Remote Access to MonosaccharideDB
MonosaccharideDB provides access to its content in a machine readable way.
- Single entries can be retrieved in xml format by adding the "output=xml" parameter to the entry's URL. A link to the xml version is also provided in the "Actions" box of the html display of the entries.
- Residue conversion via http protocol with xml formatted results is also offered (see below).
- Java code for name parsing and residue conversion is available as a .jar file for download.
- Further options for database query with xml results will be added soon.
Remote usage of MonosaccharideDB residue conversion
MonosaccharideDB can be used to convert carbohydrate residue names from one notation scheme to another one by querying the database with the residue name and looking up the corresponding alias name in the residue's entry. This method, however, is difficult to apply when a lot of residue names have to be converted, e.g. using a scripting language. Therefore, MonosaccharideDB also offers a web service for remote access to the conversion routines via http protocol; results are returned in xml format.
To use this web service a server simply has to call the convert_residue action and add the appropriate parameters.
Parameters are as follows:
- sourceScheme: The current notation scheme of the residue name to be converted.
- targetScheme: The notation scheme of the resulting residue name.
- name: The residue name to be converted.
- anomeric (optional): The anomeric state of the monosaccharide (to be used when the anomeric is encoded within the linkage and not part of the monosaccharide, as e.g. in KEGG format).
- substName (optional): The name of an external substituent.
- substMsPos (optional): The linkage position of an external substituent.
- substMsLinktype (optional): The linkage type of an external substituent.
The optional parameters substName, substMsPos and substMsLinktype can be used multiple times if more than one external substituent is present. Please make sure that the order of information is the same for all these parameters (see examples below). SourceScheme and TargetScheme may be identical to retrieve the primary alias name of a given residue name within one notation.
The result of the conversion is returned in xml format: [show | hide]
- Converting CarbBank name 'b-D-GlcpNAc' to MonosaccharideDB format:
- Converting MonosaccharideDB name 'a-lido-HEX-1:5|6:a||(2o:1)sulfate' to GlycoCT format:
- To create a unique name within one format, simply use the same format as source and target namescheme (e.g. CarbBank residue b-D-4-deoxy-Glcp):
- (further examples to be added)