basic types defined by BioTypes. SequenceML also supports a mandatory sequence id and an optional detailed sequence description.
AlignmentML BiBiServ-Team
AlignmentML is a format containing (multiple) alignment information any alignment program like DCA, Dialign or ClustalW can produce. Like in SequenceML different sequence types are supported
RNAStructML BiBiServ-Team
RNAStructML is a format for storing rna secondary structure information. One widely accepted usage for rnatools, such as RNAshapes ,RNAfold or Mfold is the proprosal of rna secondary structures, based on thermodynamic principles. RNAStructML is based on SequenceML and uses DotBracket strings for storing the structure information.
RNAStructAlignmentML BiBiServ-Team
RNAStructAlignmentML is a format for storing rna secondary structure alignments as computed by e.g. the RNAforester or RNAalifold tool. RNAStructAlignment uses a RNAStructML-like architecture, but uses AlignmentML instead of SequenceML as a basic type.

XML schemas - External
As mentioned in the section before we developed for some of our Web Services own XML schemas. However, if ever possible the usage of already existent schemas is highly recommended. There is already a broad variety of schemas for bioinformatics purposes. They emerged from single institutions as well as from international organizations. Following we collected a set of schemas usefull for the development of document-style Web Services. We try to focus on schemas with a significant visibility in the community / significant development activity.
EBI FASTA BLAST EBI The ApplicationResult.xsd used at the EBI for sequence similarity searches
  • Namespace:
  • Comments:
    Used for BLAST FASTA
GAME The Berkeley genome and sequence markup language.
  • Comments:
    Used in different Open Source Projects. Unfortunately only as DTD available.
PSI-MI Proteomics Standards Initiative
The PSI MI format is a data exchange format for protein interactions.
  • Namespace:
  • Comments: Community standard. Supported by several important protein interaction databases.
The standard for the representation of microarray expression data facilitating the exchange of microarray information between different data systems.
  • Comments: Community standard. Unfortunately a DTD.
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks.
  • Namespace:
  • Comments: Supported by over 80 software systems in systems biology.
UniProt XSD UniProt / EBI
The UniProt for protein database format.
  • Namespace:
  • Comments: Successor of the SwissProt SP-ML format. Logo
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