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.
This is a list of developed XML schemas by HOBIT.
| Grammar | maintained by | Target namespace / Description |
|---|---|---|
| Hobit Statuscode | Henning Mersch Bielefeld University |
http://hobit.sf.net/xsds/ Statuscodes for async. WebServices. See here for detailed description. |
| ProML | LMU | http://www.bio.ifi.lmu.de/2005/proml Protein and protein set descriptions. See here for detailed description. |
| SequenceML | BiBiServ-Team | http://hobit.sourceforge.net/xsds/20060201/sequenceML
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 | http://hobit.sourceforge.net/xsds/20060201/alignmentML
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 | http://hobit.sourceforge.net/xsds/20060201/rnastructML
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 |
http://hobit.sourceforge.net/xsds/20060515/rnastructAlignmentML
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.
| Schema | Origin | Description |
|---|---|---|
| EBI FASTA BLAST | EBI | The ApplicationResult.xsd used at the EBI for sequence similarity searches
|
| GAME | fruitfly.org | The Berkeley genome and sequence markup language.
|
| PSI-MI | Proteomics Standards Initiative |
The PSI MI format is a data exchange format for protein interactions.
|
| MAGE-ML | MAGE |
The standard for the representation of microarray expression data facilitating the exchange of microarray information between different data systems.
|
| SBML | SBML |
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks.
|
| UniProt XSD | UniProt / EBI |
The UniProt for protein database format.
|
