Remote Access to MonosaccharideDB

Access for Computer Programs

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:

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]

<?xml version="1.0"?>

<monosaccharide_exchange_object ms_name="" > - The outer element bracket. The "ms_name" argument contains the residue name in MonosaccharideDB notation. This name can be used to e.g. access the corresponding MonosaccharideDB entry to retrieve further properties of the residue.

  <namescheme></namescheme> - The notation scheme, in which the given residue name below is defined. Corresponds to the "targetScheme" parameter of the "convert_residue" action.

  <monosaccharide_name></monosaccharide_name>

  <external_substituents count=""> - A list of substituents, which are part of the monosaccharide and not included in the residue name but encoded separately.

    <substituent> - A member of the substituents list

      <name></name> - The name of the substituent in the target notation

      <original_name></original_name> - The name of the substituent in the source notation

      <linkage n="1"> - The linkage(s) between the monosaccharide basetype and the substituent

        <linkage_position_ms></linkage_position_ms>
        <linkage_type></linkage_type>
        <linkage_position_subst></linkage_position_subst>
        <original_linkage_type></original_linkage_type>
      </linkage>

    </substituent>

  </external_substituents>

  <orientationChanged></orientationChanged> - A flag to indicate cases where the orientation of the monosaccharide backbone was changed (klick for more info).

  <avg_mass></avg_mass>

  <monoisotopic_mass></monoisotopic_mass>

</monosaccharide_exchange_object>

Examples: